@article{
Abascal05,
   Author = {Abascal, Federico and Zardoya, Rafael and Posada, David},
   Title = {ProtTest: selection of best-fit models of protein evolution},
   Journal = {Bioinformatics},
   Volume = {21},
   Number = {9},
   Pages = {2104-2105},
   Abstract = {Summary: Using an appropriate model of amino acid replacement is very important for the study of protein evolution and phylogenetic inference. We have built a tool for the selection of the best-fit model of evolution, among a set of candidate models, for a given protein sequence alignment.  Availability: ProtTest is available under the GNU license from http://darwin.uvigo.es  Contact: fabascal@uvigo.es},
      Year = {2005} }




@article{
Abdallah89,
   Author = {Abdallah, M. M. F. and Jones, R. A. and El-Beltagy, A. S.},
   Title = {An efficient method to overcome seed dormancy in Scotch broom (Cytisus scoparius)},
   Journal = {Environmental \& Experimental Botany},
   Volume = {29},
   Number = {4},
   Pages = {499-505},
   Abstract = {Sequential, rapid immersion in hot water followed by liquid nitrogen dramatically improved seed imbibition and germination responses by as much as 3.5 fold. -from Authors},
   Keywords = {broom
dormancy
Scots broom
seed
Cytisus scoparius
Sarothamnus scoparius},
   Year = {1989} }




@article{
Adekambi01,
   Author = {Adekambi, Toidi and Drancourt, Michel},
   Title = {Dissection of phylogenetic relationships among 19 rapidly growing Mycobacterium species by 16S rRNA, hsp65, sodA, recA and rpoB gene sequencing},
   Journal = {International Journal of Systematic and Evolutionary Microbiology},
   Volume = {54},
   Number = {6},
   Pages = {2095-2105},
   Abstract = {The current classification of non-pigmented and late-pigmenting rapidly growing mycobacteria (RGM) capable of producing disease in humans and animals consists primarily of three groups, the Mycobacterium fortuitum group, the Mycobacterium chelonae-abscessus group and the Mycobacterium smegmatis group. Since 1995, eight emerging species have been tentatively assigned to these groups on the basis of their phenotypic characters and 16S rRNA gene sequence, resulting in confusing taxonomy. In order to assess further taxonomic relationships among RGM, complete sequences of the 16S rRNA gene (1483-1489 bp), rpoB (3486-3495 bp) and recA (1041-1056 bp) and partial sequences of hsp65 (420 bp) and sodA (441 bp) were determined in 19 species of RGM. Phylogenetic trees based upon each gene sequence, those based on the combined dataset of the five gene sequences and one based on the combined dataset of the rpoB and recA gene sequences were then compared using the neighbour-joining, maximum-parsimony and maximum-likelihood methods after using the incongruence length difference test. Combined datasets of the five gene sequences comprising nearly 7000 bp and of the rpoB+recA gene sequences comprising nearly 4600 bp distinguished six phylogenetic groups, the M. chelonae-abscessus group, the Mycobacterium mucogenicum group, the M. fortuitum group, the Mycobacterium mageritense group, the Mycobacterium wolinskyi group and the M. smegmatis group, respectively comprising four, three, eight, one, one and two species. The two protein-encoding genes rpoB and recA improved meaningfully the bootstrap values at the nodes of the different groups. The species M. mucogenicum, M. mageritense and M. wolinskyi formed new groups separated from the M. chelonae-abscessus, M. fortuitum and M. smegmatis groups, respectively. The M. mucogenicum group was well delineated, in contrast to the M. mageritense and M. wolinskyi groups. For phylogenetic organizations derived from the hsp65 and sodA gene sequences, the bootstrap values at the nodes of a few clusters were <70 %. In contrast, phylogenetic organizations obtained from the 16S rRNA, rpoB and recA genes were globally similar to that inferred from combined datasets, indicating that the rpoB and recA genes appeared to be useful tools in addition to the 16S rRNA gene for the investigation of evolutionary relationships among RGM species. Moreover, rpoB gene sequence analysis yielded bootstrap values higher than those observed with recA and 16S rRNA genes. Also, molecular signatures in the rpoB and 16S rRNA genes of the M. mucogenicum group showed that it was a sister group of the M. chelonae-abscessus group. In this group, M. mucogenicum ATCC 49650T was clearly distinguished from M. mucogenicum ATCC 49649 with regard to analysis of the five gene sequences. This was in agreement with phenotypic and biochemical characteristics and suggested that these strains are representatives of two closely related, albeit distinct species.},
      Year = {2004} }




@article{
Aguilar98,
   Author = {Aguilar, O. Mario and Lopez, Maria Veronica and Riccillo, Pablo M. and Gonzalez, Ramon A. and Pagano, Marcela and Grasso, Daniel H. and Puhler, Alfred and Favelukes, Gabriel},
   Title = {Prevalence of the \emph{Rhizobium etli}-Like Allele in Genes Coding for 16S rRNA among the Indigenous Rhizobial Populations Found Associated with Wild Beans from the Southern Andes in Argentina},
   Journal = {Applied and Environmental Microbiology},
   Volume = {64},
   Number = {9},
   Pages = {3520-1427},
   Abstract = {A collection of rhizobial isolates from nodules of wild beans, Phaseolus vulgaris var. aborigineus, found growing in virgin lands in 17 geographically separate sites in northwest Argentina was characterized on the basis of host range, growth, hybridization to a nifH probe, analysis of genes coding for 16S rRNA (16S rDNA), DNA fingerprinting, and plasmid profiles. Nodules in field-collected wild bean plants were largely dominated by rhizobia carrying the 16S rDNA allele of Rhizobium etli. A similar prevalence of the R. etli allele was observed among rhizobia trapped from nearby soil. Intragroup diversity of wild bean isolates with either R. etli-like or Rhizobium leguminosarum bv. phaseoli-like alleles was generally found across northwest Argentina. The predominance of the R. etli allele suggests that in this center of origin of P. vulgaris the coevolution of Rhizobium spp. and primitive beans has resulted in this preferential symbiotic association.},
      Year = {1998} }




@article{
Aguilar04,
   Author = {Aguilar, O. Mario and Riva, Omar and Peltzer, Eitel},
   Title = {Analysis of \emph{Rhizobium etli} and of its symbiosis with wild \emph{Phaseolus vulgaris} supports coevolution in centers of host diversification},
   Journal = {Proceedings of the National Academy of Sciences of the United States of America},
   Volume = {101},
   Number = {37},
   Pages = {13548-13553},
   Abstract = {Common beans (Phaseolus vulgaris) comprise three major geographic genetic pools, one in Mexico, Central America, and Colombia, another in the southern Andes, and a third in Ecuador and northern Peru. Species Rhizobium etli is the predominant rhizobia found symbiotically associated with beans in the Americas. We have found polymorphism in the common nodulation gene nodC among R. etli strains from a wide range of geographical origins, which disclosed three nodC types. The different nodC alleles in American strains show varying predominance in their regional distributions in correlation with the centers of bean genetic diversification (BD centers). By cross-inoculating wild common beans from the three BD centers with soils from Mexico, Ecuador, Bolivia, and Northwestern Argentina, the R. etli populations from nodules originated from Mexican soil again showed allele predominance that was opposite to those originated from Bolivian and Argentinean soil, whereas populations from Ecuadorian soil were intermediate. These results also indicated that the preferential nodulation of beans by geographically related R. etli lineages was independent of the nodulating environment. Coinoculation of wild common beans from each of the three BD centers with an equicellular mixture of R. etli strains representative of the Mesoamerican and southern Andean lineages revealed a host-dependent distinct competitiveness: beans from the Mesoamerican genetic pool were almost exclusively nodulated by strains from their host region, whereas nodules of beans from the southern Andes were largely occupied by the geographically cognate R. etli lineages. These results suggest coevolution in the centers of host genetic diversification.},
      Year = {2004} }




@article{
Ahmad85,
   Author = {Ahmad, M. H. and McLaughlin, W.},
   Title = {Ecology and genetics of tropical rhizobia species},
   Journal = {Biotechnol Adv},
   Volume = {3},
   Number = {2},
   Pages = {155-170},
   Abstract = {Biological nitrogen fixation (BNF) technology with special reference to Rhizobium-legume symbiosis is growing very rapidly with the hope of combatting world hunger by producing cheaper protein for animal and human consumption in the Third World. One can see rapid progress made in the biochemistry and molecular biology of symbiotic nitrogen fixation in general; however, less progress has been made on the ecological aspects despite the fact that an enormous amount of literature is available on inoculation problems and on agronomic aspects of symbiotic nitrogen fixation. So far most information on Rhizobium concerns fast-growing rhizobia and their host legume. Although it is essential that food production using BNF technology should be maximized in the Third World, the least work has been done on slow-growing rhizobia, which are generally found in tropical and sub-tropical soils. The majority of the developing countries are in tropical and sub-tropical regions. Except for R. japonicum, a microsymbiont partner of soybean (Glycine max), the majority of the slow-growing rhizobia belong to the cowpea group, and we refer to cowpea rhizobia as tropical rhizobia species. In this review we have tried to consolidate the recent progress made on ecology and genetics of tropical rhizobia. By using recombinant DNA technology techniques it is expected that super strains of rhizobia with desirable characteristics can be produced. One must evaluate the efficiency and effectiveness of these genetically manipulated laboratory strains under field conditions. In conclusion, if one aims at combatting hunger in the Third World using BNF technology, an intensive research programme on fundamental and applied aspects of tropical rhizobia species is suggested. This involves close cooperation between molecular biologists and microbial ecologists.},
      Year = {1985} }




@article{
Allen50,
   Author = {Allen, E. K. and Allen, O. N.},
   Title = {Biochemical and symbiotic properties of the rhizobia},
   Journal = {Bacteriol Rev},
   Volume = {14},
   Number = {4},
   Pages = {273-330},
      Year = {1950} }




@article{
Allen53,
   Author = {Allen, E. K. and Allen, O. N. and Newman, A. S.},
   Title = {Pseudonodulation of leguminous plants induced by 2-bromo-3,5-dichlorobenzoic acid.},
   Journal = {American Journal of Botany},
   Volume = {40},
   Pages = {725-731},
      Year = {1953} }




@article{
Allen36,
   Author = {Allen, O. N. and Allen, E. K.},
   Title = {Root nodule bacteria of some tropical leguminous plants. I. Cross nodulation studies with Vigna sinensis.},
   Journal = {Soil Science},
   Volume = {42},
   Pages = {61-77},
      Year = {1936} }




@article{
Allen39,
   Author = {Allen, O. N. and Allen, E. K.},
   Title = {Root nodule bacteria of some tropical leguminous plants. II. Cross nodulation studies with cowpea group.},
   Journal = {Soil Science},
   Volume = {47},
   Pages = {63-76},
      Year = {1939} }




@article{
Allen40,
   Author = {Allen, O. N. and Allen, E. K.},
   Title = {False nodulation on certain leguminous species},
   Journal = {Proceedings of the National Academy of Sciences of the United States of America},
   Volume = {35},
   Pages = {15-16},
      Year = {1940} }




@book{
Allen81,
   Author = {Allen, O. N. and Allen, E. K.},
   Title = {The Leguminosae, a source book of characteristics, uses, and nodulation},
   Publisher = {University of Wisconsin Press},
   Address = {Madison, Wisconsin},
      Year = {1981} }




@incollection{
Amarger01,
   Author = {Amarger, N.},
   Title = {Rhizobia in the field},
   BookTitle = {Advances in Agronomy},
   Series = {Advances in Agronomy},
   Volume = {73},
   Pages = {109-168},
      Year = {2001} }




@article{
Amarger97,
   Author = {Amarger, N. and Macheret, V. and Laguerre, G. and Amarger, N.},
   Title = {\emph{Rhizobium gallicum} sp. nov. and \emph{Rhizobium giardinii} sp. nov., from \emph{Phaseolus vulgaris} nodules},
   Journal = {International Journal of Systematic Bacteriology},
   Volume = {47},
   Number = {4},
   Pages = {996-1006},
   Abstract = {Thirty-one strains of two new genomic species (genomic species 1 and 2) of rhizobia isolated from root nodules of Phaseolus vulgaris and originating from various locations in France were compared with reference strains of rhizobia by performing a numerical analysis of 64 phenotypic features. Each genomic species formed a distinct phenon and was separated from the other rhizobial species. A comparison of the complete 16S rRNA gene sequences of a representative of genomic species 1 (strain R602sp(T)) and a representative of genomic species 2 (strain H152(T)) with the sequences of other rhizobia and related bacteria revealed that each genomic species formed a lineage independent of the lineages formed by the previously recognized species of rhizobia. Genomic species 1 clustered with the species that include the bean- nodulating rhizobia, Rhizobium leguminosarum, Rhizobium etli, and Rhizobium tropici, and branched with unclassified rhizobial strain OK50, which was isolated from root nodules of Pterocarpus klemmei in Japan. Genomic species 2 was distantly related to all other Rhizobium species and related taxa, and the most closely related organisms were Rhizobium galegae and several Agrobacterium species. On the basis of the results of phenotypic and phylogenetic analyses and genotypic data previously published and reviewed in this paper, two new species of the genus Rhizobium, Rhizobium gallicum and Rhizobium giardinii, are proposed for genomic species 1 and 2, respectively. Each species could be divided in two subgroups on the basis of symbiotic characteristics, as shown by phenotypic (host range and nitrogen fixation effectiveness) and genotypic data. For each species, one subgroup had the same symbiotic characteristics as R. leguminosarum biovar phaseoil and R. etli biovar phaseoli. The other subgroup had a species-specific symbiotic phenotype and genotype. Therefore, we propose that each species should be subdivided into two biovars, as follows: R. gallicum biovar gallicum and R. gallicum biovar phaseoil; and R. giardinii biovar giardinii and R. giardinii biovar phaseoli.},
   Keywords = {rhizobium},
   Year = {1997} }




@article{
Andre03,
   Author = {Andre, S. and Neyra, M. and Duponnois, R.},
   Title = {Arbuscular mycorrhizal symbiosis changes the colonization pattern of Acacia tortilis spp. Raddiana rhizosphere by two strains of rhizobia},
   Journal = {Microbial Ecology},
   Volume = {45},
   Number = {2},
   Pages = {137-44},
   Abstract = {The aim of the study was to assess the effect of the mycorrhizosphere of A. tortillis spp. raddiana mycorrhized with Glomus intraradices on the root nodulation by Sinorhizobium terangae (ORS 1009) and/or Mesorhizobium plurifarium (ORS 1096) in two different culture substrates (sandy soil and sand). The endomycorrhizal fungus only stimulated plant growth in the sandy soil. Moreover, arbuscular mycorrhizal infection enhanced the nodulation process in both culture substrates. Beside the stimulatory effects of the mycorrhizosphere on both rhizobia development, fungal symbiosis induces two different dynamics of each bacterial strains in the sand-grown plants. These results suggest specific relationships could occur during the development of the tripartite symbiosis, at physiological and molecular level. From a practical point of view, the role of arbuscular mycorrhizas in improving nodulation and N2 fixation is universally recognized. The fungal symbiosis could modify the development of bacterial inoculants along the root systems. This effect is of particular interest in the controlled inoculation of selected rhizobia.},
   Keywords = {Acacia/*growth \& development/*microbiology
DNA, Bacterial/chemistry/genetics
Mycorrhizae/growth \& development
Plant Roots/growth \& development/microbiology
Polymerase Chain Reaction
Polymorphism, Restriction Fragment Length
Rhizobiaceae/*growth \& development/metabolism
Sequence Analysis, DNA
Silicon Dioxide
Sinorhizobium/growth \& development
Soil
Soil Microbiology
Symbiosis
Zygomycota/*growth \& development/metabolism},
   Year = {2003} }




@article{
Andrews00,
   Author = {Andrews, J. H. and Harris, R. F.},
   Title = {The ecology and biogeography of microorganisms on plant surfaces},
   Journal = {Annual Review of Phytopathology},
   Volume = {38},
   Number = {1},
   Pages = {145-180},
   Abstract = {The vast surface of the plant axis, stretching from root tips occasionally buried deeply in anoxic sediment, to apical meristems held far aloft, provides an extraordinarily diverse habitat for microorganisms. Each zone has to a greater or lesser extent its own cohort of microorganisms, in aggregate comprising representatives from all three primary domains of life Bacteria, Archaea, and Eucarya. While the plant sets the stage for its microbial inhabitants, they, in turn, have established varied relationships with their large partner. These associations range from relatively inconsequential (transient epiphytic saprophytes) to substantial (epiphytic commensals, mutualistic symbionts, endophytes, or pathogens). Through recent technological breakthroughs, a much better perspective is beginning to emerge on the nature of these relationships, but still relatively little is known about the role of epiphytic microbial associations in the life of the plant.},
      Year = {2000} }




@article{
Antipchuk04,
   Author = {Antipchuk, A. F. and Kosenko, L. V.},
   Title = {The influence of lipopolysaccharides and glucans from two Rhizobium leguminosarum bv. viciae strains on the formation and efficiency of their symbioses with pea plants},
   Journal = {Mikrobiologiia},
   Volume = {73},
   Number = {1},
   Pages = {62-7},
   Abstract = {The influence of lipopolysaccharides (LPS), glucans, and their unseparated complexes on nodulation activity of rhizobia and efficiency of their symbioses with pea plants was studied in vegetation experiments. Two Rhizobium leguminosarum bv. viciae strains which differed in their symbiotic properties were used: strain 31 (fix+, efficient, moderately virulent, moderately competitive), and strain 248b (fix-, inefficient, highly virulent, highly competitive). Preparations of LPS-glucan complex and the respective LPS from the highly virulent strain 248b increased the nodulation activity of both strains by 10-26%. Analogous preparations from a less virulent strain 31 did not have this ability. Unseparated LPS-glucan complexes from these strains increased the productivity of plants infected with the efficient strain by 18-23% but did not change it in plants inoculated with the other, inefficient strain. No significant influence of LPS preparations on the symbiosis productivity was observed. Glucans from both strains enhanced the nodulation ability of the highly virulent strain by 36-56%. In addition, treatment of pea plants with glucan from strain 248b increased nitrogen fixation by root nodules by 27% in plants inoculated with strain 31. In general, the formation and efficiency of the symbiosis of R. leguminosarum bv. viciae with pea plants was more influenced by preparations from strain 248b, highly virulent but deficient in nitrogen fixation, than by preparations from the nitrogen fixation-proficient but less virulent strain 31.},
   Keywords = {Comparative Study
English Abstract
Glucans/pharmacology/*physiology
Lipopolysaccharides/pharmacology
Nitrogen Fixation
Peas/microbiology/*physiology
Plant Roots/microbiology/physiology
Polysaccharides, Bacterial/pharmacology/*physiology
Rhizobium leguminosarum/drug effects/metabolism/*physiology
Species Specificity
Symbiosis},
   Year = {2004} }




@article{
Anzai00,
   Author = {Anzai, Y. and Kim, H. and Park, J.-Y. and Wakabayashi, H. and Oyaizu, H.},
   Title = {Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence},
   Journal = {International Journal of Systematic and Evolutionary Microbiology},
   Volume = {50},
   Number = {4},
   Pages = {1563-1589},
   Abstract = {The broad and vague phenotypic definition allowed the genus Pseudomonas to become a dumping ground for incompletely characterized polarly flagellated, Gram-negative, rod-shaped, aerobic bacteria, and a large number of species have been accommodated in the genus Pseudomonas. The 16S rRNA sequences of 128 valid and invalid Pseudomonas species, which included almost valid species of the genus Pseudomonas listed in the Approved Lists of Bacterial Names, were obtained: sequences of 59 species were determined and those of 69 species were obtained from the GenBank/EMBL/DDBJ databases. These sequences were compared with the sequences of other species of the Proteobacteria. Fifty-seven valid or invalid species including Pseudomonas aeruginosa (type species of the genus Pseudomonas Migula 1894) belonged to the genus Pseudomonas (sensu stricto). Seven subclusters were formed in the cluster of the genus Pseudomonas (sensu stricto), and the resulting clusters conformed well to the rRNA-DNA hybridization study by Palleroni (1984). The other species did not belong to the genus Pseudomonas (sensu stricto) and were related to other genera, which were placed in four subclasses of the Proteobacteria (?, ?, ? and ?-? subclasses). Twenty-six examined species, which were not included in the cluster of the Pseudomonas (sensu stricto) and have not been transferred to other genera as yet, are listed alphabetically: 'Pseudomonas abikonensis', Pseudomonas antimicrobica, Pseudomonas beijerinckii, Pseudomonas beteli, Pseudomonas boreopolis, 'Pseudomonas butanovora', Pseudomonas carboxydohydrogena, Pseudomonas cissicola, Pseudomonas doudoroffii, Pseudomonas echinoides, Pseudomonas elongata, Pseudomonas flectens, Pseudomonas geniculata, Pseudomonas halophila, Pseudomonas hibiscicola, Pseudomonas huttiensis, Pseudomonas iners, Pseudomonas lanceolata, Pseudomonas lemoignei, Pseudomonas mephitica, Pseudomonas pictorum, Pseudomonas saccharophila, Pseudomonas spinosa, Pseudomonas stanier, Pseudomonas syzygii and Pseudomonas woodsii. The phylogenetic affiliations of these 26 pseudomonads species are shown.},
   Keywords = {16S rRNA
Phylogenetic analysis
Pseudomonads
Pseudomonas
RNA 16S
nucleotide sequence
phylogeny
Pseudomonadaceae
Pseudomonas
Pseudomonas abikonensis
Pseudomonas antimicrobica
Pseudomonas beijerinckii
Pseudomonas beteli
Pseudomonas boreopolis
Pseudomonas butanovora
Pseudomonas carboxydohydrogena
Pseudomonas cissicola
Pseudomonas doudoroffii
Pseudomonas echinoides
Pseudomonas elongata
Pseudomonas flectens
Pseudomonas geniculata
Pseudomonas halophila
Pseudomonas hibiscicola
Pseudomonas huttiensis
Pseudomonas iners
Pseudomonas lanceolata
Pseudomonas lemoignei
Pseudomonas mephitica
Pseudomonas pictorum
Pseudomonas saccharophila
Pseudomonas spinosa
Pseudomonas stanier
Pseudomonas syzygii
Pseudomonas woodsii},
   Year = {2000} }




@article{
Ardourel94,
   Author = {Ardourel, M. and Demont, N. and Debelle, F. and Maillet, F. and de Billy, F. and Prome, J.C. and Denarie, J. and Truchet, G.},
   Title = {Rhizobium meliloti lipooligosaccharide nodulation factors: Different structural requirements for bacterial entry into target root hair cells and induction of plant symbiotic developmental responses},
   Journal = {Plant Cell},
   Volume = {6},
   Number = {10},
   Pages = {1357-1374},
      Year = {1994} }




@article{
Arnold03,
   Author = {Arnold, D. L. and Pitman, A. and Jackson, R. W.},
   Title = {Pathogenicity and other genomic islands in plant pathogenic bacteria},
   Journal = {Molecular Plant Pathology},
   Volume = {4},
   Number = {5},
   Pages = {407-420},
   Abstract = {Pathogenicity islands (PAIs) were first described in uropathogenic E. coli. They are now defined as regions of DNA that contain virulence genes and are present in the genome of pathogenic strains, but absent from or only rarely present in non-pathogenic variants of the same or related strains. Other features include a variable G+C content, distinct boundaries from the rest of the genome and the presence of genes related to mobile elements such as insertion sequences, integrases and transposases. Although PAIs have now been described in a wide range of both plant and animal pathogens it has become evident that the general features of PAIs are displayed by a number of regions of DNA with functions other than pathogenicity, such as symbiosis and antibiotic resistance, and the general term genomic islands has been adopted. This review will describe a range of genomic islands in plant pathogenic bacteria including those that carry effector genes, phytotoxins and the type III protein secretion cluster. The review will also consider some medically important bacteria in order to discuss the range, acquisition and stabilization of genomic islands.},
      Year = {2003} }




@book{
Arnold-pc,
   Author = {Arnold, Greg},
   Publisher = {Landcare Research, Lincoln, New Zealand},
      Year = {personal communication} }




@article{
Arslan98,
   Author = {Arslan, E. and Schulz, H. and Zufferey, R. and Künzler, P. and Thöny-Meyer, L.},
   Title = {Overproduction of the Bradyrhizobium japonicum c-type cytochrome subunits of the cbb3 oxidase in Escherichia coli},
   Journal = {Biochemical and Biophysical Research Communications},
   Volume = {251},
   Number = {3},
   Pages = {744-747},
   Abstract = {We report on a system to improve expression of mature c-type cytochromes in Escherichia coli. It is based on the use of plasmid pEC86 that expresses the E. coli cytochrome c maturation genes ccmABCDEFGH constitutively, whereby the production of both endogenous and foreign c-type cytochromes was increased substantially. The periplasmic soluble domains of the c-type cytochrome subunits FixO and FixP of the Bradyrhizobium japonicum cbb3 oxidase could be expressed in E. coli only when pEC86 was provided in a degP-deficient strain. This shows that a stimulation of heme attachment by the Ccm maturase system combined with the diminished proteolytic activity in the periplasm can increase c-type cytochrome yields.},
      Year = {1998} }




@article{
Asai44,
   Author = {Asai, V. T.},
   Title = {\"Uber die mykorrhizenbildung der Leguminosen = pflanzen},
   Journal = {Japanese Journal of Botany},
   Volume = {13},
   Pages = {463-485},
      Year = {1944} }




@incollection{
Ausubel87,
   Author = {Ausubel, F. M. and Brent, R. and Kingston, R. E. and Moore, D. D. and Seidman, J. G. and Smith, J. A. and Struhl, K.},
   Title = {Unit 2.4 Preparation of genomic DNA from bacteria},
   BookTitle = {Current Protocols in Molecular Biology},
   Publisher = {Greene Publishing Associates and Wiley-Interscience},
   Address = {Sunderland, Massachusetts},
   Pages = {2.4.1-2.4.2},
      Year = {1987} }




@article{
Ba02,
   Author = {Ba, S. and Willems, A. and de Lajudie, P. and Roche, P. and Jeder, H. and Quatrini, P. and Neyra, M. and Ferro, M. and Prome, J. C. and Gillis, M. and Boivin-Masson, C. and Lorquin, J.},
   Title = {Symbiotic and taxonomic diversity of rhizobia isolated from Acacia tortilis subsp. raddiana in Africa},
   Journal = {Systematic and Applied Microbiology},
   Volume = {25},
   Number = {1},
   Abstract = {A collection of rhizobia isolated from Acacia tortilis subsp. raddiana from various sites in the North and South of Sahara was analysed for their diversity at both taxonomic and symbiotic levels. On the basis of whole cell protein (SDS-PAGE) and 16S rDNA sequence analysis, most of the strains were found to belong to the Sinorhizobium and Mesorhizobium genera where they may represent several different genospecies. Despite their chromosomal diversity, most A. tortilis Mesorhizobium and Sinorhizobium symbionts exhibited very similar symbiotic characters. Nodulation tests showed that the strains belong to the Acacia-Leucaena-Prosopis nodulation group, although mainly forming non-fixing nodules on species other than A. tortilis. Most of the strains tested responded similarly to flavonoid nod gene inducers, as estimated by using heterologous nodA-lacZ fusions. Thin layer chromatography analysis of the Nod factors synthesized by overproducing strains showed that most of the strains exhibited similar profiles. The structures of Nod factors produced by four different Sinorhizobium spp. strains were determined and found to be similar to other Acacia-Prosopis-Leucaena nodulating rhizobia of the Sinorhizobium-Mesorhizobium-Rhizobium branch. They are chitopentamers, N-methylated and N-acylated by common fatty acids at the terminal non-reducing sugar. The molecules can also be 6-O sulfated at the reducing end and carbamoylated at the non-reducing end. The phylogenetic analysis of available NodA sequences, including new sequences from A. tortilis strains, confirmed the clustering of the NodA sequences of members of the Acacia-Prosopis-Leucaena nodulation group.},
      Year = {2002} }




@article{
Bala01a,
   Author = {Bala, Abdullahi and Giller, Ken E.},
   Title = {Symbiotic specificity of tropical tree rhizobia for host legumes},
   Journal = {New Phytologist},
   Volume = {149},
   Number = {3},
   Pages = {495-507},
   Abstract = {Summary    . The host range and specificity is reported of a genetically diverse group of rhizobia isolated from nodules of Calliandra calothyrsus, Gliricidia sepium, Leucaena leucocephala and Sesbania sesban.    . Nodule number and nitrogen content was measured in seedlings of herbaceous and woody legume species after inoculation with rhizobial strains isolated from tropical soils, to establish symbiotic effectiveness groups for rhizobial strains and their hosts.    . Specificity for nodulation and N2 fixation varied greatly among the legumes. Symbionts of all four legumes exhibited a wide range of promiscuity and symbiotic effectiveness with isolates of S. sesban having the narrowest host range. N2 fixation varied greatly; although some strains fixed large amounts of N2 with more than one host, none was effective with all hosts. Rhizobial isolates of C. calothyrsus, G. sepium and L. leucocephala were able to effectively cross-nodulate each others' hosts as well as a number of other species.    . The complex nature of cross-nodulation relationships between diverse rhizobial strains and legume hosts is highlighted. Host plants inoculated with effective rhizobial strains showed better nitrogen use efficiency than plants supplied solely with mineral nitrogen.},
      Year = {2001} }




@article{
Bala01b,
   Author = {Bala, A. and Murphy, P. and Giller, K. E.},
   Title = {Genetic diversity of rhizobia from natural populations varies with the soil dilution sampled},
   Journal = {Soil Biology and Biochemistry},
   Volume = {33},
   Number = {6},
   Abstract = {Rhizobia were isolated from root nodules of three tree legumes (Calliandra calothyrsus, Gliricidia sepium and Leucaena leucocephala) inoculated with dilution series of two tropical soils (Yucatan, Mexico and Chitala, Malawi). The diversity of the isolates obtained from different soil dilutions was assessed by polymerase chain reaction-restriction fragment length polymorphism analysis of the internally transcribed spacer region between the 16S and 23S rRNA genes. In both soils, there was a strong effect of dilution on the genetic diversity of the populations with apparent diversity decreasing with increasing dilution.},
      Year = {2001} }




@article{
Bala02,
   Author = {Bala, A. and Murphy, P. and Giller, K. E.},
   Title = {Occurrence and genetic diversity of rhizobia nodulating Sesbania sesban in African soils},
   Journal = {Soil Biology and Biochemistry},
   Volume = {34},
   Number = {11},
   Abstract = {The distribution, diversity and relative abundance of Sesbania sesban rhizobia in African soils were investigated by host-trapping and counting of rhizobia and characterization using restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA and the internally transcribed spacer (ITS) between the 16S and 23S rRNA genes. Isolates representative of the diverse 16S rRNA groups from the various soils were selected for sequence analysis of the first 750 bp of the 16S rRNA. Compatible rhizobia were detected in only 15 out of 55 soils, and were present generally in soils with more than 10% clay, and those from low-lying areas. Populations were small, generally much less than 50 cells g-1 soil. The rhizobia nodulating S. sesban were genetically diverse, with isolates bearing 16S rRNA sequences similar to those of rhizobia belonging to the genera Rhizobium, Mesorhizobium, Sinorhizobium and Allorhizobium. Approximately 1% of the isolates recovered had sequences with close homology with Agrobacterium tumefaciens. Despite the wide phylogenetic distribution of the rhizobial isolates, the Mesorhizobium group was dominant in all soils examined, accounting for 90% of the isolates on average, with individual soil populations usually being comprised of two genera. There was a marked variability in the sequence and size of the ITS region among rhizobia nodulating Sesbania which indicates a broad diversity of 'strain' types both within and between soil populations, and within and between rhizobial genera.},
      Year = {2002} }




@article{
Bala03b,
   Author = {Bala, A. and Murphy, P. and Giller, K.E.},
   Title = {Distribution and diversity of rhizobia nodulating agroforestry legumes in soils from three continents in the tropics},
   Journal = {Molecular Ecology},
   Volume = {12},
   Number = {4},
   Pages = {917-929},
   Abstract = {The natural rhizobial populations of Calliandra calothyrsus, Gliricidia sepium, Leucaena leucocephala and Sesbania sesban were assessed in soils from nine sites across tropical areas of three continents. The rhizobial population size varied from undetectable numbers to 1.8 × 104 cells/g of soil depending on the trap host and the soil. Calliandra calothyrsus was the most promiscuous legume, nodulating in eight soils, while S. sesban nodulated in only one of the soils. Polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) analyses of the 16S rRNA gene and the internally transcribed spacer (ITS) region between the 16S and 23S rRNA genes were used to assess the diversity and relative abundance of rhizobia trapped from seven of the soils by C. calothyrsus, G. sepium and L. leucocephala. Representatives of the 16S rRNA RFLP groups were also subjected to sequence analysis of the first 950 base pairs of the 16S rRNA gene. Eighty ITS groups were obtained, with none of the ITS types being sampled in more than one soil. RFLP analysis of the 16S rRNA yielded 23 'species' groups distributed among the Rhizobium, Mesorhizobium, Sinorhizobium and Agrobacterium branches of the rhizobial phylogenetic tree. The phylogeny of the isolates was independent of the site or host of isolation, with different rhizobial groups associated with each host across the soils from widely separated geographical regions. Although rhizobial populations in soils sampled from the centre of diversity of the host legumes were the most genetically diverse, soil acidity was highly correlated with the diversity of ITS types. Our results support the hypothesis that the success of these tree legumes in soils throughout the tropics is the result of their relative promiscuity (permissiveness) allowing nodulation with diverse indigenous rhizobial types.},
   Keywords = {Bacterial diversity
Biogeography
Calliandra
Gliricidia
Leucaena
Nitrogen fixation},
   Year = {2003} }




@article{
Bala03a,
   Author = {Bala, A. and Murphy, P. J. and Osunde, A. O. and Giller, K. E.},
   Title = {Nodulation of tree legumes and the ecology of their native rhizobial populations in tropical soils},
   Journal = {Applied Soil Ecology},
   Volume = {22},
   Number = {3},
   Abstract = {A legume introduced into a new area will only form nodules and fix nitrogen if compatible rhizobia are present in the soil. Using 25 (60 in the case of Sesbania sesban) soils sampled from tropical areas of Africa, Asia and Latin America, we examined the nodulation of four agroforestry tree species (Calliandra calothyrsus, Gliricidia sepium, Leucaena leucocephala and S. sesban), their symbiotic interactions with the native rhizobial populations, and some of the ecological indicators of rhizobial population dynamics. Rhizobial population sizes estimated by the legume species ranged from undetectable numbers to 3.16x104 cells per g of soil depending on the trap host species. Although C. calothyrsus had the highest nodulation rate in the soils used, inoculation tests showed L. leucocephala to be the most promiscuous species while G. sepium had the most effective symbiosis. S. sesban was the most specific for both nodulation and symbiotic effectiveness. Symbiotic effectiveness did not bear any close relationship with specific soil parameters, but rhizobial numbers were highly correlated with soil acidity, particle size and exchangeable bases. Soil acidity was also the main factor that was highly correlated with genetic diversity among the rhizobial populations.},
      Year = {2003} }




@article{
Bala93,
   Author = {Bala, M. and Gaur, Y. D.},
   Title = {Effect of mixed inoculation with isogenic strains of Bradyrhizobium on total nodules of pigeonpea},
   Journal = {Current Science},
   Volume = {65},
   Number = {2},
   Abstract = {Competition among different strains of rhizobia for occupying infection sites on root systems is common and leads to the formation of varying proportions of nodules by competing strains. A wild-type strain of Bradyrhizobium sp. and its six spontaneous azide-resistant mutants were examined for their ability to nodulate pigeonpea as single cultures as well as in pairs with the wild-type strain. The number of nodules formed by two mutants (Azi5 and Azi50) was significantly more than the number formed by the wild-type strain. Among mixed inoculations a combination of the wild-type strain and Azi52 produced significantly more nodules than were formed by the two strains individually. This indicated that interaction between different strains affects total nodulation.},
      Year = {1993} }




@article{
Barnet91,
   Author = {Barnet, Y. M. and Catt, P. C.},
   Title = {Distribution and characteristics of root-nodule bacteria isolated from Australian \emph{Acacia} spp.},
   Journal = {Plant and Soil},
   Volume = {135},
   Number = {1},
   Pages = {109-120},
   Abstract = {Root-nodule bacteria capable of nodulating local acacias were isolated from five climatically diverse and geographically widely separated localities in New South Wales. Strains showed markedly geographic localization. Fast-growing isolates, culturally and serologically related to Rhizobium, were obtained from the arid zone but from no other area. Alpine isolates had particularly slow growth rates, with 50% taking >10 days to form colonies on yeast mannitol agar. Strains from the rainforest and coastal health areas had the characteristics of typical Bradyrhizobium. Most of the strains tested had a wide host range, nodulating members of both the Mimosaceae and the Fabaceae, although the extra-slow growing alpine isolates appeared specific for their original host. -from Authors},
      Year = {1991} }




@article{
Barnett01,
   Author = {Barnett, Melanie J. and Fisher, Robert F. and Jones, Ted and Komp, Caridad and Abola, A. Pia and Barloy-Hubler, Frederique and Bowser, Leah and Capela, Delphine and Galibert, Francis and Gouzy, Jerome and Gurjal, Mani and Hong, Andrea and Huizar, Lucas and Hyman, Richard W. and Kahn, Daniel and Kahn, Michael L. and Kalman, Sue and Keating, David H. and Palm, Curtis and Peck, Melicent C. and Surzycki, Raymond and Wells, Derek H. and Yeh, Kuo-Chen and Davis, Ronald W. and Federspiel, Nancy A. and Long, Sharon R.},
   Title = {Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid},
   Journal = {Proceedings of the National Academy of Sciences of the United States of America},
   Volume = {98},
   Number = {17},
   Pages = {9883-9888},
   Abstract = {The symbiotic nitrogen-fixing soil bacterium Sinorhizobium meliloti contains three replicons: pSymA, pSymB, and the chromosome. We report here the complete 1,354,226-nt sequence of pSymA. In addition to a large fraction of the genes known to be specifically involved in symbiosis, pSymA contains genes likely to be involved in nitrogen and carbon metabolism, transport, stress, and resistance responses, and other functions that give S. meliloti an advantage in its specialized niche.},
      Year = {2001} }




@article{
Bassett77,
   Author = {Bassett, B. and Goodman, R. N. and Novacky, A.},
   Title = {Ultrastructure of soybean nodules. I: release of rhizobia from the infection thread},
   Journal = {Canadian Journal of Microbiology},
   Volume = {23},
   Number = {5},
   Pages = {573-82},
   Abstract = {Root nodules on soybeans (var. Clark 63) were examined by transmission electron microscopy 10-12 days after seed inoculation and planting. The cell infection process appeared identical in both effective nodules, induced by Rhizobium japonicum strain 138 (USDA) and in ineffective nodules, induced by strain 8-0 (Iowa). Electron micrographs are presented which suggest that rhizobia are freed from the infection thread by disintegration of the thread wall and compartmentalization of the distintegrated wall material in membrane-bound vesicles derived from the membrane surrounding the thread. As the thread wall is removed in this manner, the bacteria are released into the host cytoplasm by a process which encloses each in an envelope also dervide from the thread membrane. Any thread wall material remaining around a bacterium after it has dissociated from the thread is removed from the envelope space by vesiculation of the membrane envelope. thus, it appears that endocytosis of both the bacteria and the material composing the infection thread wall occurs during release of rhizobia into the host cell.},
   Keywords = {Cell Wall/ultrastructure
Cytoplasm/microbiology
Endocytosis
Microscopy, Electron
*Plants/*microbiology
Rhizobium/*growth \& development/ultrastructure
*Soil Microbiology
Soybeans
Vacuoles/microbiology},
   Year = {1977} }




@article{
Batut94,
   Author = {Batut, J. and Boistard, P.},
   Title = {Oxygen control in Rhizobium},
   Journal = {Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology},
   Volume = {66},
   Number = {1-3},
   Pages = {129-50},
   Abstract = {Rhizobia are gram-negative bacteria with two distinct habitats: the soil rhizosphere in which they have a saprophytic and, usually, aerobic life and a plant ecological niche, the legume nodule, which constitutes a microoxic environment compatible with the operation of the nitrogen reducing enzyme nitrogenase. The purpose of this review is to summarize the present knowledge of the changes induced in these bacteria when shifting to a microoxic environment. Oxygen concentration regulates the expression of two major metabolic pathways: energy conservation by respiratory chains and nitrogen fixation. After reviewing the genetic data on these metabolic pathways and their response to oxygen we will put special emphasis on the regulatory molecules which are involved in the control of gene expression. We will show that, although homologous regulatory molecules allow response to oxygen in different species, they are assembled in various combinations resulting in a variable regulatory coupling between genes for microaerobic respiration and nitrogen fixation genes. The significance of coordinated regulation of genes not essential for nitrogen fixation with nitrogen fixation genes will also be discussed.},
   Keywords = {Bacterial Proteins/genetics
Electron Transport
Gene Expression Regulation, Bacterial/genetics
Genes, Nitrogen Fixation/genetics
Hydrogenase/metabolism
Monophenol Monooxygenase/genetics
Nitrogen Fixation/*physiology
Oxygen/*physiology
Oxygen Consumption
Phylogeny
Rhizobium/genetics/*metabolism
Support, Non-U.S. Gov't
Transcription Factors/genetics},
   Year = {1994} }




@article{
Batzli91,
   Author = {Batzli, J. M. and Graves, W. R. and van Berkum, P.},
   Title = {Isolation and characterization of rhizobia effective with \emph{Maackia amurensis}},
   Journal = {Journal of the American Society for Horticultural Science},
   Volume = {117},
   Number = {4},
   Pages = {612-616},
      Year = {1991} }




@book{
Baxevanis04,
   Author = {Baxevanis, A. D. and Ouellette, B. F. F.},
   Title = {Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins},
   Publisher = {Wiley-Interscience},
   Edition = {3rd},
      Year = {2004} }




@article{
Beauregard03,
   Author = {Beauregard, M.-S. and Seguin, P. and Sheaffer, C. C. and Graham, P. H.},
   Title = {Characterization and evaluation of North American Trifolium ambiguum -nodulating rhizobia},
   Journal = {Biology and Fertility of Soils},
   Volume = {38},
   Number = {5},
   Pages = {311-318},
   Abstract = {Kura clover (Trifolium ambiguum M. Bieb.) is a promising persistent forage legume, whose use is currently limited by establishment difficulties in part attributable to nodulation problems. In this study, we phenotypically characterized 18 Kura clover rhizobia including 12 newly isolated North American strains using 111 growth tests. The symbiotic performances of these 12 strains when used to inoculate hexaploid Kura clover plants were then evaluated in a growth chamber and compared to five strains commonly used in commercial Kura clover inoculants. Non-inoculated plants with or without N fertilization were used as controls. Field evaluations were also conducted in 2001 and 2002 in Montreal, Quebec and Becker, Minnesota. Hexaploid Kura clover was seeded with one of three North American strains or three commercial strains and compared to non-inoculated controls with or without N fertilizer. Phenotypic diversity observed among the 12 North American strains was limited. The North American strains were often more efficient than strains commonly used in commercial rhizobial inoculants in both growth chamber and field trials. In the growth chamber study, 60 days after seeding, shoot dry matter accumulation was overall 205% greater with North American strains than with commercial strains and 45% greater than with the best commercial strain tested. Some of the strains currently used in commercial inoculants failed to nodulate Kura clover plants effectively. North American strains tested in field trials (i.e., CT1-1, CT1-2, and WI4-4) overall increased total and shoot dry matter accumulation, 100 days after seeding, in three of four environments by 27% and 31% respectively, when compared to commercial inoculant strains. While these strains appear to have potential they still produced less dry matter than non-inoculated N-fertilized controls.},
   Keywords = {Caucasian clover
Inoculation
Kura clover
Rhizobia
Trifolium ambiguum M. Bieb},
   Year = {2003} }




@article{
Bell02,
   Author = {Bell, P. J. L. and Sunna, A. and Gibbs, M. D. and Curach, N. C. and Nevalainen, H. and Bergquist, P. L.},
   Title = {Prospecting for novel lipase genes using PCR},
   Journal = {Microbiology},
   Volume = {148},
   Number = {8},
   Pages = {2283-2291},
   Abstract = {A PCR method suitable for the isolation of lipase genes directly from environmental DNA is described. The problems associated with the low levels of similarity between lipase genes were overcome by extensive analysis of conserved regions and careful primer design. Using this method, a lipase gene (oli-lipase) was isolated directly from environmental DNA. This lipase showed less than 20% similarity with other known lipases at the amino acid level. The study also revealed that distantly related members of the ?/? hydrolase superfamily share similar conserved motifs with the lipases, thus making these genes targets for gene prospecting by PCR.},
   Keywords = {Biomass
Environment
Thermophilic
Triacylglycerol hydrolase
triacylglycerol lipase
nucleotide sequence
structural gene
Bacillus
Biomass
Chromosomes, Bacterial
Cloning, Molecular
Conserved Sequence
DNA Primers
DNA, Bacterial
Environment
Escherichia coli
Genes, Structural
Hydrolases
Lipase
Molecular Sequence Data
Polymerase Chain Reaction
Sequence Homology, Amino Acid
Support, Non-U.S. Gov't},
   Year = {2002} }




@book{
Bellich96,
   Author = {Bellich, J.},
   Title = {Making peoples: a history of the New Zealanders from Polynesian settlement to the end of the nineteenth century},
   Publisher = {Allen Lane, the Penguin Press},
   Address = {Auckland},
      Year = {1996} }




@article{
Bellingham04,
   Author = {Bellingham, P. J. and Buxton, R. P. and Duncan, R. P. and Lee, W. G.},
   Title = {Seedling growth rate and survival do not predict invasiveness in naturalized woody plants in New Zealand},
   Journal = {Oikos},
   Volume = {106},
   Number = {2},
   Pages = {308-316},
   Abstract = {We tested if plant species invasiveness (measured as rate of geographic spread in New Zealand) was positively associated with seedling relative growth rate (RGR) and survival, among 33 naturalized woody plant species in four families (Fabaceae, Mimosaceae, Pinaceae, Rosaceae). Eight disturbance and fertilization treatments were applied to seedlings in pots to mimic conditions the species are likely to encounter in the wild. We tested if seedlings of more invasive species have higher RGR and greater survival under these conditions. We also tested whether more invasive species had wider tolerance of the conditions to which they were subjected. There were no significant relationships between seedling RGR or survival and invasiveness for any of the treatments. Measures of tolerance (a species' relative performance across all treatments), based on both RGR and survival, also failed to explain differences in invasiveness. Our findings contrast with those from a recent study by Grotkopp et al. (2002) showing a positive correlation between seedling RGR and invasiveness in Pinus species, even though our study included 12 Pinus species. The findings of the two studies may differ because they focus on different stages in the invasion process. Our study tested whether RGR (and survival) was associated with the rate of spread of invasive species following naturalization, whereas Grotkopp et al. primarily tested whether RGR was associated with the probability of naturalization. We caution that relationships between RGR and measures of invasiveness are likely to be confounded with human introduction effort. Among pines, species with high RGR are more likely to have been widely cultivated, for purposes such as timber production, providing more opportunities for naturalization and spread. Associations between RGR, invasiveness and human introduction effort need to be partitioned out before we can reliably infer causal relationships.},
      Year = {2004} }




@article{
Bellingham01,
   Author = {Bellingham, P. J. and Walker, L. R. and Wardle, D. A.},
   Title = {Differential facilitation by a nitrogen-fixing shrub during primary succession influences relative performance of canopy tree species},
   Journal = {Journal of Ecology},
   Volume = {89},
   Number = {5},
   Pages = {861-875},
   Abstract = {1. The facilitative and inhibitory effects of a nitrogen-fixing shrub, Carmichaelia odorata, during primary succession were studied using both field measurements in a New Zealand temperate montane valley, and manipulative glasshouse experiments on seedlings of the three dominant tree species, Griselinia littoralis, Metrosideros umbellata and Weinmannia racemosa. 2. During a stand development chronosequence of <100 years in which Carmichaelia colonized, dominated and senesced, there was significant development of soil organic horizons and a large build-up of soil nitrogen, especially in the organic horizon. Soil organic matter and nitrogen levels across the sequence were strongly correlated with the main DCA axis of vascular plant species composition, along which there was change in dominance from herbaceous to woody species. Vegetation increased in height and light levels declined with stand development. 3. Similar responses to shade that mimicked that in mature Carmichaelia stands suggested that inhibitory effects were likely to be uniform across the three tree species. 4. Nitrogen, either added via Carmichaelia litter or in solution, enhanced shoot biomass and foliar nitrogen concentrations of all three tree species. Growth in soils of increasing development increased foliar nitrogen concentrations for Griselinia and Weinmannia, but not Metrosideros. 5. Overall, Metrosideros was the least responsive to potential facilitative effects of Carmichaelia, and Griselinia exhibited the highest degree of plasticity of response. Future forest composition and spatial patterning of species in mixed stands here, as elsewhere, is likely to result from differential facilitative responses during early primary succession.},
   Keywords = {Carmichaelia odorata
Griselinia littoralis
Inhibition
Metrosideros umbellata
Phosphorus
Specific leaf area
Temperate montane rain forest
Weinmannia racemosa
nitrogen fixation
succession (environment)
facilitation
inhibition
nitrogen fixation
primary succession
rainforest
soil organic matter
New Zealand
Carmichaelia odorata
Griselinia littoralis
Metrosideros umbellata
Weinmannia racemosa},
   Year = {2001} }




@article{
BenRomdhane05,
   Author = {Ben Romdhane, S. and Nasr, H. and Samba-Mbaye, R. and Neyra, M. and Ghorbal, M. H.},
   Title = {Diversity of Acacia tortilis rhizobia revealed by PCR/RFLP on crushed root nodules in Tunisia},
   Journal = {Annals of Microbiology},
   Volume = {55},
   Number = {4},
   Pages = {249-254},
   Abstract = {Rhizobia are used exclusively in agricultural and agroforestry systems for enhancing the ability of legumes to fix atmospheric nitrogen. Knowledge on taxonomical characteristics and ecology of the indigenous Rhizobium population is necessary for the selection of inoculant strains. In this study, we have assessed the genetic diversity of rhizobia from the host plant, Acacia tortilis ssp. raddiana along different areas of Tunisia. Thirty-one nodules were collected both directly and by trap host plants. Genetic diversity of rhizobia strains was studied by restriction fragment length polymorphism (RFLP) analysis of PCR-amplified intergenic spacer (IGS) and 16S rDNA. The PCR analysis was performed on nodules extracted-DNAs. The approaches used in this study yielded consistent results, which revealed a high degree of heterogeneity among strains and detection of 20 distinct genetic groups. These rhizobia are related to Sinorhizobium, Rhizobium, Mesorhizobium and Agrobacterium genera. This is the first report on rhizobia nodulating leguminous trees in Tunisia.},
   Keywords = {Acacia tortilis
Diversity
Nodules extracted-DNAs
PCR-RFLP
Tunisia},
   Year = {2005} }




@article{
Benhizia04,
   Author = {Benhizia, Y. and Benhizia, H. and Benguedouar, A. and Muresu, R. and Giacomini, A. and Squartini, A.},
   Title = {Gamma proteobacteria can nodulate legumes of the genus \emph{Hedysarum}},
   Journal = {Systematic and Applied Microbiology},
   Volume = {27},
   Number = {4},
   Pages = {462-468},
   Abstract = {The bacteria hosted in the root nodules of the three Mediterranean wild legume species Hedysarum carnosum, Hedysarum spinosissimum subsp. capitatum, and Hedysarum pallidum, growing in native stands in different habitats in Algeria were isolated. Bacteria were recovered on yeast-mannitol-agar or on minimal media from a total of 52 nodules. Isolates were analyzed by Amplified Ribosomal DNA Restriction Analysis (ARDRA) using the enzyme Cfol, and further sorted by RAPD fingerprinting. A total of ten different types were found and their amplified 16S rDNA was sequenced and compared to databases. The BLAST alignment indicates that all the species whose sequences share 98 to 100% identity to the bacteria found in these nodules belong to the class Gammaproteobacteria and include Pantoea agglomerans, Enterobacter kobei, Enterobacter Cloacae, Leclercia adecarboxylata, Escherichia vulneris, and Pseudomonas sp. No evidence of any rhizobial-like sequence was found even upon amplifying from the bulk of microbial cells obtained from the squashed nodules, suggesting that the exclusive occupants of the nodules formed by the three plants tested are members of the orders Enterobacteriales or Pseudomonadales. This is the first report of Gammaproteobacteria associated with legume nodules. Despite the presence of the related crop plant Hedysarum coronarium, specifically nodulated by Rhizobium sullae, these three Hedysarum species demonstrate to have undergone a separate path in terms of endophytic interactions with bacteria. An hypothesis to account for differences between the symbiotic relationships engaged by man-managed legumes, and those found in plants whose ecology is independent from human action, is discussed.},
      Year = {2004} }




@article{
Benson88,
   Author = {Benson, D. R.},
   Title = {The genus \emph{Frankia}: Actinomycete symbionts of plants},
   Journal = {Microbiol Sci},
   Volume = {5},
   Number = {1},
   Pages = {9-12},
   Abstract = {Biological N2 fixation is performed most effectively by prokaryotic diazotrophs when in mutualistic symbioses with higher plants. The most intensively studied N2-fixing symbioses involve leguminous plants and rhizobia. However, Frankia actinomycetes have attracted attention recently because they form root nodules on a broad range of non-legumes and because such nodules fix N2 as effectively as rhizobial nodules. Since the Frankia symbiosis results from an actinomycetic invasion of plant roots, it has been termed the 'actinorhizal symbiosis'.},
   Keywords = {Actinomycetaceae/genetics/*physiology/ultrastructure
Ammonia/metabolism
Bacterial Proteins/genetics/metabolism
Bacteriological Techniques
Genes, Nitrogen Fixation
*Nitrogen Fixation
Nitrogenase/antagonists \& inhibitors/genetics
Oxygen/pharmacology
Plants/*microbiology
*Symbiosis},
   Year = {1988} }




@article{
Benson93,
   Author = {Benson, D. R. and Silvester, W. B.},
   Title = {Biology of \emph{Frankia} strains, actinomycete symbionts of actinorhizal plants},
   Journal = {Microbiological Reviews},
   Volume = {57},
   Number = {2},
   Pages = {293-319},
   Abstract = {Frankia strains are N2-fixing actinomycetes whose isolation and cultivation were first reported in 1978. They induce N2-fixing root nodules on diverse nonleguminous (actinorhizal) plants that are important in ecological successions and in land reclamation and remediation. The genus Frankia encompasses a diverse group of soil actinomycetes that have in common the formation of multilocular sporangia, filamentous growth, and nitrogenase- containing vesicles enveloped in multilaminated lipid envelopes. The relatively constant morphology of vesicles in culture is modified by plant interactions in symbiosis to give a diverse array of vesicle shapes. Recent studies of the genetics and molecular genetics of these organisms have begun to provide new insights into higher-plant-bacterium interactions that lead to productive N2-fixing symbioses. Sufficient information about the relationship of Frankia strains to other bacteria, and to each other, is now available to warrant the creation of some species based on phenotypic and genetic criteria.},
      Year = {1993} }




@article{
Benton03,
   Author = {Benton, M. J. and Ayala, F. J.},
   Title = {Dating the tree of life},
   Journal = {Science},
   Volume = {300},
   Number = {5626},
   Pages = {1698-1700},
   Abstract = {The relative merits of molecular and paleontological dates of major branching points in the tree of life are currently debated. In some cases, molecular date estimates are up to twice as old as paleontological dates. However, although it is true that paleontological dates are often too young (missing fossils), molecular dates are often too old (statistical bias). Intense study of the dating of major splits in the tree of mammals has shown rapprochement as fossil dates become older and molecular dates become younger.},
      Year = {2003} }




@article{
Berck99,
   Author = {Berck, S. and Perret, X. and Quesada-Vincens, J.-C. and Prom\'e, D. and Broughton, W. J. and Jabbouri, S.},
   Title = {NolL of \emph{Rhizobium} sp. strain NGR234 is required for o-acetyltransferase activity},
   Journal = {Journal of Bacteriology},
   Volume = {181},
   Number = {3},
   Pages = {957-964},
      Year = {1999} }




@article{
Bergersen78,
   Author = {Bergersen, F. J. and Turner, G. L.},
   Title = {Activity of nitrogenase and glutamine synthetase in relation to availability of oxygen in continuous cultures of a strain of cowpea Rhizobium sp. supplied with excess ammonium},
   Journal = {Biochimica et Biophysica Acta},
   Volume = {538},
   Number = {3},
   Pages = {406-16},
   Abstract = {In samples from nitrogen-fixing continuous cultures of strain CB756 of the cowpea type rhizobia (Rhizobium sp.), newly fixed NH+4 is in equiblibrium with the medium, from where it is assimilated by the glutamine synthetase/glutamate synthase pathway. In samples from steady state cultures with different degrees of oxygen-limitation, nitrogenase activity was positively correlated with the biosynthetic of glutamine synthetase in cell free extracts. Also, activities in biosynthetic assays were positively correlated with activities in gamma-glutamyl transferase assays containing 60 mM Mg2+. Relative adenylylation of glutamine synthetase was conveniently measured in cell free extracts as the ratio of gamma-glutamyl transferase activities without and with addition of 60 mM Mg2+. Automatic control of oxygen supply was used to facilitate the study of transitions between steady-state continuous cultures with high and low nitrogenase activities. Adenylylation of glutamine synthetase and repression of nitrogenase activity in the presence of excess NH+4, were masked when oxygen strongly limited culture yield. Partial relief of the limitation in cultures supplied with 10 mM NH+4 produced early decline in nitrogenase activity and increase in relative adenylylation of glutamine synthetase. Decreased oxygen supply produced a rapid decline in relative adenylylation, followed by increased nitrogenase activity, supporting the concept that control of nitrogenase synthesis is modulated by glutamine synthetase adenylylation in these bacteria.},
   Keywords = {Ammonium Sulfate/metabolism
Glutamate-Ammonia Ligase/*metabolism
Glutamine/metabolism
Magnesium/pharmacology
Manganese/pharmacology
Nitrogen/metabolism
Nitrogenase/*metabolism
Oxygen/*pharmacology
Rhizobium/*enzymology
gamma-Glutamyltransferase/metabolism},
   Year = {1978} }




@article{
Bergsten05,
   Author = {Bergsten, Johannes},
   Title = {A review of long-branch attraction},
   Journal = {Cladistics},
   Volume = {21},
   Number = {2},
   Pages = {163-193},
   Abstract = {Abstract  The history of long-branch attraction, and in particular methods suggested to detect and avoid the artifact to date, is reviewed. Methods suggested to avoid LBA-artifacts include excluding long-branch taxa, excluding faster evolving third codon positions, using inference methods less sensitive to LBA such as likelihood, the Aguinaldo et al. approach, sampling more taxa to break up long branches and sampling more characters especially of another kind, and the pros and cons of these are discussed. Methods suggested to detect LBA are numerous and include methodological disconcordance, RASA, separate partition analyses, parametric simulation, random outgroup sequences, long-branch extraction, split decomposition and spectral analysis. Less than 10 years ago it was doubted if LBA occurred in real datasets. Today, examples are numerous in the literature and it is argued that the development of methods to deal with the problem is warranted. A 16 kbp dataset of placental mammals and a morphological and molecular combined dataset of gall waSPS are used to illustrate the particularly common problem of LBA of problematic ingroup taxa to outgroups. The preferred methods of separate partition analysis, methodological disconcordance, and long branch extraction are used to demonstrate detection methods. It is argued that since outgroup taxa almost always represent long branches and are as such a hazard towards misplacing long branched ingroup taxa, phylogenetic analyses should always be run with and without the outgroups included. This will detect whether only the outgroup roots the ingroup or if it simultaneously alters the ingroup topology, in which case previous studies have shown that the latter is most often the worse. Apart from that LBA to outgroups is the major and most common problem; scanning the literature also detected the ill advised comfort of high support values from thousands of characters, but very few taxa, in the age of genomics. Taxon sampling is crucial for an accurate phylogenetic estimate and trust cannot be put on whole mitochondrial or chloroplast genome studies with only a few taxa, despite their high support values. The placental mammal example demonstrates that parsimony analysis will be prone to LBA by the attraction of the tenrec to the distant marsupial outgroups. In addition, the murid rodents, creating the classic "the guinea-pig is not a rodent" hypothesis in 1996, are also shown to be attracted to the outgroup by nuclear genes, although including the morphological evidence for rodents and Glires overcomes the artifact. The gall wasp example illustrates that Bayesian analyses with a partition-specific GTR + Gamma + I model give a conflicting resolution of clades, with a posterior probability of 1.0 when comparing ingroup alone versus outgroup rooted topologies, and this is due to long-branch attraction to the outgroup.  c The Willi Hennig Society 2005.},
      Year = {2005} }




@article{
Beringer74,
   Author = {Beringer, J. E.},
   Title = {R factor transfer in Rhizobium leguminosarum},
   Journal = {Journal of General Microbiology},
   Volume = {84},
   Number = {1},
   Pages = {188-198},
      Year = {1974} }




@article{
Beringer79,
   Author = {Beringer, J. E. and Brewin, N. and Johnston, A. W. and Schulman, H. M. and Hopwood, D. A.},
   Title = {The \emph{Rhizobium}--legume symbiosis},
   Journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences},
   Volume = {204},
   Number = {1155},
   Pages = {219-233},
   Abstract = {The rhizobia are soil microorganisms that can interact with leguminous plants to form root nodules within which conditions are favourable for bacterial nitrogen fixation. Legumes allow the development of very large rhizobial populations in the vicinity of their roots. Infections and nodule formation require the specific recognition of host and Rhizobium, probably mediated by plant lectins. Penetration of the host by a compatible Rhizobium species usually provokes host root cell division to form the nodule, and a process of differentiation by both partners then ensues. In most cases the rhizobia alter morphologically to form bacteroids, which are usually larger than the free-living bacteria and have altered cell walls. At all stages during infection, the bacteria are bounded by host cell plasmalemma. The enzyme nitrogenase is synthesized by the bacteria and, if leghaemoglobin is present, nitrogen fixation will occur. Leghaemoglobin is a product of the symbiotic interaction, since the globin is produced by the plant while the haem is synthesized by the bacteria. In the intracellular habitat the bacteria are dependent upon the plant for supplies of energy and the bacteroids, in particular, appear to differentiate so that they are no longer able to utilize the nitrogen that they fix. Regulation of the supply of carbohydrate and the use of the fixed nitrogen thus appear to be largely governed by the host.},
   Keywords = {Leghemoglobin/physiology
Nitrogenase/metabolism
*Plant Physiology
Rhizobium/*physiology
Species Specificity
*Symbiosis},
   Year = {1979} }




@article{
Beyene04,
   Author = {Beyene, D. and Kassa, S. and Ampy, F. and Asseffa, A. and Gebremedhin, T. and van Berkum, P.},
   Title = {Ethiopian soils harbor natural populations of rhizobia that form symbioses with common bean ( Phaseolus vulgaris L.)},
   Journal = {Archives of Microbiology},
   Volume = {181},
   Number = {2},
   Pages = {129-36},
   Abstract = {The diversity and taxonomic relationships of 83 bean-nodulating rhizobia indigenous to Ethiopian soils were characterized by PCR-RFLP of the internally transcribed spacer (ITS) region between the 16S and 23S rRNA genes, 16S rRNA gene sequence analysis, multilocus enzyme electrophoresis (MLEE), and amplified fragment-length polymorphism. The isolates fell into 13 distinct genotypes according to PCR-RFLP analysis of the ITS region. Based on MLEE, the majority of these genotypes (70%) was genetically related to the type strain of Rhizobium leguminosarum. However, from analysis of their 16S rRNA genes, the majority was placed with Rhizobium etli. Transfer and recombination of the 16S rRNA gene from presumptively introduced R. etli to local R. leguminosarum is a possible theory to explain these contrasting results. However, it seems unlikely that bean rhizobia originating from the Americas (or Europe) extensively colonized soils of Ethiopia because Rhizobium tropici, Rhizobium gallicum, and Rhizobium giardinii were not detected and only a single ineffective isolate of R. etli that originated from a remote location was identified. Therefore, Ethiopian R. leguminosarum may have acquired the determinants for nodulation of bean from a low number of introduced bean-nodulating rhizobia that either are poor competitors for nodulation of bean or that failed to survive in the Ethiopian environment. Furthermore, it may be concluded from the genetic data presented here that the evidence for separating R. leguminosarum and R. etli into two separate species is inconclusive.},
   Keywords = {DNA Fingerprinting
DNA, Bacterial/analysis/chemistry/isolation \& purification
DNA, Ribosomal/analysis/chemistry/isolation \& purification
Enzymes/analysis
Ethiopia
Molecular Sequence Data
Phaseolus/*microbiology
Phylogeny
Polymorphism, Genetic
Polymorphism, Restriction Fragment Length
RNA, Ribosomal, 16S/genetics
Rhizobiaceae/*classification/*isolation \& purification/physiology
Sequence Analysis, DNA
*Soil Microbiology
*Symbiosis},
   Year = {2004} }




@book{
ILDIS,
   Author = {Bisby, F. A. and Zarucchi, J. L. and Schrire, B. D. and Roskov, Y. R. and White, R. J.},
   Title = {International Legume Database \& Information Service. Version 10},
   Publisher = {ILDIS},
   Address = {Reading},
      Year = {2005} }




@article{
Bloem01,
   Author = {Bloem, J. F. and Law, I. J.},
   Title = {Determination of competitive abilities of Bradyrhizobium japonicum strains in soils from soybean production regions in South Africa},
   Journal = {Biology and Fertility of Soils},
   Volume = {33},
   Number = {3},
   Pages = {181-189},
   Abstract = {Bradyrhizobium japonicum strain CB 1809 was recently chosen to replace strain WE 1 in commercial soybean [Glycine max (L.) Merr.] inoculants in South Africa, the selection criterion being N-2-fixing effectiveness. Nodulation competitiveness is an additional characteristic required of inoculants and was determined for CB1 809 and WB 1 as well as two other strains, USDA 110 and a Brazilian strain 965, using the gusA marker gene to identify strains. Initial experiments with plants grown in sterile sand showed that the competitive index of strain WB 1 was less than that of the other strains. Further comparisons used plants grown in five soils containing established populations of B. japonicum. When strains were applied in peat inoculum to seed at a rate of 1,000 cells per seed in a soil containing 300 rhizobia g(-1), significant differences in nodule occupancy were detected and strains ranked in the order 965>CB1809>USDA 110>WB 1. The remaining four soils each contained about 10(6) rhizobia g(-1) and 5 x 10(6) cells were applied per seed. Nodule occupancy by inoculant strains ranged from 22% to 81% between soils. In this experiment, WE 1 was consistently the poorest performer and its competitiveness was significantly less than CB 1809. The competition results supported the recent decision to replace WB 1 with CB 1809 in commercial inoculants. Although WB 1 had been used in inoculants over a period of 19 years, this strain was detected in only one soil, where it comprised 8% of isolates. In contrast, a substantial proportion (32-78%) of isolates from the soils corresponded serologically to a former inoculant strain WB 66, which had been discontinued in 1966. This illustrates the difficulty of replacing a resident population with an introduced strain. The effect of naturalized populations on the establishment of CB 1809 in South African soils will need monitoring.},
      Year = {2001} }




@article{
Bodour03,
   Author = {Bodour, A. A. and Wang, J. M. and Brusseau, M. L. and Maier, R. M.},
   Title = {Temporal change in culturable phenanthrene degraders in response to long-term exposure to phenanthrene in a soil column system},
   Journal = {Environmental Microbiology},
   Volume = {5},
   Number = {10},
   Pages = {888-895},
   Abstract = {Widespread environmental contamination by polycyclic aromatic hydrocarbons (PAH) has led to increased interest in the use of natural attenuation as a clean-up strategy. However, few bioremediation studies have investigated the behaviour of the indigenous PAH-degrading community after long-term exposure to a PAH. In this study, a column packed with sandy loam soil was exposed to a solution saturated with phenanthrene (approximate to 1.2 mg l(-1)) for a 6-month period to examine the temporal response of the indigenous phenanthrene-degrading community. Initial soil, effluent, and final soil samples were collected and analysed for phenanthrene concentration and culturable phenanthrene degraders. Phenanthrene-degrading isolates were grouped by colony morphology. For each unique group, 16S rDNA polymerase chain reaction was performed, and then sequencing analysis was used to identify the isolate at the genus level. Twenty-five phenanthrene-degrading isolates, potentially representing 19 genera, were obtained from this analysis. Of these, eight genera have not been reported previously to degrade phenanthrene, including Afipia, Janthinobacterium, Leptothrix, Massilia, Methylobacterium, Rhizobium, Sinorhizobium and Thiobacillus. Results indicate that the dominant phenanthrene-degrading population changed over the course of this 6-month experiment. Specifically, the isolates obtained initially from the soil were not subsequently found in either effluent samples or the soil at the end of the experiment. Furthermore, several isolates that were found in the soil at the end of the experiment were not observed in the soil initially or in the effluent samples. This study confirms earlier findings indicating that a diverse community participates in phenanthrene degradation in the environment, and also suggests that the composition of this community is temporally variable.},
   Keywords = {aromatic-hydrocarbon degradation; new-zealand soils; contaminant
transport; pseudomonas-putida; porous-media; bacteria; genes;
biodegradation; naphthalene; hybridization},
   Year = {2003} }




@article{
Bogusz88,
   Author = {Bogusz, D. and Appleby, C.A. and Landsmann, J. and Dennis, E. S. and Trinick, M. J. and Peacock, W. J.},
   Title = {Functioning haemoglobin genes in non-nodulating plants.},
   Journal = {Nature},
   Volume = {331},
   Number = {6152},
   Pages = {178-180},
   Abstract = {Haemoglobin has previously been recorded in plants only in the nitrogen-fixing nodules formed by symbiotic association between Rhizobium or Frankia and legume or non-legume hosts. Structural similarities amongst these and animal haemoglobins at the protein and gene level suggested a common evolutionary origin. This suggests that haemoglobin genes, inherited from an ancestor common to plants and animals, might be present in all plants. We report here the isolation of a haemoglobin gene from Trema tomentosa, a non-nodulating relative of Parasponia (Ulmaceae). The gene has three introns located at positions identical to those in the haemoglobin genes of nodulating plant species, strengthening the case for a common origin of all plant haemoglobin genes. The data argue strongly against horizontal haemoglobin gene transfer from animals to plants. The Trema gene has a tissue-specific pattern of transcription and translation, producing monomeric haemoglobin in Trema roots. We have also found that the Parasponia haemoglobin gene is transcribed in roots of non-nodulated plants. These results suggest that haemoglobin has a role in the respiratory metabolism of root cells of all plant species. We propose that its special role in nitrogen-fixing nodules has required adaptation of the haemoglobin-gene regulation pathway, to give high expression in the specialized environment of the nodule.},
      Year = {1988} }




@article{
Boivin97,
   Author = {Boivin, C. and Ndoye, I. and Molouba, F. and deLajudie, P. and Dupuy, N. and Dreyfus, B.},
   Title = {Stem nodulation in legumes: Diversity, mechanisms, and unusual characteristics},
   Journal = {Critical Reviews in Plant Sciences},
   Volume = {16},
   Number = {1},
   Pages = {1-30},
   Abstract = {Rhizobia can establish a nitrogen-fixing symbiosis with plants of the Leguminosae family. They elicit on their host plant the formation of new organs, called nodules, which develop on the roots. A few aquatic legumes, however, can form nodules on their stem at dormant root primordia. The stem-nodulating legumes described so far are all members of the genera Aeschynomene, Sesbania, Neptunia, and Discolobium. Their rhizobial symbionts belong to four genera already described: Rhizobium, Bradyrhizobium, Sinorhizobium, and Azorhizobium. This review summarizes our current knowledge on most aspects of stem nodulation in legumes, the infection process and nodule development, the characterization and unusual features of the associated bacteria, and the molecular genetics of nodulation. Potential use as green manure in lowland rice of these stem-nodulating legumes, giving them agronomical importance, is also discussed.},
      Year = {1997} }




@article{
Bonish85,
   Author = {Bonish, P. M. and Steele, K. W.},
   Title = {\emph{Rhizobium} populations in maize fields of the North Island, New Zealand},
   Journal = {New Zealand Journal of Agricultural Research},
   Volume = {28},
   Number = {2},
   Pages = {299-303},
      Year = {1985} }




@article{
Bonish91,
   Author = {Bonish, P. M. and Steele, K. W. and Neville, F. J.},
   Title = {Denitrifying and symbiotic characteristics of lotus rhizobia from two New Zealand soils},
   Journal = {New Zealand Journal of Agricultural Research},
   Volume = {34},
   Number = {2},
   Pages = {221-226},
   Abstract = {Lotus rhizobia were examined on Lotus pedunculatus vs. Maku and L. corniculatus cv. Tana. Based on colony type and growth rate, isolates from each soil were separated into two groups corresponding to Bradyrhizobium sp. (Lotus) and to Rhizobium loti. R. loti formed a significant proportion of nodules only on L. corniculatus. The bradyrhizobia were predominantly active denitrifiers. The proportion of non-denitrifying isolates found in this group different between the two soils (12 versus 4%), but there was no effect of host plant on their selection. No active denitrifiers were found among the R. loti isolates. Bradyrhizobium sp. were generally ineffective on L. corniculatus, but effective on L. pedunculatus. R. loti isolates were more effective on L. corniculatus than on L. pedunculatus. -from Authors},
   Keywords = {denitrification
nitrogen fixation
rhizobia
New Zealand
Bradyrhizobium
Lotus corniculatus
Lotus pedunculatus
Rhizobium loti},
   Year = {1991} }




@article{
Boogerd97,
   Author = {Boogerd, F. C. and vanRossum, D.},
   Title = {Nodulation of groundnut by Bradyrhizobium: a simple infection process by crack entry},
   Journal = {FEMS Microbiology Reviews},
   Volume = {21},
   Number = {1},
   Pages = {5-27},
   Abstract = {Infection of legumes by rhizobia may occur by immediate intercellular penetration of root cells (crack entry) as an alternative mode to the more elaborate infection through infection threads. The intercellular spreading mode of infection is exemplified through a comprehensive description of root infection by Bradyrhizobium and nodule organogenesis in Arachis hypogaea (groundnut). The role of axillary root hairs and the processes of plant penetration and intercellular spreading, of internalization and intracellular multiplication, and of bacteroid differentiation are described. Then flavonoids and phytoalexins, Nod factors, lectins, and surface poly(oligo)saccharides pass in review. The roles of these various (macro)molecules in the chemical communication between the two symbionts are discussed. Attention is given to special features of groundnut nodules; the presence and functions of oleosomes and other bodies, the presence and functions of nodule lectins, and the evidence for the export of amides from the nodules are discussed. Finally, a speculative model for the groundnut infection process is presented.},
      Year = {1997} }




@article{
Boot99,
   Author = {Boot, K.J.M. and Van Brussel, A.A.N. and Tak, T. and Spaink, H.P. and Kijne, J.W.},
   Title = {Lipochitin oligosaccharides from Rhizobium leguminosarum bv. viciae reduce auxin transport capacity in Vicia sativa subsp, nigra roots},
   Journal = {Molecular Plant-Microbe Interactions},
   Volume = {12},
   Number = {10},
   Pages = {839-844},
   Abstract = {Induction of the formation of root nodule primordia in legume roots by symbiotic rhizobia is probably preceded by a change in plant hormone physiology. We used a Vicia sativa (vetch) split root system to study the effect of inoculation with rhizobia or purified Nod factors (lipochitin oligosaccharides, LCOs) on polar auxin transport in roots. Addition of R. leguminosarum by. viciae, the infective symbiote of vetch, to roots of its host plant reduced polar auxin transport capacity of these roots within 24 h, in contrast to addition of non-nodulating, Sym plasmid-cured rhizobia. Addition of purified vetch-specific LCOs (NodRlv-IV/V[18:4,Ac]) caused a transient reduction in as little as 4 h after application, while after 16 h a second, stronger, and prolonged inhibition was observed that lasted at least 48 h. This reduction of auxin transport capacity was in the same order of magnitude as inhibition by N-(1-naphthyl)phthalamic acid (NPA). Purified LCOs (NodRm-IV[16:2,Ac,S]) from Sinorhizobium meliloti, the symbiote of alfalfa, and chitopentaose were inactive, which indicates a specific effect of LCOs produced by R. leguminosarum by. viciae. Auxin transport inhibition was restricted to the apical nodulation-susceptible part of the roots, whereas the upper parts of the roots showed no difference in auxin transport after treatment. The effect could be observed with as low as 10-9 M NodRlv-IV/V[18:4,Ac] LCOs. Reduction of auxin transport by LCOs could not be inhibited by nitrate. Since inhibition of auxin transport capacity preceded the first root cortical cell divisions that result in root primordium formation, our results suggest a direct relationship between LCOs, polar auxin transport, and root nodule initiation, consistent with the hypothesis of U. Mathesius, H. R. M. Schlaman, H. P. Spaink, C. Sautter, B. G. Rolfe, and M. A. Djordjevic (Plant J. 14:23-34, 1998). However, nonmitogenic NodRlv-IV/V[18:1,Ac] showed a similar effect, which suggests that mitogenicity results from additional effects, in concert with auxin transport inhibition.},
      Year = {1999} }




@article{
Boring88,
   Author = {Boring, L. R. and Swank, W. T. and Waide, J. B. and Henderson, G. S.},
   Title = {Sources, fates, and impacts of nitrogen inputs to terrestrial ecosystems: review and synthesis},
   Journal = {Biogeochemistry},
   Volume = {6},
   Number = {2},
   Pages = {119-159},
   Abstract = {The relative importance of nitrogen inputs from atmospheric deposition and biological fixation is reviewed in a number of diverse, non-agricultural terrestrial ecosystems. Bulk precipitation inputs of N (l–l2 kg N ha–1 yr–1) are the same order of magnitude as, or frequently larger than, the usual range of inputs from nonsymbiotic fixation (< 1 – 5 kg N ha–1 yr–1), especially in areas influenced by industrial activity. Bulk precipitation measurements may underestimate total atmospheric deposition by 30–40% because they generally do not include all forms of wet and dry deposition. Symbiotic fixation generally ranges from cong 10–160 kg N ha–1 yr–1) in ecosystems where N-fixing species are present during early successional stages, and may exceed the range under unusual conditions.
Rates of both symbiotic and nonsymbiotic fixation appear to be greater during early successional stages of forest development, where they have major impacts on nitrogen dynamics and ecosystem productivity. Fates and impacts of these nitrogen inputs are important considerations that are inadequately understood. These input processes are highly variable in space and time, and few sites have adequate comparative information on both nitrogen deposition and fixation.
– 	- more intensive studies of total atmospheric deposition, especially of dry deposition, are needed over a wide range of ecosystems;
– 	- additional studies of symbiotic fixation are needed that carefully quantify variation over space and time, examine more factors regulating fixation, and focus upon the availability of N and its effects upon productivity and other nutrient cycling processes;
– 	- process-level studies of associative N-fixation should be conducted over a range of ecosystems to determine the universal importance of rhizosphere fixation;
– 	- further examination of the role of free-living fixation in wood decomposition and soil organic matter genesis is needed, with attention upon spatial and temporal variation; and
– 	- investigations of long-term biogeochemical impacts of these inputs must be integrated with process-level studies using modern modelling techniques.

Key words  nitrogen input - atmospheric deposition - symbiotic nitrogen fixation - nonsymbiotic nitrogen fixation - biogeochemical cycling - decomposition - nitrogen availability - impacts - nitrogen fates},
      Year = {1988} }




@article{
Borthakur88,
   Author = {Borthakur, D. and Barker, R. F. and Latchford, J. W. and Rossen, L. and Johnston, A. W.},
   Title = {Analysis of pss genes of Rhizobium leguminosarum required for exopolysaccharide synthesis and nodulation of peas: their primary structure and their interaction with psi and other nodulation genes.},
   Journal = {Molecular and General Genetics},
   Volume = {213},
   Number = {1},
   Pages = {155-162},
   Abstract = {Strains of Rhizobium leguminosarum (R.l.) biovar viciae containing pss mutations fail to make the acidic exopolysaccharides (EPS) and are unable to nodulate peas. It was found that they also failed to nodulate Vicia hirsuta, another host of this biovar. When peas were co-inoculated with pss mutant derivatives of a strain of R.l. by viciae containing a sym plasmid plus a cured strain lacking a sym plasmid (and which is thus Nod-, but for different reasons) but which makes the acidic EPS, normal numbers of nodules were formed, the majority of which failed to fix nitrogen (the occasional Fix+ nodules were presumably induced by strains that arose as a result of genetic exchange between cells of the two inoculants in the rhizosphere). Bacteria from the Fix- nodules contained, exclusively, the strain lacking its sym plasmid. When pss mutant strains were co-inoculated with a Nod- strain with a mutation in the regulatory gene nodD (which is on the sym plasmid pRL1JI), normal numbers of Fix+ nodules were formed, all of which were occupied solely by the nodD mutant strain. Since a mutation in nodD abolishes activation of other nod genes required for early stages of infection, these nod genes appear to be dispensable for subsequent stages in nodule development. Recombinant plasmids, containing cloned pss genes, overcame the inhibitory effects of psi, a gene which when cloned in the plasmid vector pKT230, inhibits both EPS production and nodulation ability. Determination of the sequence of the pss DNA showed that one, or perhaps two, genes are required for correcting strains that either carry pss mutations or contain multi-copy psi.(ABSTRACT TRUNCATED AT 250 WORDS)},
      Year = {1988} }




@article{
Bossard92,
   Author = {Bossard, C. C. and Rejmanek, M.},
   Title = {Why Have Green Stems},
   Journal = {Functional Ecology},
   Volume = {6},
   Number = {2},
   Pages = {197-205},
   Abstract = {Photosynthetic activity of the cortical tissues of Cytisus scoparius. Link stems were examined in regard to individual biomass production and allocation, structural attributes of stem tissue, chlorophyll content, photosynthetic rates and ability to recover from herbivory. Biomass production and allocation were assessed through growth analysis of plants given one of four treatments: all stems loosely wrapped with aluminium foil; plants defoliated once; plants defoliated repeatedly; and controls. Stem photosynthesis made a significant contribution to growth and biomass production of this mesic species. Cortical stem tissue is structurally very similar to leaf tissue. Chlorophyll content and biomass accumulation of stems, leaves, roots, and nodules changed significantly with simulated herbivory. Apparently, in Cytisus scoparius, stem photosynthesis helps meet different needs, depending on which factor or combination of factors are most critical in any given habitat. For an invasive, weedy perennial like Cytisus scoparius, this flexibility may itself be the most important benefit of having photosynthetic stems. Photosynthetic stems may play an important role in the success of leguminous shrubs in general and in the success of invasive leguminous shrubs in particular.},
      Year = {1992} }




@article{
Bras00,
   Author = {Bras, C. P. and Jordá, M. A. and Wijfjes, A. H. M. and Harteveld, M. and Stuurman, N. and Spaink, H. P. and Thomas-Oates, J. E.},
   Title = {A Lotus japonicus nodulation system based on heterologous expression of the fucosyl transferase NodZ and the acetyl transferase NolL in Rhizobium leguminosarum},
   Journal = {Molecular Plant-Microbe Interactions},
   Volume = {13},
   Number = {4},
   Pages = {475-479},
   Abstract = {Heterologous expression of NodZ and NolL proteins in Rhizobium leguminosarum bv. viciae led to the production of acetyl fucosylated lipo-chitin oligosaccharides (LCOs), indicating that the NolL protein obtained from Mesorhizobium loti functions as an acetyl transferase. We show that the NolL-dependent acetylation is specific for the fucosyl penta-N-acetylglucosamine species. In addition, the NolL protein caused elevated production of LCOs. Efficient nodulation of Lotus japonicus by the NodZ/NolL-producing strain was demonstrated. Nodulation efficiency was further improved by the addition of the ethylene inhibitor L-?-(2-aminoethoxyvinyl) glycine (AVG).},
   Keywords = {Acetyl fucose
Mass spectrometry
Nod factors},
   Year = {2000} }




@article{
Bravo88,
   Author = {Bravo, A. and Mora, J.},
   Title = {Ammonium assimilation in Rhizobium phaseoli by the glutamine synthetase-glutamate synthase pathway},
   Journal = {Journal of Bacteriology},
   Volume = {170},
   Number = {2},
   Pages = {980-4},
   Abstract = {Evidence from in vitro and in vivo studies showed that in Rhizobium phaseoli ammonium is assimilated by the glutamine synthetase (GS)-glutamate synthase NADPH pathway. No glutamate dehydrogenase activity was detected. R. phaseoli has two GS enzymes, as do other rhizobia. The two GS activities are regulated on the basis of the requirement for low (GSI) or high (GSII) ammonium assimilation. When the 2-oxoglutarate/glutamine ratio decreases, GSI is adenylylated. When GSI is inactivated, GSII is induced. However, induction of GSII activity varied depending on the rate of change of this ratio. GSII was inactivated after the addition of high ammonium concentrations, when the 2-oxoglutarate/glutamine ratio decreased rapidly. Ammonium inactivation resulted in alteration of the catalytic and physical properties of GSII. GSII inactivation was not relieved by shifting of the cultures to glutamate. After GSII inactivation, ammonium was excreted into the medium. Glutamate synthase activity was inhibited by some organic acids and repressed when cells were grown with glutamate as the nitrogen source.},
   Keywords = {Ammonium Compounds/*metabolism
Culture Media
Enzyme Induction
Glutamate Synthase/*metabolism
Glutamate-Ammonia Ligase/*metabolism
Glutamates/metabolism
Glutamine/metabolism
Ketoglutaric Acids/metabolism
Rhizobium/*enzymology/growth \& development
Support, Non-U.S. Gov't
Transaminases/*metabolism},
   Year = {1988} }




@article{
Breedveld94,
   Author = {Breedveld, M. W. and Miller, K. J.},
   Title = {Cyclic $\beta$-glucans of members of the family Rhizobiaceae},
   Journal = {Microbiological Reviews},
   Volume = {58},
   Number = {2},
   Pages = {145-161},
   Abstract = {Cyclic ?-glucans are low-molecular-weight cell surface carbohydrates that are found almost exclusively in bacteria of the Rhizobiaceae family. These glucans are major cellular constituents, and under certain culture conditions their levels may reach up to 20% of the total cellular dry weight. In Agrobacterium and Rhizobium species, these molecules contain between 17 and 40 glucose residues linked solely by ?-(1,2) glycosidic bonds. In Bradyrhizobium species, the cyclic ?-glucans are smaller (10 to 13 glucose residues) and contain glucose linked by both ?-(1,6) and ?-(1,3) glycosidic bonds. In some rhizobial strains, the cyclic ?-glucans are unsubstituted, whereas in other rhizobia these molecules may become highly substituted with moieties such as sn-1-phosphoglycerol. To date, two genetic loci specifically associated with cyclic ?-glucan biosynthesis have been identified in Rhizobium (ndvA and ndvB) and Agrobacterium (chvA and chvB) species. Mutants with mutations at these loci have been shown to be impaired in their ability to grow in hypoosmotic media, have numerous alterations in their cell surface properties, and are also impaired in their ability to infect plants. The present review will examine the structure and occurrence of the cyclic ?- glucans in a variety of species of the Rhizobiaceae. The possible functions of these unique molecules in the free-living bacteria as well as during plant infection will be discussed.},
      Year = {1994} }




@incollection{
Brenner05,
   Author = {Brenner, D. J. and Staley, J. T. and Krieg, R. K.},
   Title = {Classification of procaryotic organisms and the concept of bacterial speciation},
   BookTitle = {Part A, Introductory essays, Bergey's Manual of Systematic Bacteriology},
   Editor = {Brenner, D. J. and Krieg, R. K. and Staley, J. T. and Garrity, G. M.},
   Publisher = {Springer},
   Address = {New York},
   Volume = {2},
   Edition = {2nd},
   Pages = {27-32},
      Year = {2005} }




@article{
Brewin91,
   Author = {Brewin, N. J.},
   Title = {Development of the legume root nodule},
   Journal = {Annual Review of Cell Biology},
   Volume = {7},
   Pages = {191-226},
   Keywords = {Nitrogen fixation
Rhizobium
Symbiosis},
   Year = {1991} }




@article{
Brewin93,
   Author = {Brewin, N. J.},
   Title = {The Rhizobium-legume symbiosis: plant morphogenesis in a nodule},
   Journal = {Semin Cell Biol},
   Volume = {4},
   Number = {2},
   Pages = {149-56},
   Abstract = {Development of the legume root nodule can be divided conceptually into two parallel processes. On the one hand, there is the induction of a nodule meristem and the progressive differentiation of specialised cells and tissues. On the other hand, there is cell and tissue invasion by Rhizobium, which leads ultimately to the differentiation of intracellular bacteroids as specialised nitrogen-fixing endosymbionts. The early stages of plant-microbe communication seem to be mostly mediated by the exchange of soluble, diffusible signal molecules: flavonoid compounds are secreted by plant roots, and chitin-like lipooligosaccharides are secreted by rhizobia. Further development of the nodule structure may involve the interplay of fairly conventional plant growth regulators. Direct physical contact between the cell surfaces of the symbionts also plays a prominent role in the process of tissue and cell invasion.},
   Keywords = {Extracellular Matrix/microbiology
Fabaceae/*microbiology/ultrastructure
Flavonoids/chemistry/physiology
Genes, Nitrogen Fixation
Lipopolysaccharides/metabolism
Morphogenesis
Nitrogen Fixation
*Plants, Medicinal
Rhizobium/*physiology
Signal Transduction
Support, Non-U.S. Gov't
*Symbiosis},
   Year = {1993} }




@article{
Brewin02,
   Author = {Brewin, N. J.},
   Title = {Pods and nods: A new look at symbiotic nitrogen fixing bacteria},
   Journal = {Biologist},
   Volume = {49},
   Number = {3},
   Pages = {113-117},
   Abstract = {How can growing a crop plant make fields more fertile? With legumes, this is precisely what happens. Working in partnership with symbiotic bacteria that create root nodules on their chosen host, legumes can fix atmospheric nitrogen and enhance the nitrogen status of soils. How does this symbiosis develop? And how did it evolve? Bacterial and plant genomics are beginning to provide the answers.},
   Keywords = {nitrogen fixation
symbiosis
Nitrogen Fixation
Symbiosis},
   Year = {2002} }




@article{
Brewin04,
   Author = {Brewin, N. J.},
   Title = {Plant cell wall remodelling in the rhizobium-legume symbiosis},
   Journal = {Critical Reviews in Plant Sciences},
   Volume = {23},
   Number = {4},
   Pages = {293-316},
   Abstract = {Colonization of host cells by rhizobium bacteria involves the progressive remodelling of the plant-microbial interface. Following induction of nodulation genes by legume-derived flavonoid signals, rhizobium secretes Nod-factors (lipochitin oligosaccharides) that cause root hair deformations by perturbing the growth of the plant cell wall. The infection thread arises as a tubular ingrowth bounded by plant cell wall. This serves as a conduit for colonizing bacterial cells that grow and divide in its lumen. The transcellular orientation of thread growth is controlled by the cytoskeleton and is coupled to cell cycle reactivation and cell division processes. In response to rhizobium infection, host cells synthesize several new components (early nodulins) that modify the properties of the cell wall and extracellular matrix. Root nodule extensins are a legume-specific family of hydroxyproline-rich glycoproteins targeted into the lumen of the infection thread. They have alternating extensin and arabinogalactan (AGP) glycosylation motifs. The structural characteristics of these glycoproteins suggest that they may serve to regulate fluid-to-solid transitions in the extracellular matrix. Extensibility of the infection thread is apparently controlled by peroxide-driven protein cross-linking and perhaps also by modification of the pectic matrix. Endocytosis of rhizobia from unwalled infection droplets into the host cell cytoplasm depends on physical contact between glycocalyx components of the plant and bacterial membrane surfaces. As endosymbionts, bacteroids remain enclosed within a plant-derived membrane that is topologically equivalent to the plasma membrane. This membrane acquires specialist functions that regulate metabolite exchanges between bacterial cells and the host cytoplasm. Ultimately, however, the fate of the symbiosome is to become a lysosome, causing the eventual senescence of the symbiotic interaction.},
   Keywords = {Cellulose synthesis
Extensin
Infection threads
Nitrogen fixation
Proline rich glycoproteins
Root nodules
Rhizobium},
   Year = {2004} }




@article{
Brockwell63,
   Author = {Brockwell, J.},
   Title = {Accuracy of a plant-infection technique for counting populations of Rhizobium trifolii},
   Journal = {Applied Microbiology},
   Volume = {11},
   Pages = {377-383},
      Year = {1963} }




@article{
Broos05,
   Author = {Broos, K. and Beyens, H. and Smolders, E.},
   Title = {Survival of rhizobia in soil is sensitive to elevated zinc in the absence of the host plant},
   Journal = {Soil Biology and Biochemistry},
   Volume = {37},
   Number = {3},
   Pages = {573-579},
   Abstract = {The survival of free-living rhizobia in soil is sensitive to elevated heavy metals in soil and can explain adverse effects of metals on symbiotic nitrogen fixation in soils. A survival experiment was set-up to derive critical cadmium (Cd) and zinc (Zn) concentrations in a range of field-contaminated soils in the absence of their host plant (Trifolium repens L.). Soils applied with metal salts or sewage sludge > 10 years ago were sampled and were inoculated with Rhizobium leguminosarum, bv. trifolii (10(8) cells g(-1) soil) and incubated outdoors for up to 6 months. The most probable number (MPN) decreased 1-2 orders of magnitude in uncontaminated soils during the incubation. There was no significant effect of total metal concentrations on rhizobia survival in soils contaminated with Cd salts or with high Ni/Cd sewage sludge with highest Cd concentrations between 18 and 118 mg Cd kg(-1). In contrast, survival was strongly affected in soils contaminated by sewage sludge, where Zn was the principal metal contaminant. Neither total Cd nor soil solution Cd was large enough to attribute these effects to Cd when compared with the soil series, where Cd salts had been applied. The MPN decreased at least one order of magnitude above total Zn concentrations of 233 mg Zn kg(-1) (soil pH 5.6) and 876 mg Zn kg(-1) (soil pH 6.3). The EC50s of log MPN were 204 and 604 mg Zn kg(-1), respectively, and were lower than those for the symbiotic nitrogen fixation measured in the pot trial on the same soils (respectively 602 and 737 mg Zn kg(-1)). This study corroborates the evidence that symbiotic nitrogen fixation is affected by Zn in the field when Zn decreases the free-living population of rhizobia to below a critical threshold. (C) 2004 Elsevier Ltd. All rights reserved.},
      Year = {2005} }




@article{
Broughton03,
   Author = {Broughton, W. J.},
   Title = {Roses by other names: Taxonomy of the \emph{Rhizobiaceae}},
   Journal = {Journal of Bacteriology},
   Volume = {185},
   Number = {10},
   Pages = {2975-2979},
      Year = {2003} }




@article{
Broughton00,
   Author = {Broughton, W. J. and Jabbouri, S. and Perret, X.},
   Title = {Keys to symbiotic harmony},
   Journal = {Journal of Bacteriology},
   Volume = {182},
   Number = {20},
   Pages = {5641-5652},
      Year = {2000} }




@article{
Broughton99,
   Author = {Broughton, William J. and Perret, Xavier},
   Title = {Genealogy of legume-Rhizobium symbioses},
   Journal = {Current Opinion in Plant Biology},
   Volume = {2},
   Number = {4},
   Pages = {305-311},
   Abstract = {Accumulating evidence suggests that lateral transfer of nodulation capacity s an important driving force n symbiotic evolution. As a consequence, many distantly related soil bacteria have acquired the capacity to invade plants and fix nitrogen within them. In addition to these proteins required for bacteroid development and nitrogen fixation, core symbiotic competence seems to require flavonoids, NodD proteins, lipochitooligosaccharidic Nod-factors, extra-cellular polysaccharides, as well as various exported proteins. Plants respond to different levels and combinations of these substances in species specific ways after contact has been initiated by flavonoids and NodD proteins, constant signal exchange fine-tunes these symbiotic demands, especially to overcome defence reactions.},
      Year = {1999} }




@article{
Brown03,
   Author = {Brown, J. R.},
   Title = {Ancient horizontal gene transfer},
   Journal = {Nature Reviews Genetics},
   Volume = {4},
   Number = {2},
   Pages = {121-32},
   Keywords = {Evolution, Molecular
*Gene Transfer, Horizontal
Phylogeny
Support, Non-U.S. Gov't},
   Year = {2003} }




@article{
Brownsey01,
   Author = {Brownsey, P. J.},
   Title = {New Zealand's pteridophyte flora - Plants of ancient lineage but recent arrival?},
   Journal = {Brittonia},
   Volume = {53},
   Number = {2},
   Pages = {284-303},
   Abstract = {A hypothesis is presented that most pteridophytes arrived in New Zealand relatively recently, by long-distance dispersal. The flora comprises 194 native species, of which 89 (46%) are endemic and 105 (54%) are widespread. Of the latter, 90% are shared with temperate Australasia, 53% with tropical regions, 14% with temperate southern Africa and 13% with the circum-Antarctic islands and South America. New Zealand has undergone such dramatic changes in location, land area, and topography since initial separation from Gondwana 85 Ma that it seems improbable that the 95 species shared with temperate Australasia could have remained conspecific throughout that time. Modern fossil and molecular evidence strongly suggest that many families of ferns had not even evolved prior to separation, and palynological evidence from New Zealand indicates that 78% of pteridophyte genera first appeared there only after separation from Gondwana. Present-day distributions in New Zealand suggest that ferns have greater dispersal potential than flowering plants, and that pteridophyte distributions are more heavily influenced by temperature, rainfall, and geothermal activity than by geological history. Most endemic pteridophyte species have a predominantly southern distribution pattern and are characteristic of cool, lowland to montane forest. Pteridophytes in the northern part of New Zealand show a lower level of endemism than elsewhere and tend to be widespread species that have arrived from temperate Australasian and tropical regions. There is also evidence that at least some pteridophytes have migrated from New Zealand to Australia. It is suggested that the hypothesis of long-distance dispersal of pteridophytes across the Tasman Sea could be tested by molecular techniques.},
   Keywords = {Endemism
Ferns
Long distance dispersal
New Zealand
Pteridophytes
Vicariance},
   Year = {2001} }




@article{
Bruneau01,
   Author = {Bruneau, A. and Forest, F. and Herendeen, P.S. and Klitgaard, B.B. and Lewis, G.P.},
   Title = {Phylogenetic relationships in the Caesalpinioideae (Leguminosae) as inferred from chloroplast trnL intron sequences},
   Journal = {Systematic Botany},
   Volume = {26},
   Number = {3},
   Pages = {487-514},
   Abstract = {The basal subfamily Caesalpinioideae of the Leguminosae generally is subdivided into four or five tribes, but their monophyly remains questionable. Recent cladistic analyses based on morphological characters and chloroplast rbcL sequences suggest conflicting hypotheses of relationships among tribes and subtribal groupings and of the identification of the basal Caesalpinioideae. Our phylogenetic analysis of the chloroplast trnL intron for 223 Caesalpinioideae, representing 112 genera, plus four Papilionoideae, 12 Mimosoideae and three outgroup taxa, provides some well-supported hypotheses of relationships for the subfamily. Our analysis concurs with the rbcL studies in suggesting that a monophyletic Cercideae is sister to the remainder of the Leguminosae. Among the other tribes of Caesalpinioideae, only the broadly circumscribed Detarieae (including Amherstieae or Macrolobieae) is also supported as monophyletic. The Detarieae s.l. occurs as sister to all Leguminosae, excluding Cercideae. Cassieae subtribes Dialiinae and Labicheinae together are sister to the remaining Leguminosae, which includes a monophyletic Papilionoideae, a paraphyletic Mimosoideae, and several monophyletic groups that correspond to previously defined generic groups or subtribes in the Caesalpinioideae. The trnL intron analysis suggests that basal legumes are extremely diverse in their floral morphology, and that presence of simple, actinomorphic flowers may be a derived feature in a number of lineages in the family.},
      Year = {2001} }




@article{
Bryan96,
   Author = {Bryan, J. A. and Berlyn, G. P. and Gordon, J. C.},
   Title = {Toward a new concept of the evolution of symbiotic nitrogen fixation in the leguminosae},
   Journal = {Plant and Soil},
   Volume = {186},
   Number = {1},
   Pages = {151-159},
   Abstract = {It is generally believed that only the nodulating species of the Leguminosae fix atmospheric nitrogen; however, anatomical, ecological and taxonomic considerations indicate that non-nodulating legume species may also fix nitrogen. To test whether nitrogen-fixing symbioses in the Leguminosae might extend to the non-nodulating species, a survey of the Leguminosae was conducted: living plants of non-nodulating species were assayed using acetylene reduction. Ethylene evolution, indicating apparent nitrogenase activity, was detected in non-nodulating species representing the major taxonomic groups of Caesalpinioideae as well as in non-nodulating species of the Papilionoideae and Mimosoideae. Non-nodules nitrogen fixation appears to have provided evolutionary precursors for the nodular symbiosis in the Leguminosae.},
   Keywords = {Caesalpinioideae
nitrogenase activity
nodulation
root cortex
taxonomy},
   Year = {1996} }




@article{
Buckley02,
   Author = {Buckley, T. R.},
   Title = {Model misspecification and probabilistic tests of topology: Evidence from empirical data sets},
   Journal = {Systematic Biology},
   Volume = {51},
   Number = {3},
   Pages = {509-523},
   Abstract = {Probabilistic tests of topology offer a powerful means of evaluating competing phylogenetic hypotheses. The performance of the nonparametric Shimodaira-Hasegawa (SH) test, the parametric Swofford-Olsen-Waddell-Hillis (SOWH) test, and Bayesian posterior probabilities were explored for five data sets for which all the phylogenetic relationships are known with a very high degree of certainty. These results are consistent with previous simulation studies that have indicated a tendency for the SOWH test to be prone to generating Type 1 errors because of model misspecification coupled with branch length heterogeneity. These results also suggest that the SOWH test may accord overconfidence in the true topology when the null hypothesis is in fact correct. In contrast, the SH test was observed to be much more conservative, even under high substitution rates and branch length heterogeneity. For some of those data sets where the SOWH test proved misleading, the Bayesian posterior probabilities were also misleading. The results of all tests were strongly influenced by the exact substitution model assumptions. Simple models, especially those that assume rate homogeneity among sites, had a higher Type 1 error rate and were more likely to generate misleading posterior probabilities. For some of these data sets, the commonly used substitution models appear to be inadequate for estimating appropriate levels of uncertainty with the SOWH test and Bayesian methods. Reasons for the differences in statistical power between the two maximum likelihood tests are discussed and are contrasted with the Bayesian approach.},
   Keywords = {Bayesian statistics
Markov chain Monte Carlo
Maximum likelihood
Nucleotide substitution models
Parametric bootstrapping
SH test
SOWH test
Statistical tests},
   Year = {2002} }




@article{
Buckley02a,
   Author = {Buckley, T. R.},
   Title = {A statistical future for morphological phylogenetics?},
   Journal = {Trends in Ecology and Evolution},
   Volume = {17},
   Number = {4},
   Pages = {161},
      Year = {2002} }




@article{
Buckley02b,
   Author = {Buckley, T.R. and Cunningham, C.W.},
   Title = {The effects of nucleotide substitution model assumptions on estimates of nonparametric bootstrap support},
   Journal = {Molecular Biology and Evolution},
   Volume = {19},
   Number = {4},
   Pages = {394-405},
   Abstract = {The use of parameter-rich substitution models in molecular phylogenetics has been criticized on the basis that these models can cause a reduction both in accuracy and in the ability to discriminate among competing topologies. We have explored the relationship between nucleotide substitution model complexity and nonparametric bootstrap support under maximum likelihood (ML) for six data sets for which the true relationships are known with a high degree of certainty. We also performed equally weighted maximum parsimony analyses in order to assess the effects of ignoring branch length information during tree selection. We observed that maximum parsimony gave the lowest mean estimate of bootstrap support for the correct set of nodes relative to the ML models for every data set except one. For several data sets, we established that the exact distribution used to model among-site rate variation was critical for a successful phylogenetic analysis. Site-specific rate models were shown to perform very poorly relative to gamma and invariables sites models for several of the data sets most likely because of the gross underestimation of branch lengths. The invariable sites model also performed poorly for several data sets where this model had a poor fit to the data, suggesting that addition of the gamma distribution can be critical. Estimates of bootstrap support for the correct nodes often increased under gamma and invariable sites models relative to equal rates models. Our observations are contrary to the prediction that such models cause reduced confidence in phylogenetic hypotheses. Our results raise several issues regarding the process of model selection, and we briefly discuss model selection uncertainty and the role of sensitivity analyses in molecular phylogenetics.},
   Keywords = {AIC
Maximum likelihood
Model selection
Nonparametric bootstrapping
Nucleotide substitution models
Phylogenetics},
   Year = {2002} }




@article{
Buckley01,
   Author = {Buckley, T. R. and Simon, C. and Chambers, G. K.},
   Title = {Exploring among-site rate variation models in a maximum likelihood framework using empirical data: Effects of model assumptions on estimates of topology, branch lengths, and bootstrap support},
   Journal = {Systematic Biology},
   Volume = {50},
   Number = {1},
   Pages = {67-86},
   Abstract = {We have investigated the effects of different among-site rate variation models on the estimation of substitution model parameters, branch lengths, topology, and bootstrap proportions under minimum evolution (ME) and maximum likelihood (ML). Specifically, we examined equal rates, invariable sites, gamma-distributed rates, and site-specific rates (SSR) models, using mitochondrial DNA sequence data from three protein-coding genes and one tRNA gene from species of the New Zealand cicada genus Maoricicada. Estimates of topology were relatively insensitive to the substitution model used; however, estimates of bootstrap support, branch lengths, and R-matrices (underlying relative substitution rate matrix) were strongly influenced by the assumptions of the substitution model. We identified one situation where ME and ML tree building became inaccurate when implemented with an inappropriate among-site rate variation model. Despite the fact the SSR models often have a better fit to the data than do invariable sites and gamma rates models, SSR models have some serious weaknesses. First, SSR rate parameters are not comparable across data sets, unlike the proportion of invariable sites or the alpha shape parameter of the gamma distribution. Second, the extreme among-site rate variation within codon positions is problematic for SSR models, which explicitly assume rate homogeneity within each rate class. Third, the SSR models appear to give severe underestimates of R-matrices and branch lengths relative to invariable sites and gamma rates models in this example. We recommend performing phylogenetic analyses under a range of substitution models to test the effects of model assumptions not only on estimates of topology but also on estimates of branch length and nodal support.},
   Keywords = {Among-site rate variation
Bootstrapping
Insect mitochondrial DNA
Likelihood ratio test
Maoricicada
Maximum likelihood
Nucleotide substitution models},
   Year = {2001} }




@article{
Buckley03,
   Author = {Buckley, Y. M. and Rees, M. and Downey, P. and Fowler, S. V. and Winks, C. and Hill, R. and Memmot, J. and Norambuena, H. and Pitcairn, M. and Shaw, R. and Sheppard, A. W. and Wittenberg, R.},
   Title = {Are invasives bigger? A global study of seed size variation in two invasive shrubs},
   Journal = {Ecology},
   Volume = {84},
   Number = {6},
   Pages = {1434-1440},
   Abstract = {We explored the spatial structure of seed size variation and tested whether seed size differed between native and exotic populations in two invasive species. Seed of Cytisus scoparius (Scotch broom) is significantly heavier in its exotic range, whereas seed of Ulex europaeus (European gorse) is no different between ranges. This result suggests that seed size in C. scoparius is either adaptively or phenotypically responsive to conditions in its exotic range or that plants with large seeds were preferentially introduced. We found that modern ornamental broom seed was no bigger than seed from natural or naturalized populations, suggesting that large seed size in the exotic range is not due to preferential introduction of ornamental varieties with large seeds. Most previous studies of trait differences between native and exotic ranges in invasive species have not taken variation throughout the ranges into account. This is the most comprehensive survey of seed size variation in any species, and the first time that variation in a trait of an invasive species has been studied from individual plant level up to global ranges. Demographic rates can be affected by seed attributes making this study an important first step in understanding how population processes may differ between native and exotic ranges.},
   Keywords = {Cytisus scoparius
Evolutionary change
Invasive plants
Linear mixed effects models
Phenotypic plasticity
Seed size variation
Ulex europaeus},
   Year = {2003} }




@article{
Bukvaj91,
   Author = {Bukvaj, M.},
   Title = {Production Capability of Leys with Higher Proportion of Clover Crops in Different Site Conditions},
   Journal = {Rostlinna Vyroba},
   Volume = {37},
   Number = {9-10},
   Pages = {837-844},
   Abstract = {In 1984-1988 in practical farming conditions on 47 farms in potato-, montane-, and submontane-growing region, the production ability of three herbage and three meadow mixtures with higher proportion of clover crops were studied in the area of 3,400 ha. Leguminous component in herbage mixtures was formed by white clover (the Huia variety of New Zealand) at a rate of 3 to 4 kg per ha. In meadow mixtures, clover crops were represented by mammoth red clover (the Kvarta variety) supplemented with white clover and alsike clover. An average dry matter yield from test sites amounted to 7.02 t per ha, 6.93 t per ha of it in pasture mixtures and 7.11 t per ha in meadow mixtures. The proportion of clover crops in all mixtures amounted to about 20% in all mixtures on an average for the years under study, ranging from 15 to 45%. The bred varieties of clover crops, namely Huia white clover as a decisive leguminous crop, provided high herbage yields with no respect to production region. They were withdrawing from areas where subsoil exhibited low biological activity and on the plots of strongly acid soil reaction (below pH value of 5.0). Owing to the activities of rhizobial bacteria of clover crops, it was possible to reduce significantly nitrogen application rate in commercial fertilizers what is demonstrated by an average yield in all mixtures amounting to 105.4 kg per ha. It follows from the results of dry matter yields obtained and nitrogen application rate that clover crops enriched the soil by 80 to 100 kg of N per ha.},
      Year = {1991} }




@article{
Burdon99,
   Author = {Burdon, J. J. and Gibson, A. H. and Woods, M. J. and Brockwell, J. and Searle, S. D.},
   Title = {Variation in the effectiveness of symbiotic associations between native rhizobia and temperate Australian acacia: Within-species interactions},
   Journal = {Journal of Applied Ecology},
   Volume = {36},
   Number = {3},
   Pages = {398-408},
   Abstract = {1. The ability of different rhizobial isolates collected from any one site to establish effective nitrogen-fixing associations with host-plants from that site showed significant variation in 22 host Acacia species and nearly all of 67 populations. The average Acacia host-Rhizobium strain combination was only about 70% effective. Many combinations were far poorer; in a few cases the worst combination resulted in plants less than one-tenth the size of the best combinations. 2. The ability of rhizobial isolates to form effective symbiotic interactions showed marked host population and rhizobial-isolate effects in a study of eight, four and nine populations of A. dealbata, A. implexa and A. mearnsii. A more complete trial involved three populations of each of A. dealbata, A. implexa, A. irrorata, A. mearnsii and A. melanoxylon. These were inoculated with a range of rhizobial isolates previously shown to be highly, moderately or weakly successful in forming an effective association. Evidence of marked host population and rhizobial origin effects was found but there was very little evidence of isolate-host population interaction effects. 3. The general lack of host population-rhizobial origin interaction effects suggests that rhizobial strains selected as highly effective for an Acacia species growing in a particular population will generally perform well symbiotically with that species in other populations. This will make their practical application as inoculants in revegetation and forestry situations much easier. 4. Significant host-based variability in the ability to form effective symbiotic interactions was detected in comparisons of half-sib families of A. dealbata, A. mearnsii and A. melanoxylon. In the case of A. dealbata, the interaction between half-sib family lines and rhizobial isolates was complex, with 'locally' derived isolates performing better than 'foreign' ones. There were also significant interaction effects. In A. mearnsii, on the other hand, the only significant differences were detected between the response of different half-sib families to the same rhizobial isolate. The occurrence of host-based variability indicates that in Acacia breeding programmes attention should be given to the possibility of inadvertent selection affecting these relationships.},
   Keywords = {Bradyrhizobium
Nodulation
Rhizobium
Symbiotic effectiveness},
   Year = {1999} }




@article{
Burrill17,
   Author = {Burrill, T. J. and Hansen, R.},
   Title = {Is symbiosis possible between legumes bacteria and non-legume plants?},
   Journal = {Ill Agric Exp Stn Bull},
   Volume = {202},
   Number = {115-181},
      Year = {1917} }




@article{
Burris52,
   Author = {Burris, R. H. and Wilson, P. W.},
   Title = {Effect of haemoglobin and other nitrogenous compounds on the respiration of the rhizobia},
   Journal = {Biochemical Journal},
   Volume = {51},
   Number = {1},
   Pages = {90-6},
      Year = {1952} }




@article{
Bushby95,
   Author = {Bushby, H.V.A. and Date, R.A. and Dart, P.J.},
   Title = {Tenth Australian nitrogen fixation conference. Genetics, microbial ecology and nitrogen fixation: is there a sustainable symbiosis? Brisbane, September 1993},
   Journal = {Soil Biology \& Biochemistry},
   Volume = {27},
   Number = {4-5},
   Pages = {379-738},
   Abstract = {There are 51 papers, reporting mainly Australian research, but also including studies relevant to the wider tropics. Contributions are published in sections on: metabolic pathways associated with N2 fixation, with reference to chickpea Cicer arietinum and soybean Glycine max nodules; nodulation and N2 fixation with trees and shrubs, particularly legumes such as Acacia ampliceps, Robinia pseudoacacia, Calliandra calothyrsus and Sesbania sesban; non-symbiotic N2 fixation by various soil microorganisms in rice Oryza sativa, wheat Triticum aestivum and other crop plants; microbe-plant genetic interactions in N2 fixation, including genetic analyses and molecular techniques of the study of Rhizobium populations; N2 fixation, N supply and rhizobial populations in agricultural production systems, particularly crop and pasture legume-based systems, emphasizing their role in crop yield and sustainable production; nodulation and N2 fixation under environmental stresses such as salinity or soil acidification; and advances in inoculant and seed inoculation technology. -J.W.Cooper},
      Year = {1995} }




@article{
Byzezinski04,
   Author = {Byzezinski, K. and Rogozinski, B. and St{\c e}pkowski , T. and Bujacz, G. and Jaskolski, M.},
   Title = {Cloning purification crystallization and preliminary crystallographic studies of Bradyrhizobium fucosyltransferase NodZ},
   Journal = {Acta Crystallographica},
   Volume = {60},
   Pages = {344-346},
   Abstract = {The alpha-1,6-fucosyltransferase NodZ from Bradyrhizobium sp. WM9 (Lupinus), composed of 325 amino acids with a molecular weight of 37 kDa, has been cloned, expressed and purified. Protein crystals suitable for X-ray diffraction were obtained under optimized crystallization conditions using ammonium dihydrogen phosphate as a precipitant. The crystals are hexagonal and belong to space group P6(1)22 or P6(5)22, with unit-cell parameters a = 125.5, c = 95.6 Angstrom, and contain 56.8% solvent and a single protein molecule in the asymmetric unit. Native data were collected to 2.85 Angstrom using synchrotron radiation and cryogenic conditions. The native crystals were soaked in a mother-liquor solution containing 2.5 mM [Ta6Br12](2+) cluster for derivatization and SAD data were collected to 3.4 Angstrom at the tantalum L-III absorption peak.},
      Year = {2004} }




@article{
Ceremonie98,
   Author = {C\'er\'emonie, H. and Cournoyer, B. and Normand, P. and Fernandez, M. P. and Maillet, F.},
   Title = {Genetic complementation of rhizobial \emph{nod} mutants with \emph{Frankia} DNA: Artifact or reality?},
   Journal = {Molecular and General Genetics},
   Volume = {260},
   Number = {1},
   Pages = {115-119},
   Abstract = {Two divergent reports have been published on the genetic complementation of rhizobial nod mutants using Frankia DNA. In 1991 putative Frankia cosmid library clones were reported to restore normal nodulation properties to Rhizobium leguminosarum biovar viciae nodD::Tn5, but no supporting sequence data were published. In 1992 a second group reported a failure to find any evidence of functional complementation of various rhizobial nod mutants by Frankia DNA (nodA, nodB and nodC). Complementation tests of nine Nod- R. leguminosarum bv. viciae or Sinorhizobium meliloti Tn5 mutants (nodA-, nodB-, nodC-, nodD-, nodF-, nodL-, nodH-) were thus performed using a Frankia gene library in pLAFR3 to clarify this situation. Rhizobial transconjugants obtained by tri-parental matings were screened for restoration of the nodulation phenotype on their host plants, Vicia sativa subsp. nigra or medicago sativa. Nodulation was observed on plants inoculated with transconjugants of the R. leguminosarum bv. viciae nodC::Tn5 mutant. The Nod+ rhizobial transconjugants were isolated, and analysed. The Nod+ phenotype of these transconjugants was found to be due to Tn5 excision/transposition. No functional complementation was found with any of the mutants used, suggesting that rhizobial complementation of non mutants with Frankia DNA is unlikely to occur.},
   Keywords = {Complementation
Frankia
Nodulation
Rhizobiaceae
Tn5 mutant},
   Year = {1998} }




@article{
CaetanoAnolles91,
   Author = {Caetano-Anolles, G. and Gresshoff, P. M.},
   Title = {Plant genetic control of nodulation},
   Journal = {Annual Review of Microbiology},
   Volume = {45},
   Pages = {345-382},
   Keywords = {Bradyrhizobium
legumes
molecular genetics
nitrogen fixation
Rhizobium
symbiosis},
   Year = {1991} }




@article{
Camacho02,
   Author = {Camacho, M. and Santamaria, C. and Temprano, E. and Rodriguez-Navarro, D. N. and Daza, A. and Espuny, R. and Bellog\'in, R. and Ollero, F. J. and Lyrade, Mccp and Buendia-Claveria, A. and Zhou, J. and Li, F. D. and Mateos, C. and Vel\'azquez, E. and Vinardell, J. M. and Ru\'iz-Sainz, J. E.},
   Title = {Soils of the Chinese Hubei province show a very high diversity of Sinorhizobium fredii strains},
   Journal = {Systematic and Applied Microbiology},
   Volume = {25},
   Number = {4},
   Pages = {592-602},
   Abstract = {Biodiversity studies of native soybean-nodulating rhizobia in soils from the Chinese Hubei province (Honghu county; pH 8, alluvial soil) have been carried out. Inoculation of an American (Williams) and an Asiatic (Peking) soybean cultivar with eleven soil samples led to the isolation of 167 rhizobia strains. The ratio (%) of slow-/fast-growing isolates was different depending on the trap plant used. All isolates were able to nodulate both cultivars, although the N-2-fixation efficiency (measured as plant-top dry weight) was different among them. A total of thirty-three isolates were selected for further characterisation on the basis of physiological parameters, PCR-RFLP of symbiotic genes and Low Molecular Weight RNA, lipopolysaccharide, protein and plasmid profiles. Low Molecular Weight RNA profiling indicates that all the isolates belong to species Sinorhizobium fredii. The dendrogram obtained with the physiological parameters has been useful to classify the isolates at strain level, although plasmid profiling was the most discriminating technique to detect differences among the analysed soybean-rhizobia isolates, showing there is not two isolates identical each other. Plasmid profile analyses also revealed that some of the investigated strains contain low molecular weight plasmids (7-8-kb). They are, to our knowledge, the smallest ever found in rhizobia and they could be the starting point for the construction of the first group of vectors based on a native rhizobia replicon.},
      Year = {2002} }




@article{
Cantera02b,
   Author = {Cantera, J. J. L. and Kawasaki, H. and Seki, T.},
   Title = {Evolutionary relationship of phototrophic bacteria in the ?-proteobacteria based on farnesyl diphosphate synthase},
   Journal = {Microbiology},
   Volume = {148},
   Number = {6},
   Pages = {1923-1929},
   Abstract = {Partial sequences of farnesyl diphosphate (FPP) synthase genes derived from the Rhodobacter-Rhodovulum group and from the Rhodopseudomonas palustris-Bradyrhizobium japonicum group of the ?-Proteobacteria were subjected to phylogenetic analysis to investigate the relationships of phototrophic and non-phototrophic bacteria in the ?-Proteobacteria. The four Rhodovulum species formed a monophyletic group within the Rhodobacter cluster, and Agrobacterium ferrugineum IAM 12616T intermingled with the Rhodobacter species. This topology is in good agreement with the 16S rRNA phylogeny, although the FPP synthase gene was more divergent than the 16S rRNA. On the other hand, strains of the phototrophic Rps. palustris formed a cluster far from that of the non-phototrophic Bradyrhizobium japonicum strains. Moreover, Rps. palustris strains were differentiated from the nodule-forming B. japonicum, Mezorhizobium loti MAFF 303099 and Sinorhizobium sp. NGR 234 in the FPP synthase phylogeny. This relationship does not agree with the 16S rRNA phylogeny, wherein Rps. palustris was more closely related to B. japonicum than to strains of the Rhodobacter-Rhodovulum group. These results suggest that the FPP synthase gene of Rps. palustris diverged from that of B. japonicum.},
   Keywords = {Isoprenyl diphosphare synthase
Nodule-forming bacteria
Phylogeny
Rhodobacter
Rhodopseudomonas},
   Year = {2002} }




@article{
Cantera02a,
   Author = {Cantera, J. J. L. and Kawasaki, H. and Seki, T.},
   Title = {Farnesyl diphosphate synthase gene of three phototrophic bacteria and its use as a phylogenetic marker},
   Journal = {International Journal of Systematic and Evolutionary Microbiology},
   Volume = {52},
   Pages = {1953-1960},
   Abstract = {Farnesyl diphosphate (FPP) synthase is essential not only for phototrophic bacteria in carotenoid biosynthesis, but also for non-phototrophic bacteria in the biosynthesis of physiologically important compounds. The gene encoding FPP synthase was assessed as a molecular marker to investigate the intermingled relationship between the phototropic and non-phototropic bacteria in the alpha-Proteobacteria based on 16S rRNA analysis. The FPP synthase amino acid sequences from three phototropic bacteria, Rhodobacter sphaeroides ATCC 11167(T), Rhodobacter capsulatus ATCC 11166(T) and Rhodovulum sulfidophilum W4(T), were determined and used in conjunction with sequences of other representative members of the alpha-, gamma- and epsilon-Proteobacteria and the low-G+C Gram-positive bacteria for phylogenetic analyses by the neighbour-joining and maximum-likelihood methods. The overall topology of the FPP synthase gene tree is consistent with that of the 16S rRNA tree, producing a distinct cluster of the three phototropic bacteria. A minor discordance between the two trees was observed in the cluster of the non-phototrophic Bradyrhizobium japonicum USDA 110 and Mesorhizobium loti MAFF 303099; the FPP synthase genes of these two rhizobial species are highly homologous as compared with their respective 16S rRNA. The results suggest that the FPP synthase and 16S rRNA genes have the same evolutionary pattern, evolving vertically from each common ancestral gene; the FPP synthase gene, therefore, could possibly be used for further study on the molecular systematics of photosynthetic bacteria.},
      Year = {2002} }




@article{
Cantera04,
   Author = {Cantera, Jose Jason L. and Kawasaki, Hiroko and Seki, Tatsuji},
   Title = {The nitrogen-fixing gene (\emph{nifH}) of \emph{Rhodopseudomonas palustris}: a case of lateral gene transfer?},
   Journal = {Microbiology},
   Volume = {150},
   Number = {7},
   Pages = {2237-2246},
   Abstract = {Nitrogen fixation is catalysed by some photosynthetic bacteria. This paper presents a phylogenetic comparison of a nitrogen fixation gene (nifH) with the aim of elucidating the processes underlying the evolutionary history of Rhodopseudomonas palustris. In the NifH phylogeny, strains of Rps. palustris were placed in close association with Rhodobacter spp. and other phototrophic purple non-sulfur bacteria belonging to the{alpha} -Proteobacteria, separated from its close relatives Bradyrhizobium japonicum and the phototrophic rhizobia (Bradyrhizobium spp. IRBG 2, IRBG 228, IRBG 230 and BTAi 1) as deduced from the 16S rRNA phylogeny. The close association of the strains of Rps. palustris with those of Rhodobacter and Rhodovulum, as well as Rhodospirillum rubrum, was supported by the mol% G+C of their nifH gene and by the signature sequences found in the sequence alignment. In contrast, comparison of a number of informational and operational genes common to Rps. palustris CGA009, B. japonicum USDA 110 and Rhodobacter sphaeroides 2.4.1 suggested that the genome of Rps. palustris is more related to that of B. japonicum than to the Rba. sphaeroides genome. These results strongly suggest that the nifH of Rps. palustris is highly related to those of the phototrophic purple non-sulfur bacteria included in this study, and might have come from an ancestral gene common to these phototrophic species through lateral gene transfer. Although this finding complicates the use of nifH to infer the phylogenetic relationships among the phototrophic bacteria in molecular diversity studies, it establishes a framework to resolve the origins and diversification of nitrogen fixation among the phototrophic bacteria in the{alpha} -Proteobacteria.},
      Year = {2004} }




@article{
Capela01,
   Author = {Capela, Delphine and Barloy-Hubler, Frederique and Gouzy, Jerome and Bothe, Gordana and Ampe, Frederic and Batut, Jacques and Boistard, Pierre and Becker, Anke and Boutry, Marc and Cadieu, Edouard and Dreano, Stephane and Gloux, Stephanie and Godrie, Therese and Goffeau, Andre and Kahn, Daniel and Kiss, Erno and Lelaure, Valerie and Masuy, David and Pohl, Thomas and Portetelle, Daniel and Puhler, Alfred and Purnelle, Benedicte and Ramsperger, Ulf and Renard, Clotilde and Thebault, Patricia and Vandenbol, Micheline and Weidner, Stefan and Galibert, Francis},
   Title = {Analysis of the chromosome sequence of the legume symbiont Sinorhizobium meliloti strain 1021},
   Journal = {Proceedings of the National Academy of Sciences of the United States of America},
   Volume = {98},
   Number = {17},
   Pages = {9877-9882},
   Abstract = {Sinorhizobium meliloti is an[alpha] -proteobacterium that forms agronomically important N2-fixing root nodules in legumes. We report here the complete sequence of the largest constituent of its genome, a 62.7% GC-rich 3,654,135-bp circular chromosome. Annotation allowed assignment of a function to 59% of the 3,341 predicted protein-coding ORFs, the rest exhibiting partial, weak, or no similarity with any known sequence. Unexpectedly, the level of reiteration within this replicon is low, with only two genes duplicated with more than 90% nucleotide sequence identity, transposon elements accounting for 2.2% of the sequence, and a few hundred short repeated palindromic motifs (RIME1, RIME2, and C) widespread over the chromosome. Three regions with a significantly lower GC content are most likely of external origin. Detailed annotation revealed that this replicon contains all housekeeping genes except two essential genes that are located on pSymB. Amino acid/peptide transport and degradation and sugar metabolism appear as two major features of the S. meliloti chromosome. The presence in this replicon of a large number of nucleotide cyclases with a peculiar structure, as well as of genes homologous to virulence determinants of animal and plant pathogens, opens perspectives in the study of this bacterium both as a free-living soil microorganism and as a plant symbiont.},
      Year = {2001} }




@article{
Carlson95,
   Author = {Carlson, R. W. and Reuhs, B. and Chen, T.-B. and Bhat, U. R. and Noel, K. D.},
   Title = {Lipopolysaccharide core structures in Rhizobium etli and mutants deficient in O-antigen},
   Journal = {Journal of Biological Chemistry},
   Volume = {270},
   Number = {20},
   Pages = {11783-11788},
   Abstract = {Lipopolysaccharide (LPS) is a major component of the bacterial outer membrane, and for Rhizobium spp. has been shown to play a critical role in the establishment of an effective nitrogen-fixing symbiosis with a legume host. Many genes required for O-chain polysaccharide synthesis are in the lps ? region of the CE3 genome; this region may also carry lps genes required for core oligosaccharide synthesis. The LPSs from several swains mutated in the a region were isolated, and their mild acid released oligosaccharides, purified by high performance anion-exchange chromatography, were characterized by electrospray- and fast atom bombardment-mass spectrometry, NMR, and methylation analysis. The LPSs from several mutants contained truncated O-chains, and the core region consisted of a (3-deoxy-D-manno-2- octulosomic acid) (Kdo)-(2?6)-?-Galp-(1?6)-[?-GalpA-(1?4)]-?-Manp- (1?5)-Kdop (3-deoxy-D-manno-2-octulosomic acid) (Kdo)pentasaccharide and a ?-GalpA-(1?4)-[?-GalpA-(1?5)]-Kdop trisaccharide. The pentasaccharide was altered in two mutants in that it was missing either the terminal Kdo or the GalA residue. These results indicate that the lps ? region, in addition to having the genes for O-chain synthesis, contains genes required for the transfer of these 2 residues to the core region. Also, the results show that an LPS with a complete core but lacking an O-chain polysaccharide is not sufficient for an effective symbiosis.},
   Keywords = {bacterium lipopolysaccharide
o antigen
rhizobium},
   Year = {1995} }




@article{
Carlson85,
   Author = {Carlson, T. A. and Guerinot, M. L. and Chelm, B. K.},
   Title = {Characterization of the gene encoding glutamine synthetase I (glnA) from Bradyrhizobium japonicum},
   Journal = {Journal of Bacteriology},
   Volume = {162},
   Number = {2},
   Pages = {698-703},
   Abstract = {We have isolated the Bradyrhizobium japonicum gene encoding glutamine synthetase I (glnA) from a phage lambda library by using a fragment of the Escherichia coli glnA gene as a hybridization probe. The rhizobial glnA gene has homology to the E. coli glnA gene throughout the entire length of the gene and can complement an E. coli glnA mutant when borne on an expression plasmid in the proper orientation to be transcribed from the E. coli lac promotor. High levels of glutamine synthetase activity can be detected in cell-free extracts of the complemented E. coli. The enzyme encoded by the rhizobial gene was identified as glutamine synthetase I on the basis of its sedimentation properties and resistance to heat inactivation. DNA sequence analysis predicts a high level of amino acid sequence homology among the amino termini of B. japonicum, E. coli, and Anabaena sp. strain 7120 glutamine synthetases. S1 nuclease protection mapping indicates that the rhizobial gene is transcribed from a single promoter 131 ± 2 base pairs upstream from the initiation codon. This glnA promoter is active when B. japonicum is grown both symbiotically and in culture with a variety of nitrogen and carbon sources. There is no detectable sequence homology between the constitutively expressed glnA promoter and the differentially regulated nif promoters of the same B. japonicum strain.},
      Year = {1985} }




@article{
Casida82,
   Author = {Casida, Jr., L. E.},
   Title = {\emph{Ensifer adhaerens} gen. nov., sp. nov.: A bacterial predator of bacteria in soil},
   Journal = {International Journal of Systematic Bacteriology},
   Volume = {32},
   Number = {3},
   Pages = {339-345},
      Year = {1982} }




@article{
Cavalier02,
   Author = {Cavalier-Smith, T.},
   Title = {The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification},
   Journal = {International Journal of Systematic and Evolutionary Microbiology},
   Volume = {52},
   Pages = {7-76},
   Abstract = {Prokaryotes constitute a single kingdom, Bacteria, here divided into two new subkingdoms: Negibacteria, with a cell envelope of two distinct genetic membranes, and Unibacteria, comprising the new phyla Archaebacteria and Posibacteria, with only one. Other new bacterial taxa are established in a revised higher-level classification that recognizes only eight phyla and 29 classes. Morphological, palaeontological and molecular data are integrated into a unified picture of large-scale bacterial cell evolution despite occasional lateral gene transfers. Archaebacteria and eukaryotes comprise the clade neomura, with many common characters, notably obligately co-translational secretion of N-linked glycoproteins, signal recognition particle with 75 RNA and translation-arrest domain, protein-spliced tRNA introns, eight-subunit chaperonin, prefoldin, core histones, small nucleolar ribonucleoproteins (snoRNPs), exosomes and similar replication, repair, transcription and translation machinery. Eubacteria (posibacteria and negibacteria) are paraphyletic, neomura having arisen from Posibacteria within the new subphylum Actinobacteria (possibly from the new class Arabobacteria, from which eukaryotic cholesterol biosynthesis probably came). Replacement of eubacterial peptidoglycan by glycoproteins and adaptation to thermophily are the keys to neomuran origins. All 19 common neomuran character suites probably arose essentially simultaneously during the radical modification of an actinobacterium. At least 11 were arguably adaptations to thermophily. Most unique archaebacterial characters (prenyl ether lipids; flagellar shaft of glycoprotein, not flagellin; DNA-binding protein 10b; specially modified tRNA; absence of Hsp90) were subsequent secondary adaptations to hyperthermophily and/or hyperacidity. The insertional origin of protein-spliced tRNA introns and an insertion in proton-pumping ATPase also support the origin of neomura from eubacteria. Molecular co-evolution between histones and DNA-handling proteins, and in novel protein initiation and secretion machineries, caused quantum evolutionary shifts in their properties in stem neomura. Proteasomes probably arose in the immediate common ancestor of neomura and Actinobacteria. Major gene losses (e.g. peptidoglycan synthesis, hsp90, secA) and genomic reduction were central to the origin of archaebacteria. Ancestral archaebacteria were probably heterotrophic, anaerobic, sulphur-dependent hyperthermoacidophiles; methanogenesis and halophily are secondarily derived. Multiple lateral gene transfers from eubacteria helped secondary archaebacterial adaptations to mesophily and genome re-expansion. The origin from a drastically altered actinobacterium of neomura, and the immediately subsequent simultaneous origins of archaebacteria and eukaryotes, are the most extreme and important cases of quantum evolution since cells began. All three strikingly exemplify De Beer's principle of mosaic evolution: the fact that, during major evolutionary transformations, some organismal characters are highly innovative and change remarkably swiftly, whereas others are largely static, remaining conservatively ancestral in nature. This phenotypic mosaicism creates character distributions among taxa that are puzzling to those mistakenly expecting uniform evolutionary rates among characters and lineages. The mixture of novel (neomuran or archaebacterial) and ancestral eubacteria-like characters in archaebacteria primarily reflects such vertical mosaic evolution, not chimaeric evolution by lateral gene transfer. No symbiogenesis occurred. Quantum evolution of the basic neomuran characters, and between sister paralogues in gene duplication trees, makes many sequence trees exaggerate greatly the apparent age of archaebacteria. Fossil evidence is compelling for the extreme antiquity of eubacteria [over 3500 million years (My)] but, like their eukaryote sisters, archaebacteria probably arose only 850 My ago. Negibacteria are the most ancient; radiating rapidly into six phyla. Evidence from molecular sequences, ultrastructure, evolution of photosynthesis, envelope structure and chemistry and motility mechanisms fits the view that the cenancestral cell was a photosynthetic negibacterium, specifically an anaerobic green non-sulphur bacterium, and that the universal tree is rooted at the divergence between sulphur and non-sulphur green bacteria. The negibacterial outer membrane was lost once only in the history of life, when Posibacteria arose about 2800 My ago after their ancestors diverged from Cyanobacteria.},
      Year = {2002} }




@article{
Cavalier04,
   Author = {Cavalier-Smith, T.},
   Title = {Only six kingdoms of life},
   Journal = {Proceedings of the Royal Society of London - Series B: Biological Sciences},
   Volume = {271},
   Number = {1545},
   Pages = {1251-1262},
   Abstract = {There are many more phyla of microbes than of macro-organisms, but microbial biodiversity is poorly understood because most microbes are uncultured. Phylogenetic analysis of rDNA sequences cloned after PCR amplification of DNA extracted directly from environmental samples is a powerful way of exploring our degree of ignorance of major groups. As there are only five eukaryotic kingdoms, two claims using such methods for numerous novel 'kingdom-level' lineages among anaerobic eukaryotes would be remarkable, if true. By reanalysing those data with 167 known species (not merely 8-37), I identified relatives for all 8-10 'mysterious' lineages. All probably belong to one of five already recognized phyla (Amoebozoa, Cercozoa, Apusozoa, Myzozoa, Loukozoa) within the basal kingdom Protozoa, mostly in known classes, sometimes even in known orders, families or genera. This strengthens the idea that the ancestral eukaryote was a mitochondrial aerobe. Analogous claims of novel bacterial divisions or kingdoms may reflect the weak resolution and grossly non-clock-like evolution of ribosomal rRNA, not genuine phylum-level biological disparity. Critical interpretation of environmental DNA sequences suggests that our overall picture of microbial biodiversity at phylum or division level is already rather good and comprehensive and that there are no uncharacterized kingdoms of life. However, immense lower-level diversity remains to be mapped, as does the root of the tree of life.},
      Year = {2004} }




@article{
Cha96,
   Author = {Cha, C. and Gao, P. and Chen, Y.-C. and Shaw, P. D. and Farrand, S. K.},
   Title = {Production of acyl-homoserine lactone quorum-sensing signals by gram-negative plant-associated bacteria},
   Journal = {Molecular Plant-Microbe Interactions},
   Volume = {11},
   Number = {11},
   Pages = {1119-1129},
   Abstract = {Many gram-negative bacteria regulate expression of specialized gene sets in response to population density. This regulatory mechanism, called autoinduction or quorum-sensing, is based on the production by the bacteria of a small, diffusible signal molecule called the autoinducer. In the most well-studied systems the autoinducers are Nacylated derivatives of L-homoserine lactone (acyl-HSL). Signal specificity is conferred by the length, and the nature of the substitution at C-3, of the acyl side-chain. We evaluated four acyl-HSL bioreporters, based on tra of Agrobacterium tumefaciens, lux of Vibrio fischeri, las of Pseudomonas aeruginosa, and pigment production by Chromobacterium violaceum, for their ability to detect sets of 3-oxo acyl-HSLs, 3-hydroxy acyl-HSLs, and alkanoyl-HSLs with chain lengths ranging from C4 to C12. The traG::lacZ fusion reporter from the A. tumefaciens Ti plasmid was the single most sensitive and versatile detector of the four. Using this reporter, we screened 106 isolates representing seven genera of bacteria that associate with plants. Most of the Agrobacterium, Rhizobium, and Pantoea isolates and about half of the Erwinia and Pseudomonas isolates gave positive reactions. Only a few isolates of Xanthomonas produced a detectable signal. We characterized the acyl-HSLs produced by a subset of the isolates by thin-layer chromatography. Among the pseudomonads and erwinias, most produced a single dominant activity chromatographing with the properties of N-(3-oxo-hexanoyl)-L-HSL. However, a few of the erwinias, and the P. fluorescens and Ralstonia solanacearum isolates, produced quite different signals, including 3-hydroxy forms, as well as active compounds that chromatographed with properties unlike any of our standards. The few positive xanthomonads, and almost all of the agrobacteria, produced small amounts of a compound with the chromatographic properties of N-(3-oxo-octanoyl)-L-HSL. Members of the genus Rhizobium showed the greatest diversity, with some producing as few as one and others producing as many as seven detectable signals. Several isolates produced extremely nonpolar compounds indicative of very long acyl side-chains. Production of these compounds suggests that quorum-sensing is common as a gene regulatory mechanism among gram-negative plant-associated bacteria.},
      Year = {1998} }




@article{
Chaintreuil00,
   Author = {Chaintreuil, Clemence and Giraud, Eric and Prin, Yves and Lorquin, Jean and Ba, Amadou and Gillis, Monique and de Lajudie, Philippe and Dreyfus, Bernard},
   Title = {Photosynthetic Bradyrhizobia Are Natural Endophytes of the African Wild Rice Oryza breviligulata},
   Journal = {Applied and Environmental Microbiology},
   Volume = {66},
   Number = {12},
   Pages = {5437-1427},
   Abstract = {We investigated the presence of endophytic rhizobia within the roots of the wetland wild rice Oryza breviligulata, which is the ancestor of the African cultivated rice Oryza glaberrima. This primitive rice species grows in the same wetland sites as Aeschynomene sensitiva, an aquatic stem-nodulated legume associated with photosynthetic strains of Bradyrhizobium. Twenty endophytic and aquatic isolates were obtained at three different sites in West Africa (Senegal and Guinea) from nodal roots of O. breviligulata and surrounding water by using A. sensitiva as a trap legume. Most endophytic and aquatic isolates were photosynthetic and belonged to the same phylogenetic Bradyrhizobium/Blastobacter subgroup as the typical photosynthetic Bradyrhizobium strains previously isolated from Aeschynomene stem nodules. Nitrogen-fixing activity, measured by acetylene reduction, was detected in rice plants inoculated with endophytic isolates. A 20% increase in the shoot growth and grain yield of O. breviligulata grown in a greenhouse was also observed upon inoculation with one endophytic strain and one Aeschynomene photosynthetic strain. The photosynthetic Bradyrhizobium sp. strain ORS278 extensively colonized the root surface, followed by intercellular, and rarely intracellular, bacterial invasion of the rice roots, which was determined with a lacZ-tagged mutant of ORS278. The discovery that photosynthetic Bradyrhizobium strains, which are usually known to induce nitrogen-fixing nodules on stems of the legume Aeschynomene, are also natural true endophytes of the primitive rice O. breviligulata could significantly enhance cultivated rice production.},
      Year = {2000} }




@article{
Chambers01,
   Author = {Chambers, G. K. and Boon, Wee Ming and Buckley, T. R. and Hitchmough, R. A.},
   Title = {Using molecular methods to understand the Gondwanan affinities of the New Zealand biota: Three case studies},
   Journal = {Australian Journal of Botany},
   Volume = {49},
   Number = {3},
   Pages = {377-387},
   Abstract = {The application of new molecular technologies is central to the search for causal mechanisms capable of explaining the modern-day biogeography of the southern continents. Projects have previously focused on marine mammals and birds, but in recent years they have begun to expand in scope. We now describe the results from three studies carried out recently on parakeets (genus Cyanoramphus), cicadas (genus Maoricicada) and geckos (genera Hoplodactylus and Naultinus) in the context of the Gondwanan affinities of the New Zealand biota. The work described here has been the subject of independent reports (see text for individual references) and their findings have been brought together for the first time here in a more general synthesis.},
      Year = {2001} }




@article{
Chaw04,
   Author = {Chaw, S.-M. and Chang, C.-C. and Chen, H.-L. and Li, W.-H.},
   Title = {Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes},
   Journal = {Journal of Molecular Evolution},
   Volume = {58},
   Number = {4},
   Pages = {424-441},
   Abstract = {We estimated the dates of the monocot-dicot split and the origin of core eudicots using a large chloroplast (cp) genomic dataset. Sixty-one protein-coding genes common to the 12 completely sequenced cp genomes of land plants were concatenated and analyzed. Three reliable split events were used as calibration points and for cross references. Both the method based on the assumption of a constant rate and the Li-Tanimura unequal-rate method were used to estimate divergence times. The phylogenetic analyses indicated that nonsynonymous substitution rates of cp genomes are unequal among tracheophyte lineages. For this reason, the constant-rate method gave overestimates of the monocot-dicot divergence and the age of core eudicots, especially when fast-evolving monocots were included in the analysis. In contrast, the Li-Tanimura method gave estimates consistent with the known evolutionary sequence of seed plant lineages and with known fossil records. Combining estimates calibrated by two known fossil nodes and the Li-Tanimura method, we propose that monocots branched off from dicots 140-150 Myr ago (late Jurassic-early Cretaceous), at least 50 Myr younger than previous estimates based on the molecular clock hypothesis, and that the core eudicots diverged 100-115 Myr ago (Albian-Aptian of the Cretaceous). These estimates indicate that both the monocot-dicot divergence and the core eudicot's age are older than their respective fossil records.},
   Keywords = {Age of core eudicots
Angiosperm phylogeny
Chloroplast genome
Divergence of monocot and dicot
Molecular clock
Unequal rate},
   Year = {2004} }




@article{
Chen96,
   Author = {Chen, H. and Long, B.-G. and Song, H.-Y.},
   Title = {Exopolysaccharide-deficient mutants of Astragali rhizobia are symbiotically effective on Astragalus sinicus, an indeterminate nodulating host},
   Journal = {Plant and Soil},
   Volume = {179},
   Number = {2},
   Pages = {217-221},
   Abstract = {Five exopolysaccharide-deficient mutants were isolated after rhizobial strain 107 was subjected to transposon Tn5 mutagenesis. The amount of EPS produced by the mutants was dramatically decreased to between 3% and 6% of wild-type level. All mutants carried a singel copy of Tn5. Two mutants (NA3 and NA10) were complemented by the R. meliloti exoA gene and the functionally equivalent exoD gene of Rhizobium sp. strain NGR234. Two other mutants (NA7 and NA8) were complemented by the R. meliloti exoB gene and the functionally equivalent NGR234 exoC gene. The remaining mutant (NA11) was not complemented by any exo genes of R. meliloti or Rhizobium NGR234. All mutants induced normal nitrogen-fixing nodules on Astragalus sinicus, an indeterminate nodulating host.},
   Keywords = {Astragali rhizobia
Astragalus sinicus
exopolysaccharide
symbiosis
Astragali rhizobia
Astragalus sinicus},
   Year = {1996} }




@article{
Chen93,
   Author = {Chen, H. and Richardson, A. E. and Rolfe, B. G.},
   Title = {Studies of the physiological and genetic basis of acid tolerance in Rhizobium leguminosarum biovar trifolii},
   Journal = {Applied and Environmental Microbiology},
   Volume = {59},
   Number = {6},
   Pages = {1798-1804},
   Abstract = {Acid-tolerant Rhizobium leguminosarum biovar trifolii ANU1173 was able to grow on laboratory media at a pH as low as 4.5. Transposon Tn5 mutagenesis was used to isolate mutants of strain ANU1173, which were unable to grow on media at a pH of less than 4.8. The acid-tolerant strain ANU1173 maintained a near-neutral intracellular pH when the external pH was as low as 4.5. In contrast, the acid-sensitive mutants AS25 and AS28 derived from ANU1173 had an acidic intracellular pH when the external pH was less than 5.5. The acid- sensitive R. leguminosarum biovar trifolii ANU794, which was comparatively more sensitive to low pH than mutants AS25 and AS28, showed a more acidic internal pH than the two mutants when the three strains were exposed to medium buffered at a pH of less than 5.5. The two acid-sensitive mutants had an increased membrane permeability to protons but did not change their proton extrusion activities. However, the acid-sensitive strain ANU794 exhibited both a higher membrane permeability to protons and a lower proton extrusion activity compared with the acid-tolerant strain ANU1173. DNA hybridization analysis showed that mutants AS25 and AS28 carried a single copy of Tn5 located in 13.7-kb (AS25) and 10.0-kb (AS28) EcoRI DNA fragments. The wild- type DNA sequences spanning the mutation sites of mutants AS25 and AS28 were cloned from genomic DNA of strain ANU1173. Transfer of these wild-type DNA sequences into corresponding Tn5-induced acid-sensitive mutants, respectively, restored the mutants to their acid tolerance phenotypes. Mapping studies showed that the AS25 locus was mapped to a 5.6-kb EcoRI- BamHI megaplasmid DNA fragment, whilst the AS28 locus was located in an 8.7- kb BglII chromosomal DNA fragment.},
   Keywords = {genetics
physiology},
   Year = {1993} }




@article{
Chen92,
   Author = {Chen, L. and Cui, Y. and Qin, M. and Wang, Y. and Bai, X. and Ma, Q.},
   Title = {Identification of a nodD-like gene in Frankia by direct complementation of a Rhizobium nodD-mutant},
   Journal = {Molecular and General Genetics},
   Volume = {233},
   Number = {1-2},
   Pages = {311-314},
   Abstract = {Clones from a Frankia At4 gene bank were pooled into groups and mass conjugated into a nodD mutant of Rhizobium leguminosarum bv. viciae by triparental matings. When peas were inoculated with the pooled transconjugants, nodulation was observed. A plasmid, pAt2GX containing Frankia DNA, was isolated from bacteria recovered from these nodules. This plasmid was shown to complement a nodD mutant of R. leguminosarum bv. viciae. Thus pAt2GX contains a Frankia gene that is functionally equivalent to nodD of R. leguminosarum bv. viciae.},
   Keywords = {complementation
Frankia
mutant
nod
nodule
genetic analysis
genetic complementation
mutant
Genes, Fungal},
   Year = {1992} }




@article{
Chen00a,
   Author = {Chen, Lu Shi  and Figueredo, A. and Pedrosa, F. O. and Hungria, M.},
   Title = {Genetic characterization of soybean rhizobia in Paraguay},
   Journal = {Applied and Environmental Microbiology},
   Volume = {66},
   Number = {11},
   Pages = {5099-5103},
   Abstract = {The soybean is an exotic plant introduced in Paraguay in this century; commercial cropping expanded after the 1970s. Inoculation is practiced in just 15 to 20% of the cropping areas, but root nodulation occurs in most sites where soybeans grow. Little is known about rhizobial diversity in South America, and no study has been performed in Paraguay until this time. Therefore, in this study, the molecular characterization of 78 rhizobial isolates from soybean root nodules, collected under field conditions in 16 sites located in the two main producing states, Alto Parana and Itapua, was undertaken. A high level of genetic diversity was detected by an ERIC-REP-PCR analysis, with the majority of the isolates representing unique strains. Most of the 58 isolates characterized by slow growth and alkaline reactions in a medium containing mannitol as a carbon source were clustered with strains representative of the Bradyrhizobium japonicum and Bradyrhizobium elkanii species, and the 16S ribosomal DNA (rDNA) sequences of 5 of those isolates confirmed the species identities. However, slow growers were highly polymorphic in relation to the reference strains, including five carried in commercial inoculants in neighboring countries, thus indicating that the Paraguayan isolates might represent native bradyrhizobia. Twenty isolates highly polymorphic in the ERIC-REP-PCR profiles were characterized by fast growth and acid reactions in vitro, and two of them showed high 16S rDNA identities with Rhizobium genomic species Q. However, two other fast growers showed high 16S rDNA identity with Agrobacterium spp., and both of these strains established efficient symbioses with soybean plants.},
   Keywords = {nucleotide sequence
Rhizobium
Agrobacterium
Bradyrhizobium elkanii
Bradyrhizobium japonicum},
   Year = {2000} }




@article{
Chen02a,
   Author = {Chen, L. S. and Hungria, M. and Figueredo, A. and Villani, H. and Michajluk, J.},
   Title = {Diversity and symbiotic effectiveness of rhizobia isolated from field-grown soybean nodules in Paraguay},
   Journal = {Biology and Fertility of Soils},
   Volume = {35},
   Number = {6},
   Pages = {448-457},
   Abstract = {Soybean was introduced in Paraguay in the 1920s and commercial crops have been grown since the 1970s. Root nodulation occurs at the majority of the producing sites, although inoculation has been practiced in only 15-20% of the cropping areas. The diversity and symbiotic effectiveness of soybean rhizobia was studied using 78 isolates obtained from root nodules of fieldgrown plants at 16 sites located in the two main producing states. The rhizobial isolates were characterized in relation to several parameters in vitro (colony morphology, tolerance to high temperature and salinity, intrinsic resistance to antibiotics, synthesis of indole acetic acid, profiles of proteins and lipopolysaccharides) and in vivo (nodulation, plant growth and total N accumulated in shoots). Fifty-eight isolates had slow growth rates and alkaline reaction in medium containing mannitol as the carbon source, whereas 20 had fast growth rates and an acid reaction. Most isolates did not tolerate acidity (pH 4.5) or high temperature (40°C). Very few isolates shared similar protein and lipopolysaccharide profiles; therefore a high level of diversity was detected, with most of the isolates representing unique strains. Some of the isolates with an outstanding symbiotic performance were identified, and will now be tested under field conditions in a search for efficient and competitive strains for use in commercial inoculants in Paraguay.},
   Keywords = {Bacterial diversity
Biological nitrogen fixation
Bradyrhizobium
Glycine max
Rhizobium
nitrogen fixation
nodulation
rhizobacterium
soybean
symbiosis
Rhizobiaceae
species diversity
Paraguay},
   Year = {2002} }




@article{
Chen01,
   Author = {Chen, M. and Xie, F. and Zhou, J.},
   Title = {Diversity of \emph{Sinorhizobium fredii} strains},
   Journal = {Ying Yong Sheng Tai Xue Bao},
   Volume = {12},
   Number = {4},
   Pages = {597-600. In Chinese, English summary},
   Abstract = {Rhizobial strains were isolated from soils growing with soybean cultivar Heilong 33 and Willimas. Fifty Sinorhizobium fredii strains were chosen, and their biological characteristics including growth velocity, acid-alkali endurance, resistance of intrinsic antibiotics, utilization of carbon and nitrogen sources, absorption of congo red, ability of melanin production, and plasmid profiles were comparatively researched. The dendrogram was described using the method of cluster analysis, and the biodiversity of Sinorhizobium fredii from different soils was proved.},
      Year = {2001} }




@article{
Chen05b,
   Author = {Chen, M. Z. and Xie, B. and Huang, C. H. and Xie, F. L. and Yang, J. G. and Zhou, Q. and Zhou, J. C.},
   Title = {Study on genetic diversity and phylogeny of soybean rhizobia in China},
   Journal = {Symbiosis},
   Volume = {38},
   Number = {2},
   Pages = {123-144},
   Abstract = {Fifty-two soybean rhizobia isolated from root nodules of nine soybean cultivars from soil samples collected from seven different sites in China were studied comparing with twenty three type strains of rhizobia by phenotypic characteristics, host specificity, 16S rDNA PCR-RFLP, 16S rDNA sequencing, REP-ERIC-PCR and DNA-DNA hybridization. Results of phenotypic characteristics indicated that twenty nine fast-growing strains could be distinguished with Sinorhizobium xinjiangense CCBAU110 and twenty three slow-growing strains with Bradyrhizobium elkanii USDA76, respectively. The similarities of some slow-growing strains corresponded to geographical sampling sites. All strains could be divided into two types by host specificity. Results of 16S rDNA PCR-RFLP, 16S rDNA sequence analysis, REP-ERIC-PCR and DNA-DNA hybridization revealed that twenty nine strains of fast-growing rhizobia were all clustered together with Sinorhizobium fredii USDA205 and S. xinjiangense CCBAU110. Similarly, twenty three strains of slow-growing rhizobia were highly related with B. japonicum and B. liaoningense.},
      Year = {2005} }




@article{
Chen02b,
   Author = {Chen, R. and Yaklich, R. and Keister, D. L. and Bhagwat, A. A. and Chen, R.},
   Title = {Characterization of ndvD, the third gene involved in the synthesis of cyclic ?-(1?3),(1?6)-D-glucans in Bradyrhizobium japonicum},
   Journal = {Canadian Journal of Microbiology},
   Volume = {48},
   Number = {11},
   Pages = {1008-1016},
   Abstract = {Previously, we identified two genes in Bradyrhizobium japonicum (ndvB, ndvC) that are required for cyclic ?-(1?3),(1?6)-D-glucan synthesis and successful symbiotic interaction with soybean (Glycine max). In this study, we report a new open reading frame (ORF1) located in the intergenic region between ndvB and ndvC, which is essential for ?-glucan synthesis and effective nodulation of G. max. This new gene is designated ndvD (nodule development). The ndvD translation product has a predicted molecular mass of 26.4 kDa with one transmembrane domain. Genetic experiments involving gene deletion, Tn5 insertion, and gene complementation revealed that the mutation of ndvD generated pleiotropic phenotypes, including hypoosmotic sensitivity, reduced motility, and defects in conjugative gene transfer, in addition to symbiotic ineffectiveness. Although deficient in in vivo ?-glucan synthesis, membrane preparations from the ndvD mutant synthesized neutral ?-glucans in vitro. Therefore, ndvD does not appear to be a structural gene for ?-glucan synthesis. Our hypothesis for the mechanism of ?-(1?3),(1?6)-D-glucan synthesis is presented.},
   Keywords = {?-glucans
Bradyrhizobium
Nitrogen fixation
Soybean
Biological membranes
Genes
Organic compounds
Osmosis
Mutation
Microbiology
beta glucan
carbohydrate derivative
cyclic beta (1-3),(1-6) dextro glucan
nitrogen fixation
rhizobacterium
carbohydrate synthesis
gene identification
nucleotide sequence
Rhizobium japonicum
Symbiosis
Bradyrhizobium japonicum
Glycine max},
   Year = {2002} }




@article{
Chen95,
   Author = {Chen, W. and Wang, E. and Wang, S. and Li, Y. and Chen, X.},
   Title = {Characteristics of \emph{Rhizobium tianshanense} sp. nov., a moderately and slowly growing root nodule bacterium isolated from an arid saline environment in Xinjiang, People's Republic of China},
   Journal = {International Journal of Systematic Bacteriology},
   Volume = {45},
   Number = {1},
   Pages = {153-159},
   Abstract = {We performed a numerical analysis of 148 phenotypic characteristics of 20 strains of root nodule bacteria isolated from an arid saline desert soil in the Xinjiang region of northwestern People's Republic of China and compared these organisms with 28 Rhizobium and Bradyrhizobium strains obtained from different regions of the People's Republic of China and from other countries, including nine type strains of different species. All of the strains examined clustered into two groups at a similarity level of more than 63%. Group I included all of the previously described Rhizobium species and was divided into eight subgroups, which corresponded to previously described Rhizobium species, at a similarity level of more than 82%. Group II was divided into the following three subgroups at a similarity level of more than 80% Bradyrhizobium japonicum, a cluster containing 17 moderately and slowly growing strains isolated in the Xinjiang region, and a small subgroup containing three fast-growing strains. The generation times of the moderately and slowly growing strains were 5 to 15 h, and these organisms produced acid in medium containing mannitol. The DNA G+C contents of the members of this group ranged from 59 to 63 mol%. DNA-DNA hybridization experiments revealed that the levels of DNA homology among all of the moderately and slowly growing strains obtained from Xinjiang were more than 70% and that the levels of DNA homology between representative strains of this group and the type strains of all previously described species of root- and stem-nodulating bacteria were low. All of our experimental data indicated that the moderately and slowly growing rhizobia isolated from Xinjiang are members of a new species. Partial 16S rRNA gene sequencing of the type strain. A-1BS (= CCBAU3306), and a comparison of the resulting sequence with the sequences of previously described species revealed that strain A-1BS is closely related to Rhizobium loti, Rhizobium huakuii, and Rhizobium galegae, but not to B. japonicum and Azorhizobium caulinodans. On the basis of our results, we propose that the strains which we studied are members of a new species, Rhizobium tianshanense. The type strain, A-1BS (= CCBAU3306), has been deposited in the Culture Collection of Beijing Agricultural University, Beijing, People's Republic of China.},
   Keywords = {rhizobium},
   Year = {1995} }




@article{
Chen03a,
   Author = {Chen, W. M. and James, E. K. and Prescott, A. R. and Kierans, M. and Sprent, J. I.},
   Title = {Nodulation of \emph{Mimosa} spp. by the beta-proteobacterium \emph{Ralstonia taiwanensis}},
   Journal = {Molecular Plant-Microbe Interactions},
   Volume = {16},
   Number = {12},
   Pages = {1051-1061},
   Abstract = {Several beta-proteobacteria have been isolated from legume root nodules and some of these are thought to be capable of nodulating and fixing N-2. However, in no case has there been detailed studies confirming that they are the active symbionts. Here, Ralstonia taiwanensis LMG19424, which was originally isolated from Mimosa pudica nodules, was transformed to carry the green fluorescent protein (gfp) reporter gene before being used to inoculate axenically-grown seedlings of M. pudica and M. diplotricha. Plants were harvested at various intervals for 56 days after inoculation, then examined for evidence of infection and nodule formation. Nodulation of both Mimosa spp. was abundant, and acetylene reduction assays confirmed that nodules had nitrogenase activity. Confocal laser scanning microscopy (CLSM) showed that fresh M. pudica nodules with nitrogenase activity had infected cells containing bacteroids expressing gfp. In parallel, fixed and embedded nodules from both Mimosa spp. were sectioned for light and electron microscopy, followed by immunogold labeling with antibodies raised against gfp and nitrogenase Fe (nifH) protein. Significant immunolabeling with these antibodies confirmed that R. taiwanensis LMG19424 is an effective N-2-fixing symbiont of Mimosa spp. Both species were infected via root hairs and, in all respects, the nodule ontogeny and development was similar to that described for other mimosoid legumes. The nodules were indeterminate with a persistent meristem, an invasion zone containing host cells being invaded via prominent infection threads, and an N-2-fixing zone with infected cells containing membrane-bound symbiosomes.},
      Year = {2003} }




@article{
Chen03b,
   Author = {Chen, W. M. and Moulin, L. and Bontemps, C. and Vandamme, P. and Bena, G. and Boivin-Masson, C.},
   Title = {Legume symbiotic nitrogen fixation by beta-proteobacteria is widespread in nature},
   Journal = {Journal of Bacteriology},
   Volume = {185},
   Number = {24},
   Pages = {7266-72},
   Abstract = {Following the initial discovery of two legume-nodulating Burkholderia strains (L. Moulin, A. Munive, B. Dreyfus, and C. Boivin-Masson, Nature 411:948-950, 2001), we identified as nitrogen-fixing legume symbionts at least 50 different strains of Burkholderia caribensis and Ralstonia taiwanensis, all belonging to the beta-subclass of proteobacteria, thus extending the phylogenetic diversity of the rhizobia. R. taiwanensis was found to represent 93% of the Mimosa isolates in Taiwan, indicating that beta-proteobacteria can be the specific symbionts of a legume. The nod genes of rhizobial beta-proteobacteria (beta-rhizobia) are very similar to those of rhizobia from the alpha-subclass (alpha-rhizobia), strongly supporting the hypothesis of the unique origin of common nod genes. The beta-rhizobial nod genes are located on a 0.5-Mb plasmid, together with the nifH gene, in R. taiwanensis and Burkholderia phymatum. Phylogenetic analysis of available nodA gene sequences clustered beta-rhizobial sequences in two nodA lineages intertwined with alpha-rhizobial sequences. On the other hand, the beta-rhizobia were grouped with free-living nitrogen-fixing beta-proteobacteria on the basis of the nifH phylogenetic tree. These findings suggest that beta-rhizobia evolved from diazotrophs through multiple lateral nod gene transfers.},
   Keywords = {Acyltransferases/genetics
Amidohydrolases/genetics
Burkholderia/*genetics
Fabaceae/microbiology
Gene Transfer, Horizontal/genetics
Mimosa/microbiology
Molecular Sequence Data
Nitrogen Fixation/*genetics
Oxidoreductases/genetics
*Phylogeny
Ralstonia/*genetics
Support, Non-U.S. Gov't
Taiwan},
   Year = {2003} }




@article{
Chen01x,
   Author = {Chen, W.-M. and Laevens, S. and Lee, T.-M. and Coenye, T. and De Vos, P. and Mergeay, M. and Vandamme, P.},
   Title = {\emph{Ralstonia taiwanensis} sp. nov., isolated from root nodules of \emph{Mimosa} species and sputum of a cystic fibrosis patient},
   Journal = {International Journal of Systematic and Evolutionary Microbiology},
   Volume = {51},
   Number = {5},
   Pages = {1729-1735},
   Abstract = {A polyphasic taxonomic study, including 16S rDNA sequence analysis, DNA-DNA hybridizations, DNA base ratio determinations, amplified 16S rDNA restriction analysis, whole-cell protein analyses and extensive biochemical characterization, was conducted to clarify the relationships of eight isolates from root nodules of Mimosa species and one isolate from sputum of a cystic fibrosis patient. All nine isolates were classified as a novel Ralstonia species, for which the name Ralstonia taiwanensis sp. nov. is proposed. The type strain is LMG 19424T (= CCUG 44338T). R. taiwanensis effectively nodulated the Mimosa species and is the first ?-proteobacterium that is known to be capable of root nodule formation and nitrogen fixation.},
   Keywords = {Mimosa
Ralstonia taiwanensis sp. nov.
Root nodules
Taxonomy},
   Year = {2001} }




@article{
Chen00b,
   Author = {Chen, W.-M. and Lee, T.-M. and Lan, C.-C. and Cheng, C.-P.},
   Title = {Characterization of halotolerant rhizobia isolated from root nodules of Canavalia rosea from seaside areas},
   Journal = {FEMS Microbiology Ecology},
   Volume = {34},
   Number = {1},
   Pages = {9-16},
   Abstract = {Twelve nodule isolates from Canavalia rosea, an indigenous leguminous halophyte growing in the seaside areas of southern Taiwan, were effective symbionts for the original host and able to grow at NaCl concentrations up to 3-3.5% (w/v). The taxonomy of these isolates was investigated using a polyphasic approach, including phenotypic characteristics, banding patterns of total proteins from sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), genomic fingerprint patterns from random amplified polymorphic DNA (RAPD) analysis, pulsed-field gel electrophoresis (PFGE) analysis, amplified 16S rDNA restriction analysis (ARDRA), 16S rRNA gene sequencing, and nifH gene sequencing. Based on the SDS-PAGE, RAPD, PFGE and ARDRA results, the 12 isolates are highly diverse. The 16S rRNA and nifH gene sequences were determined for isolates with distinct ARDRA patterns and compared with other members of the rhizobial species. We propose these isolates should be classified into the genus Sinorhizobium and distinguished from the current species of this genus. Copyright (C) 2000 Federation of European Microbiological Societies.},
   Keywords = {16S rRNA gene
Canavalia rosea
Halotolerant
nifH gene
Sinorhizobium
Symbiosis
genetic analysis
Rhizobium
Sinorhizobium
Canavalia rosea
Sinorhizobium},
   Year = {2000} }




@article{
Chen91,
   Author = {Chen, W. X. and Li, G. S. and Qi, Y. L. and Wang, E. T. and Yuan, H. L. and Li, J. L.},
   Title = {\emph{Rhizobium huakuii} sp. nov. isolated from the root nodules of \emph{Astragalus sinicus}},
   Journal = {International Journal of Systematic Bacteriology},
   Volume = {41},
   Number = {2},
   Pages = {275-280},
   Abstract = {Nine bacterial strains isolated from root nodules of Astragalus sinicus were compared with 41 reference strains, including the type strains of the type species of the genera Rhizobium, Bradyrhizobium, and Agrobacterium, by performing a numerical analysis of 200 phenotype features. Representative strains belonging to different clusters were further compared with similar bacteria by using data from gel electrophoresis of whole-cell proteins, DNA G+C content data, and DNA-DNA hybridization data. The rhizobial strains isolated from nodules of a. sinicus constitute a distinct homology group that is quite different from previously described Rhizobium, Bradyrhizobium, and Agrobacterium species and from strains isolated from other Astragalus species. We propose the name Rhizobium huakuii sp. nov. for the strains isolated from A. sinicus. Type strain CCBAU 2609 (= 103) has been deposited in the Culture Collection of Beijing Agricultural University, Beijing, People's Republic of China.},
   Keywords = {rhizobium},
   Year = {1991} }




@article{
Chen97,
   Author = {Chen, W. X. and Tan, Z. Y. and Gao, J. L. and Li, Y. and Wang, E. T.},
   Title = {\emph{Rhizobium hainanense} sp. nov, isolated from tropical legumes},
   Journal = {International Journal of Systematic Bacteriology},
   Volume = {47},
   Number = {3},
   Pages = {870-873},
   Abstract = {A fast-growing rhizobial group isolated from leguminous plants in Hainan Province, a tropical region of China, is proposed as a new Rhizobium species on the basis of 16S rRNA gene sequencing, DNA-DNA hybridization, and phenotypic characterization. This new species belongs to the phylogenetic branch which includes Rhizobium leguminosarum. We propose the name Rhizobium hainanense sp. nov. for this species. The strain CCBAU 57015 (I66) is the type strain; it has been deposited in the culture collection of Beijing Agricultural University, People's Republic of China.},
      Year = {1997} }




@incollection{
Chen05a,
   Author = {Chen, W. X. and Wang, E. T. and Kuykendall, L. D.},
   Title = {Genus VI. \emph{Mesorhizobium} Jarvis, van Berkum, Chen, Nour, Fernandez, Cleyet-Marel and Gillis 1997, 897$^{\mathrm{VP}}$},
   BookTitle = {Part C, The Alpha-, Beta-, Delta-, and Epsilonproteobacteria, Bergey's Manual of Systematic Bacteriology},
   Editor = {Brenner, D. J. and Krieg, R. K. and Staley, J. T. and Garrity, G. M.},
   Series = {Bergey's Manual of Systematic Bacteriology},
   Publisher = {Springer},
   Address = {New York},
   Volume = {2},
      Year = {2005} }




@article{
Chen88,
   Author = {Chen, W. X. and Yan, G. H. and Li, J. L.},
   Title = {Numerical taxonomic study of fast-growing soybean rhizobia and a proposal that \emph{Rhizobium fredii} be assigned to \emph{Sinorhizobium} gen. nov.},
   Journal = {International Journal of Systematic Bacteriology},
   Volume = {38},
   Number = {4},
   Pages = {392-397},
   Abstract = {A total of 33 strains of fast-growing soybean rhizobia isolated from soil and soybean nodules collected in China and 25 strains belonging to the genera Rhizobium, Bradyrhizobium, and Agrobacterium were compared by numerical taxonomic techniques, using 240 different characters. Our results indicated that all of the strains of fast-growing soybean rhizobia which we examined are closely related (guanine-plus-cytosine content, 59.9 to 63.8 mol%) and are separated from Rhizobium and Bradyrhizobium at the generic level. Based on numerical taxonomy, deoxyribonucleic acid (DNA) base ratio determinations, DNA-DNA hybridization data, serological analysis data, the composition of extracellular gum, bacteriophage typing data, and soluble protein patterns, we propose that the fast-growing soybean rhizobia represent members of a new genus rather than a species of Rhizobium (Rhizobium fredii); we propose Sinorhizobium gen. nov. as an appropriate generic name. The type species of the new genus is Sinorhizobium fredii comb. nov. (basonym, Rhizobium fredii Scholla and Elkan 1984), and the type strain is strain ATCC 35423 (= USDA 205). For the other species we propose the name Sinorhizobium xinjiangensis sp. nov.; the type strain of this species is strain CCBAU 110, which has been deposited in the Beijing Agricultural University Culture Collection, Beijing, People's Republic of China.},
   Keywords = {rhizobium fredii},
   Year = {1988} }




@article{
Chhonkar66,
   Author = {Chhonkar, P. K. and Subba-Rao, N. S.},
   Title = {Fungi associated with legume root nodules and their effect on rhizobia},
   Journal = {Canadian Journal of Microbiology},
   Volume = {12},
   Number = {6},
   Pages = {1253-61},
   Keywords = {Anti-Bacterial Agents/biosynthesis/*pharmacology
Aspergillus/isolation \& purification
Fungi/*isolation \& purification
Mitosporic Fungi/*isolation \& purification
Penicillium/isolation \& purification
*Plants
Rhizobium/*drug effects
Rhizopus/isolation \& purification
*Soil Microbiology},
   Year = {1966} }




@article{
Chimote03,
   Author = {Chimote, V. and Kashyap, L. R.},
   Title = {Organization pattern of common nod genes in Mesorhizobium ciceri strain MC 18-7},
   Journal = {Journal of Plant Biochemistry and Biotechnology},
   Volume = {12},
   Number = {1},
   Pages = {57-59},
   Abstract = {The common nodulation genes (nod ABC) are normally present together as a single operon in most rhizobia; however, there are few exceptions. Fast growing Mesorhizobium ciceri strain MC 18-7 was examined for structural organization of the nodABC genes by PCR amplification. Results indicated that in Mesorhizobium ciceri strain MC 18-7 nodA and nodC genes are present together under same nod box, while nodB gene has a separate nod box present immediately upstream to it, just like in its close relative Mesorhizobium loti.},
      Year = {2003} }




@article{
Choi96,
   Author = {Choi, B.-H. and Ohashi, H.},
   Title = {Pollen Morphology and Taxonomy of Hedysarum and Its Related Genera of the Tribe Hedysareae (Leguminosae-Papilionoideae)},
   Journal = {Journal of Japanese Botany},
   Volume = {71},
   Number = {4},
   Pages = {191-213},
   Abstract = {Pollen morphology of 51 species of the genera Alhagi, Corethrodendron, Ebenus, Eversmannia, Hedysarum, Onobrychis, Stracheya and Taverniera of the tribe Hedysareae was investigated. Three pollen types are recognized, i.e., tricolporoidate, tricolpate and tricolporate. The tricolporoidate type exhibits tricolporoidate apertures and perforate tectum, while the tricolpate or the tricolporate type are those with tricolpate or tricolporate apertures, respectively, with reticulate tectum. The tricolporoidate type is observed in Alhagi, Corethrodendron, Eversmannia, Hedysarum (section Membranacea of subgenus Gamotion and subgenus Heteroloma) and Taverniera. The tricolpate type is found in Ebenus, Hedysarum (sections Crinifera, Gamotion, Multicaulia and Subacaulia of subgenus Gamotion), Onobrychis and Stracheya, and is the most common in the tribe. The tricolporate type is found only in Hedysarum (subgenus Hedysarum). The tricolpate and tricolporate types are supposed to be derived from the tricolporoidate type, which is recognized here as most primitive in the tribe Hedysareae. Pollen morphological data of our study show that subgenus Hedysarum is separated from other infrageneric groups of Hedysarum, and that there is no substantial basis for separating Corethrodendron, Stracheya and Taverniera from Hedysarum as distinct genera. The former two are allied with the subgenus Heteroloma and the latter with the subgenus Gamotion.},
      Year = {1996} }




@article{
Choma00,
   Author = {Choma, A. and Urbanik-Sypniewska, T. and Russa, R. and Kutkowska, J. and Mayer, H.},
   Title = {Occurrence and taxonomic significance of oxo-fatty acids in lipopolysaccharides from members of Mesorhizobium},
   Journal = {Systematic and Applied Microbiology},
   Volume = {23},
   Number = {2},
   Pages = {185-90},
   Abstract = {Lipopolysaccharides (LPSs) isolated from seven strains of Mesorhizobium were studied for the presence of fatty acids with particular attention for 27-oxooctacosanoic acid and 4-oxo fatty acids. The LPSs from all analysed strains contained various amounts of 27-oxo-28:0 and all of them, with the exception of Mesorhizobium tianshanense, contained also 4-oxo fatty acids (4-oxo-20:0, 4-oxo-i-21:0, 4-oxo-22:0). The group of amide-linked fatty acids consisted of a wide range of 3-hydroxylated and 4-oxo fatty acids whereas all the nonpolar as well as the (omega-1) hydroxylated long-chain acids and the 27-oxo-28:0 fatty acids were ester-linked. The characteristic spectrum of 3-hydroxy fatty acids and presence of 27-OH-28:0 as well as 27-oxo-28:0 acid in LPSs of Mesorhizobium showed that these strains were closely related. Therefore the lipid A fatty acid pattern could be a useful chemotaxonomic marker which helps to isolate the Mesorhizobium group from rhizobium bacteria during the classification process.},
   Keywords = {Amides
chemistry
Bacterial Typing Techniques
Comparative Study
Esters
Fatty Acids
isolation \& purification
Lipid A
Plants
microbiology
Rhizobiaceae
classification
Support
Non-U.S.Gov't},
   Year = {2000} }




@article{
Chung06,
   Author = {Chung, S.-M. and Vaidya, M. and Tzfira, T.},
   Title = {Agrobacterium is not alone: Gene transfer to plants by viruses and other bacteria},
   Journal = {Trends in Plant Science},
   Volume = {11},
   Number = {1},
   Pages = {1-4},
   Abstract = {Agrobacterium-mediated genetic transformation is the most widely used technology for obtaining the overexpression of recombinant proteins in plants. However, complex patent issues related to the use of Agrobacterium as a tool for plant genetic engineering and the general requirement of establishing transgenic plants can create obstacles in using this technology for speedy research and development and for agricultural improvements in many plant species. Recent studies addressing these issues have shown that virus-based vectors can be efficiently used for high transient expression of foreign proteins in transfected plants and that non-Agrobacterium bacterial species can be used for the production of transgenic plants, laying the foundation for alternative tools for future plant biotechnology. © 2005 Elsevier Ltd. All rights reserved.},
      Year = {2006} }




@article{
Clemens01,
   Author = {Clemens, J.},
   Title = {The wild origins of \emph{Clianthus} cultivars and their value for \emph{ex situ} conservation},
   Journal = {International Plant Propagators' Society. Combined Proceedings of Annual Meetings},
   Volume = {51},
   Pages = {92-93},
   Abstract = {Clianthus is an endangered genus endemic to Mew Zealand. Random amplified polymorphic DMA (RAPD) analysis, followed by hierarchical cluster analysis, showed that Clianthus cultivars are not representative of the remaining range of wild populations. As such, they constitute minimal value for the ex situ conservation of Clianthus diversity. Cultiver 'White Heron' probably comes from close to the most north-easterly extremity of the distribution of C. maximus in the wild (near East Cape). Cultivars Kaka King® (Naturally Native New Zealand Plants Ltd.), 'Maximus', and 'Red Cardinal' are very closely related (or Indistinguishable), and also originate from the north-eastern range of this species. Cultiver 'Flamingo' associates with the more south-westerly populations of this species.},
   Keywords = {Composition
DNA
Genetic engineering
Cultivars
Biodiversity},
   Year = {2001} }




@article{
Clos96,
   Author = {Clos, D},
   Title = {Caract\`eres ext\'erieurs et modes de r\'epartition des petits tubercules ou tuberculo\"ides des l\'egumineuses},
   Journal = {C. R. Acad. Sci.},
   Volume = {123},
   Pages = {407-410},
      Year = {1896} }




@article{
Cohan01,
   Author = {Cohan, F. M.},
   Title = {Bacterial species and speciation},
   Journal = {Systematic Biology},
   Volume = {50},
   Number = {4},
   Pages = {513-524},
   Abstract = {Bacteria are profoundly different from eukaryotes in their patterns of genetic exchange. Nevertheless, ecological diversity is organized in the same way across all of life: individual organisms fall into more or less discrete clusters on the basis of their phenotypic, ecological, and DNA sequence characteristics. Each sequence cluster in the bacterial world appears to correspond to an "ecotype," defined as a population of cells in the same ecological niche, which would all be out-competed by any adaptive mutant coming from the population. Ecotypes, so defined, share many of the dynamic properties attributed to eukaryotic species: genetic diversity within an ecotype is limited by a force of cohesion (in this case, periodic selection); different ecotypes are free to diverge without constraint from one another; and ecotypes are ecologically distinct. Also, ecotypes can be discovered and classified as DNA sequence clusters, even when we are ignorant of their ecology. Owing to the rarity and promiscuity of bacterial genetic exchange, speciation in the bacterial world is expected to be much less constrained than in the world of animals and plants.},
      Year = {2001} }




@article{
Cohan02b,
   Author = {Cohan, F. M.},
   Title = {Sexual isolation and speciation in bacteria},
   Journal = {Genetica},
   Volume = {116},
   Number = {2-3},
   Pages = {359-370},
   Abstract = {Like organisms from all other walks of life, bacteria are capable of sexual recombination. However, unlike most plants and animals, bacteria recombine only rarely, and when they do they are extremely promiscuous in their choice of sexual partners. There may be no absolute constraints on the evolutionary distances that can be traversed through recombination in the bacterial world, but interspecies recombination is reduced by a variety of factors, including ecological isolation, behavioral isolation, obstacles to DNA entry, restriction endonuclease activity, resistance to integration of divergent DNA sequences, reversal of recombination by mismatch repair, and functional incompatibility of recombined segments. Typically, individual bacterial species are genetically variable for most of these factors. Therefore, natural selection can modulate levels of sexual isolation, to increase the transfer of genes useful to the recipient while minimizing the transfer of harmful genes. Interspecies recombination is optimized when recombination involves short segments that are just long enough to transfer an adaptation, without co-transferring potentially harmful DNA flanking the adaptation. Natural selection has apparently acted to reduce sexual isolation between bacterial species. Evolution of sexual isolation is not a milestone toward speciation in bacteria, since bacterial recombination is too rare to oppose adaptive divergence between incipient species. Ironically, recombination between incipient bacterial species may actually foster the speciation process, by prohibiting one incipient species from out-competing the other to extinction. Interspecific recombination may also foster speciation by introducing novel gene loci from divergent species, allowing invasion of new niches.},
      Year = {2002} }




@article{
Cohan02a,
   Author = {Cohan, F. M.},
   Title = {What are bacterial species?},
   Journal = {Annual Review of Microbiology},
   Volume = {56},
   Pages = {457-487},
   Abstract = {Bacterial systematics has not yet reached a consensus for defining the fundamental unit of biological diversity, the species. The past half-century of bacterial systematics has been characterized by improvements in methods for demarcating species as phenotypic and genetic clusters, but species demarcation has not been guided by a theory-based concept of species. Eukaryote systematists have developed a universal concept of species: A species is a group of organisms whose divergence is capped by a force of cohesion; divergence between different species is irreversible; and different species are ecologically distinct. In the case of bacteria, these universal properties are held not by the named species of systematics but by ecotypes. These are populations of organisms occupying the same ecological niche, whose divergence is purged recurrently by natural selection. These ecotypes can be discovered by several universal sequence-based approaches. These molecular methods suggest that a typical named species contains many ecotypes, each with the universal attributes of species. A named bacterial species is thus more like a genus than a species.},
      Year = {2002} }




@article{
Cohn72,
   Author = {Cohn, F.},
   Title = {Untersuchungen \"uber Bacterien. II.},
   Journal = {Beir\"age zur Biologie der Pflanzen},
   Volume = {1},
   Pages = {127-224},
      Year = {1872} }




@article{
Cohn98,
   Author = {Cohn, Jonathan and Day, R. Bradley and Stacey, Gary},
   Title = {Legume nodule organogenesis},
   Journal = {Trends in Plant Science},
   Volume = {3},
   Number = {3},
   Pages = {105-110},
      Year = {1998} }




@article{
Colebatch02,
   Author = {Colebatch, G. and Trevaskis, B. and Udvardi, M.},
   Title = {Symbiotic nitrogen fixation research in the postgenomics era},
   Journal = {New Phytologist},
   Volume = {153},
   Number = {1},
   Abstract = {Nitrogen-fixing symbioses between legumes and rhizobia are important for sustainable agriculture and contribute significantly to the global nitrogen cycle. The genomes of two rhizobial species, Mesorhizobium loti and Sinorhizobium meliloti, have now been completely sequenced. Hundreds of thousands of expressed sequence tags representing tens of thousands of different genes from three major legume species, soyabean, Medicago truncatula and Lotus japonicus [L. corniculatus var. japonicus], have also been deposited in the public domain. L. japonicus recently became the focus of a genome project that aims to sequence one third of the entire genome over the next 5 years. With this as a backdrop, the stage is set for a renaissance in symbiosis research, which will provide new insight into the complex molecular interplay that underpins symbiotic nitrogen fixation. This review considers how functional genomics might contribute to this renaissance.},
      Year = {2002} }




@article{
Collins02,
   Author = {Collins, M. T. and Thies, J. E. and Abbott, L. K.},
   Title = {Diversity and symbiotic effectiveness of Rhizobium leguminosarum bv. trifolii isolates from pasture soils in south-western Australia},
   Journal = {Australian Journal of Soil Research},
   Volume = {40},
   Number = {8},
   Pages = {1319-1329},
   Abstract = {The abundance of the Australian inoculant strain of Rhizobium leguminosarum bv. trifolii for subterraneum clover (WU95) and the diversity of naturalised rhizobia were assessed in 3 subterranean clover pastures in the Albany region of south-western Western Australia. Most probable number, enzyme linked immunosorbent assay (ELISA), and polymerase chain reaction (PCR) techniques were used. A putative strain similar to inoculant strain WU96 was uncommon at one site (South Stirling) and not isolated at 2 other sites. Randomly amplified polymorphic DNA (RAPD) PCR fingerprinting using the RPO1 primer identified 45 different profiles amongst the 208 isolates examined. RAPD-PCR fingerprinting using the primers RPO4 and RPO5 confirmed most groupings based on RPO1 fingerprint patterns and revealed further genetic diversity within some groups. Overall, 54 putative strains were defined by RAPD-PCR fingerprint profiles across the 3 sites. Subterranean clover rhizobia at the Manypeaks and Mount Shadforth sites were dominated by isolates with 1 or 2 RPO1 RAPD profiles at 2 sampling times, while the population at South Stifling was much more diverse. The symbiotic effectiveness of 11 rhizobial isolates, representing the major RPO1 RAPD profile groups within naturalised rhizobial populations, were compared in pot culture with those of the 2 commercial inoculant strains for subterranean clover, WU95 and TA1, on 3 cultivars. Differences in effectiveness among 3 of the 11 isolates were observed in comparison to both the commercial strains and other naturalised isolates. The nitrogen fixing effectiveness of 8 isolates representing different subgroups from one RP01 group was not the same. The use of all 3 primers increased the precision in defining putative strains of Rhizobium leguminosarum bv. trifolii, and although naturalised rhizobia from these pastures are saprophytically competent, their dominance in nodules does not appear to be linked to symbiotic effectiveness.},
   Keywords = {Diversity
ELISA
MPN
PCR
Rhizobia
Subterranean clover},
   Year = {2002} }




@article{
Colwell70,
   Author = {Colwell, R. R.},
   Title = {Polyphasic taxonomy of the genus  \emph{Vibrio}: numerical taxonomy of  \emph{Vibrio cholerae},  \emph{Vibrio parahaemolyticus}, and related  \emph{Vibrio} species.},
   Journal = {Journal of Bacteriology},
   Volume = {104},
   Number = {1},
   Pages = {410-433},
      Year = {1970} }




@article{
Cook04,
   Author = {Cook, D. R.},
   Title = {Unraveling the mystery of Nod factor signaling by a genomic approach in Medicago trunactula},
   Journal = {Proceedings of the National Academy of Sciences of the United States of America},
   Volume = {101},
   Number = {13},
   Pages = {4339-4340},
      Year = {2004} }




@article{
Cook05,
   Author = {Cook, L. G. and Crisp, M. D.},
   Title = {Not so ancient: The extant crown group of \emph{Nothofagus} represents a post-Gondwanan radiation},
   Journal = {Proceedings of the Royal Society of London - Series B: Biological Sciences},
   Volume = {272},
   Number = {1580},
   Pages = {2535-2544},
   Abstract = {This study uses a molecular-dating approach to test hypotheses about die biogeography of Nothofagus. The molecular modelling suggests that the present-day subgenera and species date from a radiation that most likely commenced between 55 and 40 Myr ago. This rules out the possibility of a reconciled all-vicariance hypothesis for the biogeography of extant Nothofagus. However, the molecular dates for divergences between Australasian and South American taxa are consistent with the rifting of Australia and South America from Antarctica. The molecular dates further suggest a dispersal of subgenera Lophozonia and Fuscospora between Australia and New Zealand after the onset of the Antarctic Circumpolar Current and west wind drift. It appears likely that the New Caledonian lineage of subgenus Brassospora diverged from the New Guinean lineage elsewhere, prior to colonizing New Caledonia. The molecular approach strongly supports fossil-based estimates that Nothofagus diverged from the rest of Fagales more than 84 Myr ago. However, the mid-Cenozoic estimate for the diversification of the four extant subgenera conflicts with the palynological interpretation because pollen fossils, attributed to all four extant subgenera, were widespread across the Weddellian province of Gondwana about 71 Myr ago. The discrepancy between the pollen and molecular dates exists even when confidence intervals from several sources of error are taken into account. In contrast, the molecular age estimates are consistent with macrofossil dates. The incongruence between pollen fossils and molecular dates could be resolved if the early pollen types represent extinct lineages, with similar types later evolving independently in the extant lineages. © 2005 The Royal Society.},
   Keywords = {Biogeography
Dispersal
Gondwana
Molecular dating
Nothofagus
Vicariance},
   Year = {2005} }




@article{
Cooper93,
   Author = {Cooper, R. A. and Millener, P. R.},
   Title = {The New Zealand biota: Historical background and new research},
   Journal = {Tree},
   Volume = {8},
   Number = {12},
   Pages = {429-433},
      Year = {1993} }




@article{
Coplin89,
   Author = {Coplin, D. L.},
   Title = {Plasmids and their role in the evolution of plant pathogenic bacteria},
   Journal = {Annual Review of Phytopathology},
   Volume = {27},
   Pages = {187-212},
      Year = {1989} }




@article{
Correa99,
   Author = {Correa, O. S. and Rivas, E. A. and Barneix, A. J.},
   Title = {Cellular envelopes and tolerance to acid pH in Mesorhizobium loti},
   Journal = {Current Microbiology},
   Volume = {38},
   Number = {6},
   Pages = {329-34},
   Abstract = {Changes in the cell envelopes in response to acidity were studied in two strains of Mesorhizobium loti differing in their tolerance to pH. When the less acid-tolerant strain LL22 was grown at pH 5.5, membrane phosphatidylglycerol decreased and phosphatidylcholine increased, compared with cells grown at pH 7.0. On the other hand, when the more acid-tolerant strain LL56 was grown at pH 5.5, phosphatidylglycerol, phosphatidylethanolamine, and lysophospholipid decreased 25%, 39%, and 51% respectively, while phosphatidyl-N-methylethanolamine and cardiolipin increased 26% and 65% respectively compared with cells grown at pH 7.0. The longest-chain fatty acids (19:0 cy and 20:0) increased in both strains at pH 5.5, while in LL56 these fatty acids increased still further at pH 4.0. Variations in other wall and membrane properties such as cell hydrophobicity, lypopolysaccharides, and protein composition of the outer membrane in relation to acid pH are also discussed.},
   Keywords = {Bacterial Outer Membrane Proteins/*analysis
Cell Membrane/*chemistry
Fatty Acids/analysis
Hydrogen-Ion Concentration
Lipopolysaccharides/*analysis
Membrane Lipids/*analysis
Phospholipids/analysis
Rhizobiaceae/chemistry/*physiology
Support, Non-U.S. Gov't},
   Year = {1999} }




@incollection{
Coutinho00,
   Author = {Coutinho, H. L. C. and de Olivera, V. M. and Moreira, F. M.},
   Title = {Systematics of legume nodule nitrogen fixing bacteria: Agronomic and ecological applications},
   BookTitle = {Applied Microbial Systematics},
   Editor = {Preist, F. G. and Goodfellow, M.},
   Publisher = {Kluwer Academic Publishers},
   Address = {Dordrecht},
   Pages = {107-134},
      Year = {2000} }




@article{
Crespi94,
   Author = {Crespi, M. D. and Jurkevitch, E. and Poiret, M. and Petrovics, G. and Kondorosi, E. and Kondorosi, A. and D'Aubenton-Carafa, Y.},
   Title = {Enod40, a gene expressed during nodule organogenesis, codes for a non-translatable RNA involved in plant growth},
   Journal = {EMBO Journal},
   Volume = {13},
   Number = {21},
   Pages = {5099-5112},
   Abstract = {Rhizobium meliloti can interact symbiotically with Medicago plants, thereby inducing root nodules. However, certain Medicago plants can form nodules spontaneously, in the absence of rhizobia. A differential screening was performed using spontaneous nodule versus root cDNAs from Medicago sativa ssp. varia. Transcripts of a differentially expressed clone, Msenod40, were detected in all differentiating cells of nodule primordia and spontaneous nodules, but were absent in fully differentiated cells. Msenod40 showed homology to a soybean early nodulin gene, Gmenod40, although no significant open reading frame (ORF) or coding capacity was found in the Medicago sequence. Furthermore, in the sequences of cDNAs and a genomic clone (Mtenod40) isolated from Medicago truncatula, a species containing a unique copy of this gene, no ORFs were found either. In vitro translation of purified Mtenod40 transcripts did not reveal any protein product. Evaluation of the RNA secondary structure indicated that both Msenod40 and Gmenod40 transcripts showed a high degree of stability, a property shared with known non-coding RNAs. The Mtenod40 RNA was localized in the cytoplasm of cells in the nodule primordium. Infection with Agrobacterium tumefaciens strains bearing antisense constructs of Mtenod40 arrested callus growth of Medicago explants, while overexpressing Mtenod40 embryos developed into teratomas. These data suggest that the enod40 genes might have a role in plant development, acting as 'riboregulators', a novel class of untranslated RNAs associated with growth control and differentiation.},
   Keywords = {Differentiation-related RNA
Early nodulin
Medicago
Plant riboregulator
Spontaneous nodules},
   Year = {1994} }




@article{
Crisp04,
   Author = {Crisp, M. and Cook, L. and Steane, D.},
   Title = {Radiation of the Australian flora: What can comparisons of molecular phylogenies across multiple taxa tell us about the evolution of diversity in present-day communities?},
   Journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences},
   Volume = {359},
   Number = {1450},
   Pages = {1551-1571},
   Abstract = {The Australian fossil record shows that from ca. 25 Myr ago, the aseasonal-wet biome (rainforest and wet heath) gave way to the unique Australian sclerophyll biomes dominated by eucalypts, acacias and casuarinas. This transition coincided with tectonic isolation of Australia, leading to cooler, drier, more seasonal climates. From 3 Myr ago, aridification caused rapid opening of the central Australian arid zone. Molecular phylogenies with dated nodes have provided new perspectives on how these events could have affected the evolution of the Australian flora. During the Mid-Cenozoic (25-10 Myr ago) period of climatic change, there were rapid radiations in sclerophyll taxa, such as Banksia, eucalypts, pea-flowered legumes and Allocasuarina. At the same time, taxa restricted to the aseasonal-wet biome (Nothofagus, Podocarpaceae and Araucariaceae) did not radiate or were depleted by extinction. During the Pliocene aridification, two Eremean biome taxa (Lepidium and Chenopodiaceae) radiated rapidly after dispersing into Australia from overseas. It is clear that the biomes have different histories. Lineages in the aseasonal-wet biome are species poor, with sister taxa that are species rich, either outside Australia or in the sclerophyll biomes. In conjunction with the fossil record, this indicates depletion of the Australian aseasonal-wet biome from the Mid-Cenozoic. In the sclerophyll biomes, there have been multiple exchanges between the southwest and southeast, rather than single large endemic radiations after a vicariance event. There is need for rigorous molecular phylogenetic studies so that additional questions can be addressed, such as how interactions between biomes may have driven the speciation process during radiations. New studies should include the hitherto neglected monsoonal tropics.},
   Keywords = {Australia
Cenozoic
Climate change
Extinction
Molecular dating
Rapid radiation},
   Year = {2004} }




@incollection{
Crisp00,
   Author = {Crisp, M. D. and Gilmore, S. and Van Wyk, B.-E.},
   Title = {Molecular phylogeny of the genistoid tribes of papilionoid legumes},
   BookTitle = {Advances in Legume Systematics,  PART 9},
   Editor = {Herendeen, P. S and Bruneau, A.},
   Publisher = {Royal Botanic Gardens, Kew},
   Address = {London},
   Pages = {249-276},
      Year = {2000} }




@article{
Crow81,
   Author = {Crow, V. L. and Jarvis, B. D. W. and Greenwood, R. M.},
   Title = {Deoxyribonucleic acid homologies among acid-producing strains of \emph{Rhizobium}},
   Journal = {International Journal of Systematic Bacteriology},
   Volume = {31},
   Number = {2},
   Pages = {152-172},
   Keywords = {dna dna hybridization
rhizobium
taxonomy},
   Year = {1981} }




@article{
Cubas02,
   Author = {Cubas, P. and Pardo, C. and Tahiri, H.},
   Title = {Molecular approach to the phylogeny and systematics of Cytisus (Leguminosae) and related genera based on nucleotide sequences of nrDNA (ITS region) and cpDNA (trnL-trnF intergenic spacer)},
   Journal = {Plant Systematics and Evolution},
   Volume = {233},
   Number = {3 - 4},
   Pages = {223-242},
      Year = {2002} }




@article{
Cullimore01,
   Author = {Cullimore, J. V. and Ranjeva, R. and Bono, J. J.},
   Title = {Perception of lipo-chitooligosaccharidic Nod factors in legumes},
   Journal = {Trends in Plant Science},
   Volume = {6},
   Number = {1},
   Pages = {24-30},
   Abstract = {Lipo-chitooligosaccharides produced by rhizobia are a class of signalling molecules that mediate recognition and nodule organogenesis in the legume-rhizobia symbiosis. Their synthesis is specified by the nodulation genes of rhizobia and hence they are commonly known as Nod factors. They are amphiphilic molecules and induce a variety of responses in the roots of the legume hosts. Studies using plant and rhizobial mutants and purified molecules suggest that Nod factors are recognized by more than one receptor. In this article, we review evidence about the affinity, specificity and location of these putative receptors and describe recent studies with regard to their identification.},
   Keywords = {Carbohydrate Conformation
Fabaceae
metabolism
Lipopolysaccharides
chemistry
Nitrogen Fixation
Plants
Medicinal},
   Year = {2001} }




@article{
Denarie96,
   Author = {D\'enarie, J. and Debell\'e, F. and Prom\'e, J.-C.},
   Title = {Rhizobium lipo-chitooligosaccharide nodulation factors: Signaling molecules mediating recognition and morphogenesis},
   Journal = {Annual Review of Biochemistry},
   Volume = {65},
   Pages = {503-535},
   Abstract = {Rhizobia elicit on their specific leguminous hosts the formation of new organs, called nodules, in which they fix nitrogen. The rhizobial nodulation genes specify the synthesis of lipo-chitooligosaccharide signals, the Nod factors (NFs). Each rhizobial species has a characteristic set of nodulation genes that specifies the length of the chitooligosaccharide backbone and the type of substitutions at both ends of the molecule, thus making the NFs specific for a given plant host. At extremely low concentrations, purified NFs are capable of eliciting on homologous legume hosts many of the plant developmental responses characteristic of the bacteria themselves, including cell divisions, and the triggering of a plant organogenic program. This review summarizes our current knowledge on the biosynthesis, structure, and function of this new class of signaling molecules. Finally we discuss the possibility that these signals could be part of a new family of plant lipo- chitooligosaccharide growth regulators.},
   Keywords = {chitin oligomers
host specificity
Nod factors
oligosaccharins
plant organogenesis},
   Year = {1996} }




@book{
Dangeard26,
   Author = {Dangeard, P. A.},
   Title = {Recherches sur les tubercules radicaux des l\'egumineuses},
   Publisher = {Le Botaniste},
   Address = {Paris},
   Series = {Series 16},
      Year = {1926} }




@article{
Danso75,
   Author = {Danso, S. K. and Keya, S. O. and Alexander, M.},
   Title = {Protozoa and the decline of Rhizobium populations added to soil},
   Journal = {Canadian Journal of Microbiology},
   Volume = {21},
   Number = {6},
   Pages = {884-95},
   Abstract = {A fall in Rhizobium abundance occurred in nonsterile soil inoculated with large numbers of the root-nodule bacteria, but many of the rhizobia still survived. No such decline was evident in sterile soil. Protozoa feeding on these bacteria were isolated from soil and other environments. As the abundance of Rhizobium meliloti and a cowpea Rhizobium strain in soil decreased, the protozoan density increased. The inability of the predators to eliminate their prey from soil was not the result of the presence of organisms feeding on the protozoa because many rhizobia survived in sterile soil inoculated with the prey and cultures of individual protozoa, nor was it the result of the rapid multiplication of the bacteria to replace those consumed because survivors were still numerous in essentially organic matter free soil in which the bacteria did not grow appreciably. The lack of elimination also was not associated with a protective effect of soil particles because survivors were still abundant in solutions inoculated with protozoa and bacteria. It is suggested that the size of the prey population diminishes until a density is attained at which the energy used by the predator in hunting for the survivors equals that obtained from the feeding.},
   Keywords = {Amoeba/isolation \& purification
Animals
Bacteria
Bacteriophages
Ciliophora/isolation \& purification
Ecology
Germ-Free Life
Mastigophora/isolation \& purification
*Protozoa/growth \& development/isolation \& purification
Rhizobium/*growth \& development
Sewage
*Soil Microbiology
Sterilization
Tetrahymena/isolation \& purification
Xanthomonas},
   Year = {1975} }




@article{
DAntuono05,
   Author = {D'Antuono, A. L. and Ugalde, R. A. and Lepek, V. C. and Casabuono, A. and Couto, A.},
   Title = {Nodule development induced by Mesorhizobium loti mutant strains affected in polysaccharide synthesis},
   Journal = {Molecular Plant-Microbe Interactions},
   Volume = {18},
   Number = {5},
   Pages = {446-457},
   Abstract = {The role of Mesorhizobium loti surface polysaccharides on the nodulation process is not yet fully understood. In this article, we describe the nodulation phenotype of mutants affected in the synthesis of lipopolysaccharide (LPS) and ?(1,2) cyclic glucan. M. loti lps?2 mutant produces LPS with reduced amount of O-antigen, whereas M. loti lps?1 mutant produces LPS totally devoid of O-antigen. Both genes are clustered in the chromosome. Based on amino acid sequence homology, LPS sugar composition, and enzymatic activity, we concluded that lps?2 codes for an enzyme involved in the transformation of dTDP-glucose into dTDP-rhamnose, the sugar donor of rhamnose for the synthesis of O-antigen. On the other hand, Ips?1 codes for a glucosyltransferase involved in the biosynthesis of the O-antigen. Although LPS mutants elicited normal nodules, both show reduced competitiveness compared with the wild type. M. loti ?(1-2) cyclic glucan synthase (cgs) mutant induces white, empty, ineffective pseudonodules in Lotus tenuis. Cgs mutant induces normal root hair curling but is unable to induce the formation of infection threads. M. loti cgs mutant was more sensitive to deoxycholate and displayed motility impairment compared with the wild-type strain. This pleiotropic effect depends on calcium concentration and temperature. © 2005 The American Phytopathological Society.},
   Keywords = {Epimerase/dehydratase family
Glycosyltransferases
LPS and ?(1-2) cyclic glucan mutants},
   Year = {2005} }




@book{
Darwin09,
   Author = {Darwin, Charles},
   Title = {The voyage of the Beagle},
   Publisher = {P. F. Collier and Son},
   Address = {Cambridge},
      Year = {1909} }




@article{
Dauga02,
   Author = {Dauga, C.},
   Title = {Evolution of the gyrB gene and the molecular phylogeny of Enterobacteriaceae: A model molecule for molecular systematic studies},
   Journal = {International Journal of Systematic and Evolutionary Microbiology},
   Volume = {52},
   Number = {2},
   Pages = {531-547},
   Abstract = {Phylogenetic trees showing the evolutionary relatedness of Enterobacteriaceae based upon gyrB and 16S rRNA genes were compared. Congruence among trees of these molecules indicates that the genomes of these species are not completely mosaic and that molecular systematic studies can be carried out. Phylogenetic trees based on gyrB sequences appeared to be more reliable at determining relationships among Serratia species than trees based on 16S rRNA gene sequences. gyrB sequences from Serratia species formed a monophyletic group validated by significant bootstrap values. Serratia fonticola had the most deeply branching gyrB sequence in the Serratia monophyletic group, which was consistent with its atypical phenotypic characteristics. Klebsiella and Enterobacter genera seemed to be polyphyletic, but the branching patterns of gyrB and 16S rRNA gene trees were not congruent. Enterobacter aerogenes was grouped with Klebsiella pneumoniae on the gyrB phylogenetic tree, which supports that this species could be transferred to the Klebsiella genus. Unfortunately, 16S rRNA and gyrB phylogenetic trees gave conflicting evolutionary relationships for Citrobacter freundii because of its unusual gyrB evolutionary process. gyrB lateral gene transfer was suspected for Hafnia alvei. Saturation of gyrB genes was observed by the pairwise comparison of Proteus spp., Providencia alcalifaciens and Morganella morganii sequences. Depending on their level of variability, 16S rRNA gene sequences were useful for describing phylogenetic relationships between distantly related Enterobacteriaceae, whereas gyrB sequence comparison was useful for inferring intra- and some intergeneric relationships.},
   Keywords = {16S rRNA
Enterobacteriaceae
Evolutionary systematic studies
gyrB},
   Year = {2002} }




@article{
David88,
   Author = {David, M. and Daveran, M.-L. and Batut, J. and Dedieu, A. and Domergue, O. and Ghai, J. and Hertig, C. and Boistard, P. and Kahn, D.},
   Title = {Cascade regulation of nif gene expression in Rhizobium meliloti},
   Journal = {Cell},
   Volume = {54},
   Number = {5},
   Pages = {671-683},
   Abstract = {We report the discovery of two genes from Rhizobium meliloti, fixL and fixJ, which are positive regulators of symbiotic expression of diverse nitrogen fixation (nif and fix) genes. nif gene regulation is shown to consist of a cascade: the fixLJ genes activate nifA, which in turn activates nifHDK and fixABCX. Like nifA, fixN can be induced in free-living microaerobic cultures of R. meliloti, indicating a major physiological role for oxygen in nif and fix gene regulation. Microaerobic expression of fixN and nifA depends on fixL and fixJ. The FixL and FixJ proteins belong to a family of two-component regulatory systems widely spread among prokaryotes and responsive to the cell environment. We propose that FixL, which has features of a transmembrane protein, senses an environmental signal and transduces it to FixJ, a transcriptional activator of nif and fix genes.},
      Year = {1988} }




@article{
Davison99,
   Author = {Davison, J.},
   Title = {Genetic exchange between bacteria in the environment},
   Journal = {Plasmid},
   Volume = {42},
   Number = {2},
   Pages = {73-91},
   Abstract = {Nucleotide sequence analysis, and more recently whole genome analysis, shows that bacterial evolution has often proceeded by horizontal gene flow between different species and genera. In bacteria, gene transfer takes place by transformation, transduction, or conjugation and this review examines the roles of these gene transfer processes, between different bacteria, in a wide variety of ecological niches in the natural environment. This knowledge is necessary for our understanding of plasmid evolution and ecology, as well as for risk assessment. The rise and spread of multiple antibiotic resistance plasmids in medically important bacteria are consequences of intergeneric gene transfer coupled to the selective pressures posed by the increasing use and misuse of antibiotics in medicine and animal feedstuffs. Similarly, the evolution of degradative plasmids is a response to the increasing presence of xenobiotic pollutants in soil and water. Finally, our understanding of the role of horizontal gene transfer in the environment is essential for the evaluation of the possible consequences of the deliberate environmental release of natural or recombinant bacteria for agricultural and bioremediation purposes.},
   Keywords = {Antibiotic resistance
Bacterial biodiversity
Conjugation
Molecular ecology
Plasmid evolution
Transduction
Transformation
Transposition
Xenobiotic degradation},
   Year = {1999} }




@book{
Dawkins82,
   Author = {Dawkins, R.},
   Title = {The extended phenotype},
   Publisher = {WH Freeman},
   Address = {Oxford},
      Year = {1982} }




@book{
Dawkins86,
   Author = {Dawkins, R.},
   Title = {The blind watchmaker},
   Publisher = {Longman Scientific and Technical},
   Address = {Harlow},
      Year = {1986} }




@article{
Dawkins79,
   Author = {Dawkins, R. and Krebs, J. R.},
   Title = {Arms races between and within species},
   Journal = {Proceedings of the Royal Society of London - Series B: Biological Sciences},
   Volume = {205},
   Number = {1161},
   Pages = {489-511},
      Year = {1979} }




@article{
Dawson00,
   Author = {Dawson, M.},
   Title = {Further observations on the nature and functions of the nodules of leguminous plants},
   Journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences},
   Volume = {193},
   Number = {1},
   Pages = {51-67},
      Year = {1900} }




@article{
deBruijn92,
   Author = {de Bruijn, F. J.},
   Title = {Use of repetitive (repetitive extragenic palindromic and enterobacterial repetitive intergeneric consensus) sequences and the polymerase chain reaction to fingerprint the genomes of Rhizobium meliloti isolates and other soil bacteria},
   Journal = {Applied and Environmental Microbiology},
   Volume = {58},
   Number = {7},
   Pages = {2180-2187},
   Abstract = {The distribution of dispersed repetitive DNA (repetitive extragenic palindromic [REP] and enterobacterial repetitive intergenic consensus [ERIC]) sequences in the genomes of a number of gram-negative soil bacteria was examined by using conserved primers corresponding to REP and ERIC sequences and the polymerase chain reaction (PCR). The patterns of the resulting PCR products were analyzed on agarose gels and found to be highly specific for each strain. The REP and ERIC PCR patterns of a series of Rhizobium meliloti isolates, previously ordered in a phylogenetic tree based on allelic variations at 14 enzyme loci (B. D. Eardly, L. A. Materon, N. H. Smith, D. A. Johnson, M. D. Rumbaugh, and R. K. Selander, Appl. Environ. Microbiol. 56:187-194), were determined. Isolates which had been postulated to be closely related by multilocus enzyme electrophoresis also revealed similar REP and ERIC PCR patterns, suggesting that the REP and ERIC PCR method is useful for the identification and classification of bacterial strains.},
      Year = {1992} }




@article{
DeFaria89,
   Author = {de Faria, S. M. and Lewis, G. P. and Sprent, J. I. and Sutherland, J. M.},
   Title = {Occurrence of nodulation in the Leguminosae},
   Journal = {New Phytologist},
   Volume = {111},
   Number = {4},
   Pages = {607-619},
   Abstract = {In the subfamily Caesalpinioideae, nodulation is largely restricted to the tribe Caesalpinieae and the genus Chamaecrista from the Cassieae. All nodules studied have rhizobia retained within infection threads during the N-fixing period. In the Mimosoideae, nodulation is general, except for 4 groups within the tribe Mimoseae, and a very few species of Acacia. The only tribe from the Papilionoideae which appears not to nodulate is the Dipterygeae, although the monogeneric Euchresteae has not been examined. A number of genera in the Swartzieae do not nodulate. -from Authors},
   Keywords = {nitrogen fixation
nodulation
Acacia
Caesalpinioideae
Chamaecrista
Dipterygeae
Euchresteae
Leguminosae
Mimosoideae
Papilionoideae
Swartzieae},
   Year = {1989} }




@article{
deJong93,
   Author = {de Jong, A. J. and Heidstra, R. and Hartog, M. V. and Meijer, E. A. and Hendriks, T. and Bisseling, T. and Van Kammen, A. and De Vries, S. C. and Spaink, H. P. and Lo Schiavo, F. and Terzi, M.},
   Title = {Rhizobium lipooligosaccharides rescue a carrot somatic embryo mutant},
   Journal = {Plant Cell},
   Volume = {5},
   Number = {6},
   Pages = {615-620},
   Abstract = {At a nonpermissive temperature, somatic embryos of the temperature-sensitive (ts) carrot cell mutant ts11 only proceed beyond the globular embryo stage in the presence of medium conditioned by wild-type embryos. The causative component in the conditioned medium has previously been identified as a 32-kD acidic endochitinase. In search of a function for this enzyme in plant embryogenesis, several compounds that contain oligomers of N-acetylglucosamine were tested for their ability to promote ts11 embryo formation. Of these compounds, only the Rhizobium lipooligosaccharides or nodulation (Nod) factors were found to be effective in rescuing the formation of ts11 embryos. These results suggest that N-acetylglucosamine-containing lipooligosaccharides from bacterial origin can mimic the effect of the carrot endochitinase. This endochitinase may therefore be involved in the generation of plant analogs of the Rhizobium Nod factors.},
      Year = {1993} }




@article{
deLajudie98a,
   Author = {de Lajudie, P. and Laurent-Fulele, E. and Willems, A. and Torck, U. and Coopman, R. and Collins, M. D. and Kersters, K. and Dreyfus, B. and Gillis, M.},
   Title = {\emph{Allorhizobium undicola} gen. nov., sp. nov., nitrogen-fixing bacteria that efficiently nodulate \emph{Neptunia natans} in Senegal},
   Journal = {International Journal of Systematic Bacteriology},
   Volume = {48},
   Number = {4},
   Pages = {1277-1290},
   Abstract = {A group of nodule isolates from Neptunia natans, an indigenous stem-nodulated tropical legume found in waterlogged areas of Senegal, was studied. Polyphasic taxonomy was performed, including SDS-PAGE of total proteins, auxanography using API galleries, host-plant specificity, PCR-RFLP of the internal transcribed spacer region between the 16S and the 23S rRNA coding genes, 16S rRNA gene sequencing and DNA-DNA hybridization. It was demonstrated that this group is phenotypically and phylogenetically separate from the known species of Rhizobium, Sinorhizobium, Mesorhizobium, Agrobacterium, Bradyrhizobium and Azorhizobium, Its closest phylogenetic neighbour, as deduced by 16S rRNA gene sequencing, is Agrobacterium vitis (96.2 % sequence homology). The name Allorhizobium undicola gen, nov., sp. nov., is proposed for this group of bacteria, which are capable of efficient nitrogen-fixing symbiosis with Neptunia natans, and the type strain is ORS 992(T)(= LMC 11875(T)).},
      Year = {1998} }




@article{
deLajudie99,
   Author = {de Lajudie, P. and Willems, A. and Nick, G. and Mohamed, S. H. and Torck, U. and Coopman, R. and Filali-Maltouf, A. and Kersters, K. and Dreyfus, B. and Lindstr\"om, K. and Gillis, M.},
   Title = {\emph{Agrobacterium} bv. 1 strains isolated from nodules of tropical legumes},
   Journal = {Systematic and Applied Microbiology},
   Volume = {22},
   Number = {1},
   Pages = {119-132},
   Abstract = {Bacterial strains were isolated from root nodules of various legumes, mainly trees, from different places in Africa. Polyphasic taxonomy, including numerical analysis of comparative whole-cell protein patterns obtained by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), 16S rRNA gene sequencing, auxanographic tests (API 50), and DNA:DNA hybridizations indicated that these strains belonged to Agrobacterium biovar 1. These strains were not capable of inducing any nodule or tumor formation on plants. No PCR amplification was observed using nif H primers, suggesting that they do not carry symbiotic genes. Biological implications of the presence of Agrobacterium in nodules are discussed.},
      Year = {1999} }




@article{
deLajudie98b,
   Author = {de Lajudie, P. and Willems, A. and Nick, G. and Moreira, F. and Molouba, F. and Hoste, B. and Torck, U. and Neyra, M. and Collins, M. D. and Lindstr\"om, K. and Dreyfus, B. and Gillis, M.},
   Title = {Characterization of tropical tree rhizobia and description of \emph{Mesorhizobium plurifarium} sp. nov},
   Journal = {International Journal of Systematic Bacteriology},
   Volume = {48},
   Number = {2},
   Pages = {369-382},
   Abstract = {A collection of strains isolated from root nodules of Acacia species in Senegal was analysed previously by electrophoresis of total cell protein, auxanographic tests, rRNA-DNA hybridization, 16S rRNA gene sequencing, DNA base composition and DNA-DNA hybridization [de Lajudie, P., Willems, A., Pot, B. \& 7 other authors (1994). Int I Syst Bacteriol 44, 715-733]. Strains from Acacia were shown to belong to two groups, Sinorhizobium terangae, and a so-called gel electrophoretic cluster U, which also included some reference strains from Brazil. Further taxonomic characterization of this group using the same techniques plus repetitive extragenic palindromic-PCR and nodulation tests is presented in this paper. Reference strains from Sudan and a number of new rhizobia isolated from nodules of Acacia senegal, Acacia tortilis subsp. raddiana and Prosopis juliflora in Senegal were included. As a result of this polyphasic approach, the creation of a new species, Mesorhizobium plurifarium, is proposed for a genotypically and phenotypically distinct group corresponding to the former cluster U and containing strains isolated from Acacia, Leucaena, Prosopis and Chamaecrista in West Africa (Senegal), East Africa (Sudan) and South America (Brazil). The type strain of Mesorhizobium plurifarium ORS 1032 has been deposited in the LMG collection as LMC 11892.},
      Year = {1998} }




@article{
deLajudie94,
   Author = {de Lajudie, P. and Willems, A. and Pot, B. and Dewettinck, D. and Maestrojuan, G. and Neyra, M. and Collins, M. D. and Dreyfus, B. and Kersters, K. and Gillis, M.},
   Title = {Polyphasic taxonomy of rhizobia: Emendation of the genus \emph{Sinorhizobium} and description of \emph{Sinorhizobium meliloti} comb. nov., \emph{Sinorhizobium saheli} sp. nov., and \emph{Sinorhizobium teranga} sp. nov.},
   Journal = {International Journal of Systematic Bacteriology},
   Pages = {715-733},
   Abstract = {A total of 80 bacterial strains isolated from different Sesbania and Acacia species growing in various sites in Senegal (West Africa) were compared with 35 reference strains of Rhizobium, Bradyrhizobium, Azorhizobium, and Agrobacterium species and with 33 representative strains of the different groups of Brazilian isolates described on the basis of the results of a numerical analysis of the whole-cell protein patterns obtained by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Fifty-two strains could be placed in three protein electrophoretic clusters, two of which were different from the clusters containing various reference or representative strains, while 30 other strains could not be placed in any group. The strains belonging to the three clusters were studied by determining their nodulation host ranges and their morphological, physiological, and auxanographic characteristics. Representative strains of the three clusters were also genotypically characterized by determining their DNA base compositions, by performing DNA-DNA and DNA-rRNA hybridization experiments, and by determining their 16S rRNA gene sequences. Our results showed that two of the clusters identified on the basis of SDS-PAGE data are genotypically and phenotypically distinct groups that belong on the Rhizobium meliloti-Rhizobium fredii rRNA branch. The third cluster is localized on the Rhizobium loti rRNA branch in the vicinity of Rhizobium huakuii and contains strains isolated in Africa, in Brazil, and in New Zealand from different leguminous species. On the basis of the results of the present study, we propose to emend the genus Sinorhizobium and to reclassify R. meliloti as Sinorhizobium meliloti comb. nov. In addition, two new species, Sinorhizobium saheli and Sinorhizobium teranga, are proposed for isolates from Senegal.},
   Keywords = {agriculture
rhizobiaceae},
   Year = {1994} }




@article{
deLange99,
   Author = {de Lange, P. J. and Heenan, P. B. and Given, D. R. and Norton, D. A. and Ogle, C. C. and Johnson, P. N. and Cameron, E. K.},
   Title = {Threatened and uncommon plants of New Zealand},
   Journal = {New Zealand Journal of Botany},
   Volume = {37},
   Number = {4},
   Pages = {603-628},
   Abstract = {A reappraisal of the conservation status of New Zealand's threatened and uncommon vascular plants is presented. The list comprises 511 taxa (22% of New Zealand's indigenous vascular flora) in the following categories: Presumed Extinct 5 taxa, Threatened 107 taxa (comprising 24 taxa Critically Endangered, 33 taxa Endangered, 50 taxa Vulnerable), Declining 60 taxa, Recovering 17 taxa (comprising 14 taxa Conservation Dependent and 3 taxa undergoing Natural Population Recovery), Naturally Uncommon 204 taxa (comprising 62 taxa rated as Sparse, 17 taxa Vagrant, 125 taxa Range Restricted). Lack of information on the threat status of a further 26 taxa caused these to be listed as Insufficiently Known. Ninety-two taxa are listed as Taxonomically Indeterminate, being those which probably belong in one or other off he preceding lists but which are currently unnamed or where there are other doubts about their taxonomic status. About half of the Taxonomically Indeterminate taxa are probably threatened. Thirty-three taxa formerly considered at risk; are removed from the threatened and uncommon vascular plant lists. A concordance of plant names is provided.},
      Year = {1999} }




@article{
deLange04b,
   Author = {de Lange, P. J. and Norton, D. A. and Heenan, P. B. and Courtney, S. P. and Molloy, B. P. J. and Ogle, C. C. and Rance, B. D. and Johnson, P. N. and Hitchmough, R.},
   Title = {Erratum: Threatened and uncommon plants of New Zealand (New Zealand Journal of Botany (2004) 42 (45-76))},
   Journal = {New Zealand Journal of Botany},
   Volume = {42},
   Number = {4},
   Pages = {715},
      Year = {2004} }




@article{
deLange04,
   Author = {de Lange, P. J and Norton, D. A. and Heenan, P. B. and Molloy, B. P. J. and Ogle, C. C. and Rance, B. D. and Courtney, S. P. and Johnson, P. N. and Hitchmough, R.},
   Title = {Threatened and uncommon plants of New Zealand},
   Journal = {New Zealand Journal of Botany},
   Volume = {42},
   Number = {4},
   Pages = {45-76},
      Year = {2004} }




@article{
DeQueiroz92,
   Author = {de Queiroz, K. and Gauthier, J.},
   Title = {Phylogenetic taxonomy},
   Journal = {Annual Review of Ecology and Systematics},
   Volume = {23},
   Number = {1},
   Pages = {449-480},
   Keywords = {Cladistics
Classification
Nomenclature
Systemics
Taxon names},
   Year = {1992} }




@article{
Souza06,
   Author = {de Souza Moreira, F. M. and Cruz, L. and de Faria, S. M. and Marsh, T. and Mart\'inez-Romero, E. and de Oliveira Pedrosa, F. and Pitard, R. M. and Young, J. P. W.},
   Title = {\emph{Azorhizobium doebereinerae} sp. nov. microsymbiont of \emph{Sesbania virgata} (Caz.) Pers.},
   Journal = {Systematic and Applied Microbiology},
   Volume = {29},
   Number = {3},
   Pages = {197-206},
   Abstract = {Thirty-four rhizobium strains were isolated from root nodules of the fast-growing woody native species Sesbania virgata in different regions of southeast Brazil (Minas Gerais and Rio de Janeiro States). These isolates had cultural characteristics on YMA quite similar to Azorhizobium caulinodans (alkalinization, scant extracellular polysaccharide production, fast or intermediate growth rate). They exhibited a high similarity of phenotypic and genotypic characteristics among themselves and to a lesser extent with A. caulinodans. DNA:DNA hybridization and 16SrRNA sequences support their inclusion in the genus Azorhizobium, but not in the species A. caulinodans. The name A. doebereinerae is proposed, with isolate UFLA1-100 (=BR5401, =LMG9993=SEMIA 6401) as the type strain.},
      Year = {2006} }




@article{
Deans93,
   Author = {Deans, J. D. and Ali, O. M. and Lindley, D. K. and Nour, H. O. A.},
   Title = {Rhizobial nodulation of Acacia tree species in Sudan: soil inoculum potential and effects of peat},
   Journal = {Journal of Tropical Forest Science},
   Volume = {6},
   Number = {1},
   Pages = {56-64},
   Abstract = {The inoculum potential of the soil in Sudan was high, but nodulation in the field was inhibited by lack of water. Seedlings of A. melifera, A. senegal and A. seyal grown in a tree nursery in Sudan produced substantial numbers of nodules when peat was added to the Nile silt/sand medium. Improved aeration seemed the most likely reason for the stimulation of nodule production. -from Authors},
   Keywords = {nodulation
soil aeration
Sudan
Acacia mellifera
Acacia senegal
Acacia seyal
Rhizobium},
   Year = {1993} }




@article{
Debelle01,
   Author = {Debell\'e, F. and Moulin, L. and Mangin, B. and D\'enarie, J. and Boivin, C.},
   Title = {Nod genes and Nod signals and the evolution of the rhizobium legume symbiosis},
   Journal = {Acta Biochimica Polonica},
   Volume = {48},
   Number = {2},
   Pages = {359-65},
   Abstract = {The establishment of the nitrogen-fixing symbiosis between rhizobia and legumes requires an exchange of signals between the two partners. In response to flavonoids excreted by the host plant, rhizobia synthesize Nod factors (NFs) which elicit, at very low concentrations and in a specific manner, various symbiotic responses on the roots of the legume hosts. NFs from several rhizobial species have been characterized. They all are lipo-chitooligosaccharides, consisting of a backbone of generally four or five glucosamine residues N-acylated at the non-reducing end, and carrying various O-substituents. The N-acyl chain and the other substituents are important determinants of the rhizobial host specificity. A number of nodulation genes which specify the synthesis of NFs have been identified. All rhizobia, in spite of their diversity, possess conserved nodABC genes responsible for the synthesis of the N-acylated oligosaccharide core of NFs, which suggests that these genes are of a monophyletic origin. Other genes, the host specific nod genes, specify the substitutions of NFs. The central role of NFs and nod genes in the Rhizobium-legume symbiosis suggests that these factors could be used as molecular markers to study the evolution of this symbiosis. We have studied a number of NFs which are N-acylated by alpha,beta-unsaturated fatty acids. We found that the ability to synthesize such NFs does not correlate with taxonomic position of the rhizobia. However, all rhizobia that produce NFs such nodulate plants belonging to related tribes of legumes, the Trifolieae, Vicieae, and Galegeae, all of them being members of the so-called galegoid group. This suggests that the ability to recognize the NFs with alpha-beta-unsaturated fatty acids is limited to this group of legumes, and thus might have appeared only once in the course of legume evolution, in the galegoid phylum.},
      Year = {2001} }




@article{
Debelle96,
   Author = {Debell\'e, F. and Plazanet, C. and Roche, P. and Pujol, C. and Rosenberg, C. and D\'enarie, J. and Savagnac, A. and Prom\'e, J.-C.},
   Title = {The NodA proteins of \emph{Rhizobium meliloti} and \emph{Rhizobium tropici} specify the N-acylation of Nod factors by different fatty acids},
   Journal = {Molecular Microbiology},
   Volume = {22},
   Number = {2},
   Pages = {303-314},
   Abstract = {Rhizobia synthesize mono-N-acylated chitooligosaccharide signals, called Nod factors, that are required for the specific infection and nodulation of their legume hosts. The biosynthesis of Nod factors is under the control of nodulation (nod) genes, including the nodABC genes present in all rhizobial species. The N-acyl substitution can vary between species and can play a role in host specificity. In Rhizobium meliloti, an alfalfa symbiont, the acyl chain is a C16 unsaturated or a (?-1) hydroxylated fatty acid, whereas in Rhizobium tropici, a bean symbiont, it is vaccenic acid (C18:1). We constructed R. meliloti derivatives having a nonpolar deletion of nodA, and carrying a plasmid with either the R. meliloti or the R. tropici nodA gene. The strain with the R. tropici nodA gene produced Nod factors acylated by vaccenic acid, instead of the C16 unsaturated or hydroxylated fatty acids characteristic of R. meliloti Nod factors, and infected and nodulated alfalfa with a significant delay. These results show that NodA proteins of R. meliloti and R. tropici specify the N-acylation of Nod factors by different fatty acids, and that allelic variation of the common nodA gene can contribute to the determination of host range.},
   Keywords = {rhizobium
rhizobium meliloti},
   Year = {1996} }




@article{
Debelle92,
   Author = {Debell\'e, F. and Rosenberg, C. and D\'enarie, J.},
   Title = {The Rhizobium, Bradyrhizobium, and Azorhizobium NodC proteins are homologous to yeast chitin synthases},
   Journal = {Molecular Plant-Microbe Interactions},
   Volume = {5},
   Number = {5},
   Pages = {443-6},
   Abstract = {The nodABC genes of rhizobia are essential for the synthesis of lipo-oligosaccharidic (N-acylated chitin oligomers) nodulation signals. nodC gene products from Rhizobium, Bradyrhizobium, and Azorhizobium exhibit extensive homology with chitin synthases, suggesting that the NodC proteins are involved in the synthesis of the chitin oligomer backbone by catalyzing the beta-1,4-linkage between N-acetyl-D-glucosamine residues.},
   Keywords = {Bacterial Proteins/*genetics
Carbohydrate Sequence
Chitin Synthase/*genetics
Comparative Study
Genes, Bacterial
*N-Acetylglucosaminyltransferases
Rhizobiaceae/*genetics
Sequence Homology, Amino Acid
Support, Non-U.S. Gov't
Yeasts/genetics},
   Year = {1992} }




@article{
Decorosi05,
   Author = {Decorosi, F. and Viti, C. and Giovannetti, L. and Mengoni, A. and Bazzicalupo, M.},
   Title = {Improvement of the cDNA-AFLP method using fluorescent primers for transcription analysis in bacteria},
   Journal = {Journal of Microbiological Methods},
   Volume = {63},
   Number = {2},
   Pages = {211-215},
   Abstract = {Here the cDNA-fluorescent amplified fragment length polymorphism (cDNA-FAFLP) technique, an improvement of cDNA-AFLP method, was used in order to analyse expression profiling in bacteria. The obtained results were validated by real-time PCR. This is the first report that validates the foreseen transcription pattern by cDNA-FAFLP with the application of real-time PCR in bacteria. This new protocol offers the possibility of quick and reliable analysis of transcription profiles, also avoids the problem linked with the use of radioisotopes, and allows a quick identification of genes differentially expressed in bacteria. © 2005 Elsevier B.V. All rights reserved.},
   Keywords = {cDNA-AFLP
cDNA-FAFLP
Chromate
Cupriavidus metallidurans (formerly Ralstonia metallidurans)
Real-time PCR
Transcription analysis},
   Year = {2005} }




@article{
delPapa99,
   Author = {del Papa, Maria F. and Balague, Laura J. and Sowinski, Susana Castro and Wegener, Caren and Segundo, Eduardo and Abarca, Francisco Martinez and Toro, Nicolas and Niehaus, Karsten and Puhler, Alfred and Aguilar, O.Mario and Martinez-Drets, Gloria and Lagares, Antonio},
   Title = {Isolation and Characterization of Alfalfa-Nodulating Rhizobia Present in Acidic Soils of Central Argentina and Uruguay},
   Journal = {Applied and Environmental Microbiology},
   Volume = {65},
   Number = {4},
   Pages = {1420-1427},
   Abstract = {We describe the isolation and characterization of alfalfa-nodulating rhizobia from acid soils of different locations in Central Argentina and Uruguay. A collection of 465 isolates was assembled, and the rhizobia were characterized for acid tolerance. Growth tests revealed the existence of 15 acid-tolerant (AT) isolates which were able to grow at pH 5.0 and formed nodules in alfalfa with a low rate of nitrogen fixation. Analysis of those isolates, including partial sequencing of the genes encoding 16S rRNA and genomic PCR-fingerprinting with MBOREP1 and BOXC1 primers, demonstrated that the new isolates share a genetic background closely related to that of the previously reported Rhizobium sp. Or191 recovered from an acid soil in Oregon (B. D. Eardly, J. P. Young, and R. K. Selander, Appl. Environ. Microbiol. 58:1809-1815, 1992). Growth curves, melanin production, temperature tolerance, and megaplasmid profiles of the AT isolates were all coincident with these characteristics in strain Or191. In addition to the ability of all of these strains to nodulate alfalfa (Medicago sativa) inefficiently, the AT isolates also nodulated the common bean and Leucaena leucocephala, showing an extended host range for nodulation of legumes. In alfalfa, the time course of nodule formation by the AT isolate LPU 83 showed a continued nodulation restricted to the emerging secondary roots, which was probably related to the low rate of nitrogen fixation by the largely ineffective nodules. Results demonstrate the complexity of the rhizobial populations present in the acidic soils represented by a main group of N2-fixing rhizobia and a second group of ineffective and less-predominant isolates related to the AT strain Or191.},
      Year = {1999} }




@article{
Demezas91,
   Author = {Demezas, D. H. and Reardon, T. B. and Watson, J. M. and Gibson, A. H.},
   Title = {Genetic diversity among Rhizobium leguminosarum bv. trifolii strains revealed by allozyme and restriction fragment length polymorphism analyses},
   Journal = {Applied and Environmental Microbiology},
   Volume = {57},
   Number = {12},
   Pages = {3489-3495},
   Abstract = {Allozyme electrophoresis and restriction fragment length polymorphism (RFLP) analyses were used to examine the genetic diversity of a collection of 18 Rhizobium leguminosarum bv. trifolii, 1 R. leguminosarum bv. viciae, and 2 R. meliloti strains. Allozyme analysis at 28 loci revealed 16 electrophoretic types. The mean genetic distance between electrophoretic types of R. leguminosarum and R. meliloti was 0.83. Within R. leguminosarum, the single strain of bv. viciae differed at an average of 0.65 from strains of bv. trifolii, while electrophoretic types of bv. trifolii differed at a range of 0.23 to 0.62. Analysis of RFLPs around two chromosomal DNA probes also delineated 16 unique RFLP patterns and yielded genetic diversity similar to that revealed by the allozyme data. Analysis of RFLPs around three Sym (symbiotic) plasmid-derived probes demonstrated that the Sym plasmids reflect genetic divergence similar to that of their bacterial hosts. The large genetic distances between many strains precluded reliable estimates of their genetic relationships.},
      Year = {1991} }




@article{
Demina78,
   Author = {Demina, N. S.},
   Title = {Ability of free-living nodule bacteria to fix atmospheric nitrogen},
   Journal = {Biol Bull Acad Sci USSR},
   Volume = {5},
   Number = {3},
   Pages = {281-8},
   Abstract = {Literature material is presented on the ability of free-living nodule bacteria for asymbiotic nitrogen fixation, detected for the first time in 1975. Necessary components of the nutrient medium in the use of which the nitrogen-fixing ability of rhizobia in pure cultures is manifested, proved to be sugars and intermediates of the citric acid cycle, as well as small quantities of bound nitrogen. The experimental data available in the literature are evidence of the presence of a complete assortment of genes for the synthesis of the nitrogenase enzyme complex in free-living nodule bacteria.},
   Keywords = {Ammonia/metabolism
Citric Acid Cycle
Nitrates/metabolism
*Nitrogen Fixation
Nitrogenase/metabolism
Rhizobium/genetics/*metabolism/physiology},
   Year = {1978} }




@article{
Denarie93,
   Author = {Denarie, J. and Cullimore, J.},
   Title = {Lipo-oligosaccharide nodulation factors: A minireview new class of signaling molecules mediating recognition and morphogenesis},
   Journal = {Cell},
   Volume = {74},
   Number = {6},
   Pages = {951-954},
      Year = {1993} }




@article{
Denarie92,
   Author = {Denarie, J. and Debelle, F. and Rosenberg, C.},
   Title = {Signalling and host range variation in nodulation},
   Journal = {Annual Review of Microbiology},
   Volume = {46},
   Pages = {497-531},
   Abstract = {Rhizobium, Bradyrhizobium, and Azorhizobium strains, collectively referred to as rhizobia, elicit on their leguminous hosts, in a specific manner, the formation of nodules in which they fix nitrogen. Rhizobial nod genes, which determine host specificity, infection, and nodulation, are involved in the exchange of low molecular weight signal molecules between the plant and the bacteria as follows. Transcription of the nod operons is under the control of NodD regulatory proteins, which are specifically activated by plant flavonoid signals. The common and species-specific structural nod genes are involved in turn in the synthesis of specific lipo-oligosaccharides that signal back to the plant to elicit root-hair deformations, cortical-cell divisions, and nodule-meristem formation.},
   Keywords = {bradyrhizobium
host specificity
legumes
nitrogen fixation
nodulation factors
rhizobium
symbiosis},
   Year = {1992} }




@article{
Denison03,
   Author = {Denison, R. F. and Bledsoe, C. and Kahn, M. and O'Gara, F. and Simms, E. L. and Thomashow, L. S.},
   Title = {Cooperation in the rhizosphere and the ``free rider'' problem},
   Journal = {Ecology},
   Volume = {84},
   Number = {4},
   Pages = {838-845},
   Abstract = {Rhizobial bacteria, endomycorrhizal fungi (also known as arbuscular mycorrhizas), and pseudomonad bacteria associated with plant roots can provide substantial benefits to the plants by fixing nitrogen, supplying phosphorus, or controlling root pathogens, respectively. A significant fraction of plant photosynthetic carbon may be used by these associated microorganisms, both to support their beneficial activities and for microbial growth and reproduction. Because many microbial individuals are associated with each individual plant, the individual benefit to a microbe that allocates more resources to its own reproduction (thereby allocating less to fixing N2, supplying P, or producing antifungal metabolites) would exceed its individual loss from any resulting reduction in collective benefits (mainly plant carbon substrates). An initially rare "free rider" mutant strain might therefore be expected to displace its more cooperative parental strain. Yet, the mycorrhizal and legume-rhizobium mutualisms have persisted (often coexisting with "cheating") for millions of years. This paper discusses the importance of microbial cooperation (with plants and with other microbes) and possible reasons for its evolutionary persistence in the rhizosphere. In undisturbed soils, spatial structure can favor kin selection, but this may be counterbalanced by the increased likelihood that future competitors will be among the beneficiaries of current cooperation. In loose associations, direct fitness benefits to microorganisms may explain the evolutionary persistence of activities (e.g., production of antifungal compounds) that can benefit plants as a side effect. In closer, more symbiotic, relationships, host sanctions against individuals or clones that fail to perform their symbiotic function may be more important. New molecular methods and other research tools are facilitating research on this topic, and some of these conclusions soon may be revised.},
   Keywords = {Cheating
Kin selection
Mutualism
Mycorrhizae
Pseudomonads
Rhizobia
Roots
Tragedy of the Commons},
   Year = {2003} }




@article{
Denison04a,
   Author = {Denison, R. F. and Kiers, E. T.},
   Title = {Lifestyle alternatives for rhizobia: mutualism, parasitism, and forgoing symbiosis},
   Journal = {FEMS Microbiology Letters},
   Volume = {237},
   Number = {2},
   Pages = {187-193},
   Abstract = {Strains of rhizobia within a single species can have three different genetically determined strategies. Mutualistic rhizobia provide their legume hosts with nitrogen. Parasitic rhizobia infect legumes, but fix little or no nitrogen. Nonsymbiotic strains are unable to infect legumes at all. Why have rhizobium strains with one of these three strategies not displaced the others? A symbiotic (mutualistic or parasitic) rhizobium that succeeds in founding a nodule may produce many millions of descendants. The chances of success can be so low, however, that nonsymbiotic rhizobia can have greater reproductive success. Legume sanctions against nodules that fix little or no nitrogen favor more mutualistic strains, but parasitic strains that use plant resources only for their own reproduction may do well when they share nodules with mutualistic strains.},
   Keywords = {Alphaproteobacteria/growth \& development/physiology
Fabaceae/microbiology
Host-Parasite Relations
Nitrogen Fixation
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Rhizobium/growth \& development/*physiology
Symbiosis},
   Year = {2004} }




@article{
Denison04b,
   Author = {Denison, R. F. and Kiers, E. T.},
   Title = {Why are most rhizobia beneficial to their plant hosts, rather than parasitic?},
   Journal = {Microbes and Infection},
   Volume = {6},
   Number = {13},
   Pages = {1235-1239},
   Abstract = {Multiple strains per plant and root-to-root (not seed-borne) transmission should favor rhizobia that invest in their own reproduction, rather than symbiotic N2 fixation, as analogous factors may favor pathogen virulence. But legumes can select for greater mutualism, controlling nodule O2 supply and reducing reproduction of rhizobia that fix less N 2. © 2004 Elsevier SAS. All rights reserved.},
   Keywords = {Evolution
Fabaceae
Nitrogen fixation
Oxygen
Rhizobium
Symbiosis
Virulence},
   Year = {2004} }




@incollection{
Dennill99,
   Author = {Dennill, G. B and Donnelly, D. and Stewart, K. and Impson, F. A. C.},
   Title = {Insect agents for the biological control of Australian \emph{Acacia} species and \emph{Paraserianthes lophantha} (Willd.) Nielson (Fabaceae) in South Africa},
   BookTitle = {Biological control of weeds in South Africa (1990-1998), African Entomology Memoir 1},
   Editor = {Olckers, T. and Hill, M. P.},
   Publisher = {Entomological Society of Southern Africa},
   Address = {Johannesburg},
   Pages = {46-55},
      Year = {1999} }




@article{
Diabate05,
   Author = {Diabate, M. and Munive, A. and de Faria, S. M. and Ba, A. and Dreyfus, B. and Galiana, A.},
   Title = {Occurrence of nodulation in unexplored leguminous trees native to the West African tropical rainforest and inoculation response of native species useful in reforestation},
   Journal = {New Phytologist},
   Volume = {166},
   Number = {1},
   Pages = {231-9},
   Abstract = {Summary * Despite the abundance and diversity of timber tree legumes in the West African rainforest, their ability to form nitrogen-fixing nodules in symbiosis with rhizobia, and their response to rhizobial inoculation, remain poorly documented. * In the first part of this study the occurrence of nodulation was determined in 156 leguminous species growing in six natural forest areas in Guinea, mostly mature trees. In the second part, an in situ experiment of rhizobial inoculation was performed on eight selected tree species belonging to three genera: Albizia, Erythrophleum and Millettia. * Of the 97 plant species and 14 genera that had never been examined before this study, 31 species and four genera were reported to be nodulated. After 4 months of growing in a nursery and a further 11 months after transplantation of plants to the field, we observed a highly significant (P < 0.001) and positive effect of inoculation with Bradyrhizobium sp. strains on the growth of the eight tree species tested. * The importance of determining the nodulation ability of unexplored local trees and subsequently using this information for inoculation in reforestation programmes was demonstrated. New Phytologist (2005) doi: 10.1111/j.1469-8137.2005.01318.x (c)New Phytologist (2005).},
      Year = {2005} }




@article{
Dincturk01,
   Author = {Dincturk, H. B.},
   Title = {Glutamate synthase: an archaeal horizontal gene transfer?},
   Journal = {J Biosci},
   Volume = {26},
   Number = {1},
   Pages = {13-4},
   Keywords = {Archaea/enzymology/*genetics
*Gene Transfer, Horizontal
Glutamate Synthase/*genetics
Open Reading Frames
Species Specificity},
   Year = {2001} }




@article{
Ditta80,
   Author = {Ditta, G. and Stanfield, S. and Corbin, D. and Helinski, D. R.},
   Title = {Broad host range DNA cloning system for Gram-negative bacteria: Construction of a gene bank of Rhizobium meliloti},
   Journal = {Proceedings of the National Academy of Sciences of the United States of America},
   Volume = {77},
   Number = {12 II},
   Pages = {7347-7351},
      Year = {1980} }




@article{
Dixon69,
   Author = {Dixon, R. O.},
   Title = {Rhizobia (with particular reference to relationships with host plants)},
   Journal = {Annual Review of Microbiology},
   Volume = {23},
   Pages = {137-58},
   Keywords = {Bacteroides/enzymology
Calcium/metabolism
Cell Division
DNA Replication
Enzyme Induction
Hydrogen-Ion Concentration
Indoleacetic Acids/pharmacology
Infection
Nitrogen Fixation
Plants/enzymology
*Rhizobium/classification/growth \& development/immunology/metabolism
Rickettsiaceae/enzymology
Symbiosis},
   Year = {1969} }




@article{
Djordjevic87,
   Author = {Djordjevic, S. P. and Chen, H. and Batley, M.},
   Title = {Nitrogen fixation ability of exopolysaccharide synthesis mutants of Rhizobium sp. strain NGR234 and Rhizobium trifolii is restored by the addition of homologous exopolysaccharides},
   Journal = {Journal of Bacteriology},
   Volume = {169},
   Number = {1},
   Pages = {53-60},
   Keywords = {nitrogenase
polysaccharide
nitrogen fixation
rhizobium trifolii
Mutation
Nitrogen Fixation},
   Year = {1987} }




@article{
Djordjevic88,
   Author = {Djordjevic, S. P. and Ridge, R. W. and Chen, H. C. and Redmond, J. W. and Batley, M. and Rolfe, B. G.},
   Title = {Induction of pathogenic-like responses in the legume Macroptilium atropurpureum by a transposon-induced mutant of the fast-growing, broad-host-range Rhizobium strain NGR234.},
   Journal = {Journal of Bacteriology},
   Volume = {170},
   Number = {4},
   Pages = {1848-1857},
   Abstract = {Mutant strain ANU2861, a transposon Tn5 mutant of the fast-growing, broad-host-range Rhizobium strain ANU280 (NGR234 Smr Rfr) overproduces polysaccharide, is an ade auxotroph, and induces poorly developed nodules on Leucaena leucocephala and Lablab purpureus (H.C. Chen, M. Batley, J.W. Redmond, and B.G. Rolfe, J. Plant Physiol. 120:331-349, 1985). Strain ANU2861 cannot form nodules on Macroptilium atropurpureum Urb. (siratro) or on Desmodium intortum and D. uncinatum and the nonlegume Parasponia. The parent strain, ANU280, effectively nodulates all these legume species except Parasponia, on which it forms ineffective nodules. Ultrastructural examination of infection sites on the legume siratro showed that mutant strain ANU2861 caused root hair curling (Hac+ phenotype), some cortical cell division (Noi+), but no infection threads (Inf-). Localized cellular responses, known to occur in phytopathological interactions, were observed in electron micrographs of the epidermal tissue at or near the infection zone after inoculation with strain ANU2861 but not the wild-type parental strain. These include (i) the rapid (within 20 h) accumulation of osmiophilic droplets attached to membranes at potential sites of strain ANU2861 penetration and (after 48 h) in the epidermal cells in the immediate region of the curled root hairs, and (ii) localized cell death of the epidermal cells. In addition, strain ANU2861 can initiate a systemic response in split-root siratro plants which prevents the successful nodulation of strain ANU280. A 6.3-kilobase fragment of wild-type genomic DNA, which includes the site of Tn5 insertion in strain ANU2861, was cloned and introduced to strain ANU2861. All the phenotypic defects of the mutant strain were corrected by the introduction of this DNA fragment. This indicates that the original Tn5 insertion is responsible for the phenotype.},
   Keywords = {medicinal plant
Plants, Medicinal},
   Year = {1988} }




@article{
Dobrindt04,
   Author = {Dobrindt, U. and Hochhut, B. and Hentschel, U. and Hacker, J.},
   Title = {Genomic islands in pathogenic and environmental microorganisms},
   Journal = {Nature Reviews Microbiology},
   Volume = {2},
   Number = {5},
   Pages = {414-424},
   Abstract = {Horizontal gene transfer is an important mechanism for the evolution of microbial genomes. Pathogenicity islands - mobile genetic elements that contribute to rapid changes in virulence potential - are known to have contributed to genome evolution by horizontal gene transfer in many bacterial pathogens. Increasing evidence indicates that equivalent elements in nonpathogenic species - genomic islands - are important in the evolution of these bacteria, influencing traits such as antibiotic resistance, symbiosis and fitness, and adaptation in general. This review discusses the recent lessons that have been learned from pathogenicity islands in pathogenic microorganisms and how they apply to the role of genomic islands in commensal, symbiotic and environmental bacteria.},
      Year = {2004} }




@book{
Stanley05,
   Author = {DoC},
   Title = {Wild kakabeak close to extinction},
   Publisher = {Department of Conservation (DoC)},
      Year = {2005} }




@book{
DoC06,
   Author = {DoC},
   Title = {National Parks},
   Publisher = {Department of Conservation (DoC)},
      Year = {2006} }




@article{
Doignon99,
   Author = {Doignon-Bourcier, F. and Sy, A. and Willems, A. and Torck, U. and Dreyfus, B. and Gillis, M. and de Lajudie, P.},
   Title = {Diversity of bradyrhizobia from 27 tropical Leguminosae species native of Senegal},
   Journal = {Systematic and Applied Microbiology},
   Volume = {22},
   Number = {4},
   Pages = {647-661},
   Abstract = {We isolated 71 slow-growing bacterial strains from nodules of 27 native leguminous plants species in Senegal (West-Africa) belonging to the genera Abrus, Alysicarpus, Bryaspis, Chamaecrista, Cassia, Crotalaria, Desmodium, Eriosema, Indigofera, Moghania, Rhynchosia, Sesbania, Tephrosia, and Zornia playing an ecological role and having agronomic potential in arid regions. The isolates were characterised by restriction fragment length polymorphism (RFLP) analysis of PCR-amplified 16S rDNA and comparative SDS-PAGE of whole-cell proteins; reference strains of the different known rhizobial species and groups were included as references. We conclude that these nodule isolates are diverse, and form several phylogenetic subgroups inside Bradyrhizobium. Nodulation tests performed on 5 plant species demonstrated host specificity among the strains studied.},
      Year = {1999} }




@article{
Doignon00,
   Author = {Doignon-Bourcier, F. and Willems, A. and Coopman, R. and Laguerre, G. and Gillis, M. and de Lajudie, P.},
   Title = {Genotypic characterization of Bradyrhizobium strains nodulating small Senegalese legumes by 16S-23S rRNA intergenic gene spacers and amplified fragment length polymorphism fingerprint analyses},
   Journal = {Applied and Environmental Microbiology},
   Volume = {66},
   Number = {9},
   Pages = {3987-3997},
   Abstract = {We examined the genotypic diversity of 64 Bradyrhizobium strains isolated from nodules from 27 native leguminous plant species in Senegal (West Africa) belonging to the genera Abrus, Alysicarpus, Bryaspis, Chamaecrista, Cassia, Crotalaria, Desmodium, Eriosema, Indigofera, Moghania, Rhynchosia, Sesbania, Tephrosia, and Zornia, which play an ecological role and have agronomic potential in arid regions. The strains were characterized by intergenic spacer (between 16S and 23S rRNA genes) PCR and restriction fragment length polymorphism (IGS PCR-RFLP) and amplified fragment length polymorphism (AFLP) fingerprinting analyses. Fifty-three reference strains of the different Bradyrhizobium species and described groups were included for comparison. The strains were diverse and formed 27 groups by AFLP and 16 groups by IGS PCR-RFLP. The sizes of the IGS PCR products from the Bradyrhizobium strains that were studied varied from 780 to 1,038 bp and,cere correlated with the IGS PCR-RFLP results. The grouping of strains was consistent by the three methods AFLP, IGS PCR-RFLP, and previously reported 16S amplified ribosomal DNA restriction analysis. For investigating the whole genome, AFLP was the most discriminative technique, thus being of particular interest for future taxonomic studies in Bradyrhizobium, for which DNA is difficult to obtain in quantity and quality to perform extensive DNA:DNA hybridizations.},
      Year = {2000} }




@article{
Donnelly04,
   Author = {Donnelly, D. and Hoffmann, J. H.},
   Title = {Utilization of an unpredictable food source by Melanterius ventralis, a seed-feeding biological control agent of Acacia longifolia in South Africa},
   Journal = {BioControl},
   Volume = {49},
   Number = {2},
   Pages = {225-235},
   Abstract = {A seed-feeding weevil, Melanterius ventralis (Coleoptera: Curculionidae), has been introduced into South Africa to supplement a gall wasp, Trichilogaster acaciaelongifoliae (Hymenoptera: Pteromalidae), in the biological control programme against an alien invasive tree, Acacia longifolia (Mimosaceae), from Australia. The gall wasp debilitates most of the flower buds on A. longifolia and reduces seed-set by >95%. The intended role for M. ventralis is to destroy the residual seeds. To achieve this, the gravid females need to be able to locate a food source that is both heterogeneously dispersed and frequently scarce due to damage caused by T. acaciaelongifoliae. Observations showed that M. ventralis females are meticulous in choosing sites to oviposit so that larvae do not become overcrowded and food limited. Cage tests and field observations revealed that females located pods regardless of density and position, and that the duration of time spent on branches was proportional to the number of pods on the branches and to the condition of pods. The females spent little time on branches of acacia species other than A. longifolia, but some time was spent on branches with pods of A. melanoxylon that had been coated with juice extracted from A. longifolia. All indications are that M. ventralis has the attributes needed to be an excellent supplementary biological control agent to T. acaciaelongifoliae and the progress of the weevil continues to be monitored.},
   Keywords = {Biological weed control
Oviposition behaviour
Pre-dispersal seed damage
Seed pod density
beetle
biological control
host location
oviposition
seed predation
seed set
weed control
Africa
South Africa
Southern Africa
Sub-Saharan Africa
Acacia longifolia
Acacia melanoxylon
Coleoptera
Curculionidae
Hymenoptera
Melanterius ventralis
Mimosaceae
Pteromalidae
Trichilogaster acaciaelongifoliae},
   Year = {2004} }




@article{
Doolittle90,
   Author = {Doolittle, R. F. and Feng, D. F. and Anderson, K. L. and Alberro, M. R.},
   Title = {A naturally occurring horizontal gene transfer from a eukaryote to a prokaryote},
   Journal = {J Mol Evol},
   Volume = {31},
   Number = {5},
   Pages = {383-8},
   Abstract = {Naturally occurring horizontal gene transfers between nonviral organisms are difficult to prove. Only with the availability of sequence data from a wide variety of organisms can a convincing case be made. In the case of putative gene transfers between prokaryotes and eukaryotes, the minimum requirements for inferring such an event include (1) sequences of the transferred gene or its product from several appropriately divergent eukaryotes and several prokaryotes, and (2) a similar set of sequences from the same (or closely related organisms) for another gene or genes. Given these criteria, we believe that a strong case can be made for Escherichia coli having acquired a second glyceraldehyde-3-phosphate dehydrogenase gene from some eukaryotic host. Ancillary observations on the general rate of change and the time of the prokaryote-eukaryote divergence support the notion.},
   Keywords = {Amino Acid Sequence
Escherichia coli/enzymology/*genetics
Euryarchaeota/enzymology/*genetics
Glyceraldehyde-3-Phosphate Dehydrogenases/*genetics
Molecular Sequence Data
Phosphoglycerate Kinase/genetics
*Phylogeny
Rhizobium/enzymology/*genetics
Support, U.S. Gov't, P.H.S.
*Transfection},
   Year = {1990} }




@article{
Douglas98,
   Author = {Douglas, A. E.},
   Title = {Nutritional interactions in insect-microbial symbioses: Aphids and their symbiotic bacteria Buchnera},
   Journal = {Annual Review of Entomology},
   Volume = {43},
   Pages = {17-37},
   Abstract = {Most aphids possess intracellular bacteria of the genus Buchnera. The bacteria are transmitted vertically via the aphid ovary, and the association is obligate for both partners: Bacteria-free aphids grow poorly and produce few or no offspring, and Buchnera are both unknown apart from aphids and apparently unculturable. The symbiosis has a nutritional basis. Specifically, bacterial provisioning of essential amino acids has been demonstrated. Nitrogen recycling, however, is not quantitatively important to the nutrition of aphid species studied, and there is strong evidence against bacterial involvement in the lipid and sterol nutrition of aphids. Buchnera have been implicated in various non-nutritional functions. Of these, just one has strong experimental support: promotion of aphid transmission of circulative viruses. It is argued that strong parallels may exist between the nutritional interactions (including the underlying mechanisms) in the aphid-Buchnera association and other insect symbioses with intracellular microorganisms.},
   Keywords = {Amino acids
Arthropod
Endosymbiosis
Mycetocyte
Nutrition},
   Year = {1998} }




@article{
Downie94,
   Author = {Downie, J. A.},
   Title = {Signalling strategies for nodulation of legumes by rhizobia},
   Journal = {Trends in Microbiology},
   Volume = {2},
   Number = {9},
   Pages = {318-24},
   Abstract = {During the formation of nitrogen-fixing root nodules, the establishment of the symbiotic relationship between rhizobia and leguminous plants depends on a highly specific exchange of signals. The products of several of the rhizobial nodulation (nod) genes are involved in the biosynthesis of host-specific lipo-oligosaccharide signalling molecules that can induce nodule morphogenesis on legume roots. Such signalling may point to a more widespread cell-to-cell signalling system in plants.},
   Keywords = {Fabaceae/*physiology
Gene Expression Regulation, Bacterial
Genes, Plant/*physiology
Microtubule Proteins/genetics/metabolism/*physiology
Nitrogen Fixation/genetics/*physiology
*Plants, Medicinal
Rhizobiaceae/genetics/*physiology
Signal Transduction/physiology
Support, Non-U.S. Gov't},
   Year = {1994} }




@article{
Downie02,
   Author = {Downie, J. A. and Parniske, M.},
   Title = {Plant biology - Fixation with regulation},
   Journal = {Nature},
   Volume = {420},
   Number = {6914},
   Pages = {369-370},
      Year = {2002} }




@article{
Downie99,
   Author = {Downie, J. A. and Walker, S. A.},
   Title = {Plant responses to nodulation factors},
   Journal = {Current Opinion in Plant Biology},
   Volume = {2},
   Number = {6},
   Pages = {483-489},
   Abstract = {The focus of research on signalling in Rhizobium-legume interactions has moved from understanding the structure and synthesis of rhizobially made Nod factors, towards an analysis of how they function in plants. Nod-factor-induced changes in ion fluxes across membranes, followed by establishment of an oscillation of intracellular Ca2+ concentration, point to the involvement of a receptor-mediated signal transduction pathway. Progress towards the identification of components in this pathway is being made by identifying Nod-factor binding proteins, isolating plant mutants that are defective in signalling and analysing plant responses to Nod factors.},
      Year = {1999} }




@article{
Doyle94,
   Author = {Doyle, J. J.},
   Title = {Phylogeny of the Legume Family - an Approach to Understanding the Origins of Nodulation},
   Journal = {Annual Review of Ecology and Systematics},
   Volume = {25},
   Pages = {325-349},
   Abstract = {Members of Leguminosae (legumes), the third largest family of flowering plants, are cosmopolitan in distribution, diverse in form, and of considerable ecological, agricultural, and scientific importance. Objective phylogeny reconstruction at all taxonomic levels is in the process of reshaping the taxonomy of the family as well as providing new hypotheses concerning the affinities of the family with other angiosperms. Cladistic analyses of morphological and DNA variation for the entire family are in relatively good agreement and echo long-held beliefs, based on more intuitive methods, that many recognized taxa are unnatural. Of the three subfamilies, Mimosoideae and Papilionoideae are most probably monophyletic, while Caesalpinioideae, as suspected, is a paraphyletic grade of basal elements. Phylogenetic hypotheses are being used to address a diversity of questions including biogeography, evolution of pollination systems, origins of economically important species, and genome evolution. Phylogenetic considerations suggest that the ability of legumes to fix atmospheric nitrogen in symbiosis with soil bacteria (nodulation) has arisen several times in the family. Nodules appear to be structurally homologous across the family. The orthology relationships and expression patterns of genes expressed solely or predominantly in the nodule (nodulins) may eventually provide additional criteria for elucidating homologies.},
      Year = {1994} }




@article{
Doyle98,
   Author = {Doyle, J. J.},
   Title = {Phylogenetic perspectives on nodulation: evolving views of plants and symbiotic bacteria},
   Journal = {Trends in Plant Science},
   Volume = {3},
   Number = {12},
   Pages = {473-478},
   Abstract = {Phylogenetic studies are contributing greatly to our knowledge of relationships on both sides of the plant-bacteria nodulation symbiosis. Multiple origins of nodulation (perhaps even within the legume family) appear likely. However, all nodulating flowering plants are more closely related than previously suspected, suggesting that the predisposition to nodulate might have arisen only once. Phylogenies of 16S rRNA genes highlight the evolutionary diversity of symbiotic bacteria and appear to rule out any broad coevolution with their plant hosts, but high levels of gene transfer might obscure the relevant pattern. The origins of nodulation, and the extent to which developmental programs are conserved in nodules remain unclear, but an improved understanding of the relationships between nodulin genes is providing some clues.},
      Year = {1998} }




@incollection{
Doyle00,
   Author = {Doyle, J. J. and Chappill, J. A. and Bailey, D. C. and Kajita, T.},
   Title = {Towards a comprehensive phylogeny of legumes: evidence from \emph{rbcL} sequences and non-molecular data},
   BookTitle = {Advances in Legume Systematics},
   Editor = {Herendeen, P. S.  and Bruneau, A.},
   Publisher = {Royal Botanic Gardens},
   Address = {Kew},
   Pages = {1-20},
      Year = {2000} }




@article{
Doyle88,
   Author = {Doyle, J. J. and Doyle, J. L. and Ballenger, J. A. and Dickson, E. E. and Kajita, T. and Ohashi, H.},
   Title = {A phylogeny of the chloroplast gene rbcL in the leguminosae: Taxonomic correlations and insights into the evolution of nodulation},
   Journal = {American Journal of Botany},
   Volume = {84},
   Number = {4},
   Pages = {541-554},
   Abstract = {Phylogenetic analyses of the chloroplast-encoded rbcL gene in Leguminosae are consistent with previous hypotheses in suggesting that the family as a whole is monophyletic, but that only two of its three subfamilies are natural. The earliest dichotomics in the family appear to have involved tribes Cercideae or Cassieae (subtribe Dialiinae), followed by Detarieae/Macrolobieae, all of which are members of subfamily Caesalpinioideae. The remainder of the family is divided into two clades: (1) Mimosoideac and the caesalpinioid tribes Caeasalpinieae and Cassieae (subtribes Ceratoniinae and Cassiinae); (2) Papilionoideae. Basal groups within Papilionoideae are, as expected, elements of the grade tribes Sophoreae and Swartzieae. Major clades within Papilionoideae include: (1) a Genistoid Alliance comprising Genisteae, Crotalarieae, Podalyrieae, Thermopsideae, Euchrcsteae, and also some Sophoreae; (2) a clade marked by the absence of one copy of the chloroplast inverted repeat, with which are associated Robinieae, Loteae, and some Sophoreae; (3) Phaseoleae, Desmodieae, Psoraleeae, and most Millettieae, a group also marked by presence of pseudoracemose inflorescences; and (4) a well-supported clade comprising Acschynomeneae, Adesmieae, and some Dalbergieae. Nodulation is most parsimoniously optimized on the rbcL strict consensus tree as three parallel gains, occurring in Papilionoideae, the caesalpinioid ancestors of Mimosoideae, and in the genus Chamaecrista (Caesalpinieae: Cassieae).},
   Keywords = {Leguminosae
Nodulation
Phylogeny
RbcL
Taxonomy},
   Year = {1997} }




@article{
Doyle03,
   Author = {Doyle, J. J. and Luckow, M. A.},
   Title = {The rest of the iceberg. Legume diversity and evolution in a phylogenetic context},
   Journal = {Plant Physiology},
   Volume = {131},
   Number = {3},
   Pages = {900-910},
   Keywords = {genetic variability
plant evolution
Evolution, Molecular
Phylogeny},
   Year = {2003} }




@article{
Droge99,
   Author = {Dr\"oge, M. and P\"uhler, A. and Selbitschka, W.},
   Title = {Horizontal gene transfer among bacteria in terrestrial and aquatic habitats as assessed by microcosm and field studies},
   Journal = {Biology and Fertility of Soils},
   Volume = {29},
   Number = {3},
   Pages = {221-245},
   Abstract = {Genetic interactions among bacteria are mediated by one of the three distinct gene-exchange mechanisms: conjugation, transformation or transduction. Conjugative gene exchange relies on mobile elements, such as plasmids, which transfer between donor and recipient cells. In natural transformation, competent cells take up DNA and incorporate it into their genome. Gene transfer via transduction is mediated by bacteriophages which accidentally package donor DNA in their phage head and transfer it to recipient cells. Driven mainly by biosafety research and research into the rapid dissemination of antibiotic resistance, the evaluation of gene flux among bacteria in their natural habitats has become a focus of scientific interest in recent years. Accordingly, gene transfer has been assessed in laboratory-based studies employing model ecosystems, as well as in field experiments. Conjugative gene exchange has been shown to occur under a wide range of environmental conditions. Factors identified as conducive for conjugation include the presence of nutrients provided by the rhizosphere of plants. Studies addressing gene transfer via transformation have demonstrated that naturally transformable bacteria develop competence and take up DNA under in situ conditions. Moreover, DNA has been shown to persist to some extent in the environment, and thus be available for uptake by naturally competent cells. Gene exchange via transduction has been demonstrated under conditions of nutrient depletion and low densities of host cells. Whereas gene transfer is readily observed in the laboratory, more importantly, field studies have provided direct evidence that all three gene transfer mechanisms also occur in nature. DNA transfer frequencies observed in the environment in some cases differed considerably from those obtained under laboratory conditions. Transfers of low frequency observed in laboratory-based experiments have been readily detected in the environment in the presence of selective forces.},
   Keywords = {Biosafety
Conjugation
Rhizobium
Transduction
Transformation},
   Year = {1999} }




@article{
Dreyfus88,
   Author = {Dreyfus, B. and Garcia, J. L. and Gillis, M.},
   Title = {Characterization of \emph{Azorhizobium caulinodans} gen. nov., sp. nov., a stem-nodulating nitrogen-fixing bacterium isolated from \emph{Sesbania rostrata}},
   Journal = {International Journal of Systematic Bacteriology},
   Volume = {38},
   Number = {1},
   Pages = {89-98},
      Year = {1988} }




@article{
Droge98,
   Author = {Droge, M. and Puhler, A. and Selbitschka, W.},
   Title = {Horizontal gene transfer as a biosafety issue: a natural phenomenon of public concern},
   Journal = {J Biotechnol},
   Volume = {64},
   Number = {1},
   Pages = {75-90},
   Abstract = {The transfer of genetic information between distantly or even unrelated organisms during evolution had been inferred from nucleotide sequence comparisons. These studies provided circumstantial evidence that in rare cases genes had been laterally transmitted amongst organisms of the domains bacteria, archaea and eukarya. Laboratory-based studies confirmed that the gene pools of the various domains of organisms are linked. Amongst the bacterial gene exchange mechanisms transduction, transformation and conjugation, the latter was identified as the mechanism with potentially the broadest host range of transfer. Previously, the issue of horizontal gene transfer has become important in the context of biosafety. Gene transfer studies carried out under more natural conditions such as in model ecosystems or in the environment established that all gene transfer mechanisms worked under these conditions. Moreover, environmental hot-spots were identified where favourable conditions such as nutrient enrichment increased the probability of genetic exchange among bacteria. In particular, the phytosphere was shown to provide conducive conditions for conjugative gene exchange. Concern has been expressed that transfer of recombinant DNA (e.g. antibiotic resistance genes) from genetically modified organisms (GMOs) such as transgenic plants to phytosphere bacteria may occur and thus contribute to the undesirable spread of antibiotic resistance determinants. Studies which were performed to address this issue clearly showed that such a transfer occurs, if at all, at extremely low frequency.},
   Keywords = {Evolution
*Gene Transfer, Horizontal/adverse effects
Plants/genetics
Recombination, Genetic
Soil Microbiology
Species Specificity
Support, Non-U.S. Gov't},
   Year = {1998} }




@article{
Drummond01,
   Author = {Drummond, A. and Strimmer, K.},
   Title = {PAL: An object-oriented programming library for molecular evolution and phylogenetics},
   Journal = {Bioinformatics},
   Volume = {17},
   Number = {7},
   Pages = {662-663},
      Year = {2001} }




@article{
Dunican74,
   Author = {Dunican, L. K. and Tierney, A. B.},
   Title = {Genetic transfer of nitrogen fixation from Rhizobium trifolii to Klebsiella aerogenes},
   Journal = {Biochemical and Biophysical Research Communications},
   Volume = {57},
   Number = {1},
   Pages = {62-72},
   Abstract = {The transfer of genes controlling N2 fixation from Rhizobium trifolii to Klebsiella aerogenes 418, a strain incapable of fixing nitrogen, is reported. This intergeneric transfer was mediated by an F like R factor which had previously been transferred into the R. trifolii. The Nif operon was transferred at a frequency of 10-7 or higher. The K. aerogenes hybrids reduced acetylene at rates similar to a naturally occurring N2 fixing strain, K. pneumonia M5al. Acetylene reduction was suppressed in the presence of oxygen or combined nitrogen. While the results presented are consistent with the general conclusion that Nif genes were transferred from R. trifolii to K. aerogenes, the possibility that the transfer of genetic material from R. trifolii permitted the expression of latent Nif genes in K. aerogenes must remain an alternate consideration.},
      Year = {1974} }




@article{
Duponnois97,
   Author = {Duponnois, R. and Cadet, P. and Senghor, K. and Sougoufara, B.},
   Title = {Susceptibility of some Australian acacias to the root-knot nematode Meloidogyne javanica},
   Journal = {Annales des Sciences Forestieres},
   Volume = {54},
   Number = {2},
   Pages = {181-190},
   Abstract = {The susceptibility of seven Australian acacias (Acacia hilliana, A holosericea, A lysiphloia, A mangium, A sclerosperma, A trachycarpa and A tumida) to Meloidogyne javanica has been studied with different rates of nematode inoculums (100, 500 and 1000 juveniles per pot). All these Acacia species are susceptible to the root-knot nematode. A sclerosperma, A hilliana, A holosericea and A mangium are better hosts for M javanica than A trachycarpa. A tumida and A lysiphloia. The root-knot nematode only inhibits the development of A holosericea and stimulates the growth of A tumida. A negative effect of the nematode has been measured with the nitrogen fixation with A mangium and A holosericea but, on the contrary. M javanica stimulates this symbiosis with A tunida and A hilliana. In this case, it can be calculated that 1 mg of dry weight of nodule induces 98 and 88 mg of shoot dry weight respectively.},
   Keywords = {Acacia spp
Meloidogyne javanica
pathogenicity
rhizobium},
   Year = {1997} }




@article{
Duponnois99,
   Author = {Duponnois, R. and Neyra, M. and Senghor, K. and Bâ, A. M.},
   Title = {Effects of the root-knot nematode Meloidogyne javanica on the symbiotic relationships between different strains of Rhizobia and Acacia holosericea (A Cunn. ex G. Don)},
   Journal = {European Journal of Soil Biology},
   Volume = {35},
   Number = {2},
   Pages = {99-105},
   Abstract = {Several strains of Bradyrhizobium, Mesorhizobium and Sinorhizobium strains were tested for their compatibility with an Australian acacia: Acacia holosericea. All bacterial strains induced some nodule formation on roots. However, the rhizobia which greatly increased the development of seedlings belonged to the Bradyrhizobium genus. The root-knot nematode Meloidogyne javanica, strongly inhibited the symbiosis with most of the rhizobial strains. The rhizobia had no effect on nematode multiplication except for bacterial strain ORS 1020 where the final nematode population was higher than in the control treatment. The hypothesis concerning the interactions between nematodes and the nitrogen fixative process are discussed. Moreover, this investigation underlines the decreasing effect of nematodes on the potential benefits that may result from growing A. holosericea inoculated with selected rhizobial strains. (C) 2000 Editions scientifiques et medicales Elsevier SAS.},
   Keywords = {Acacia holosericea
Bradyrhizobium sp.
Forest tree
Meloidogyne javanica
Mesorhizobium plurifarium
Nematode
Rhizobia
Sinorhizobium terangae},
   Year = {1999} }




@article{
Durner99,
   Author = {Durner, Jorg and Klessig, Daniel F.},
   Title = {Nitric oxide as a signal in plants},
   Journal = {Current Opinion in Plant Biology},
   Volume = {2},
   Number = {5},
   Pages = {369-374},
   Abstract = {Molecular, genetic and biochemical studies have identified key players in the signaling pathways regulating growth and development, as well as defense responses in plants. Recently, nitric oxide (NO) -- the versatile and powerful effector of animal redox-regulated signaling and immune responses -- was shown to mediate plant defense responses against pathogens. Interestingly, several key components involved in NO-mediated signaling in animals also appear to be operative in plants.},
      Year = {1999} }




@article{
Dutta,
   Author = {Dutta, C. and Pan, A.},
   Title = {Horizontal gene transfer and bacterial diversity},
   Journal = {J Biosci},
   Volume = {27},
   Number = {1 Suppl 1},
   Pages = {27-33},
   Abstract = {Bacterial genomes are extremely dynamic and mosaic in nature. A substantial amount of genetic information is inserted into or deleted from such genomes through the process of horizontal transfer. Through the introduction of novel physiological traits from distantly related organisms, horizontal gene transfer often causes drastic changes in the ecological and pathogenic character of bacterial species and thereby promotes microbial diversification and speciation. This review discusses how the recent influx of complete chromosomal sequences of various microorganisms has allowed for a quantitative assessment of the scope, rate and impact of horizontally transmitted information on microbial evolution.},
   Keywords = {Animals
Bacteria/*genetics/metabolism
*Evolution
Gene Transfer, Horizontal/*physiology
Genes, Bacterial/*genetics
Support, Non-U.S. Gov't},
   Year = {2002} }




@article{
Duzan05,
   Author = {Duzan, H. M. and Mabood, F. and Zhou, X. and Souleimanov, A. and Smith, D. L.},
   Title = {Nod factor induces soybean resistance to powdery mildew},
   Journal = {Plant Physiology and Biochemistry},
   Volume = {43},
   Number = {10-11},
   Pages = {1022-1030},
   Abstract = {Plants possess highly sensitive perception systems by which microbial signal molecules are recognized. In the Bradyrhizobium-soybean (Glycine max (L.) Merr.) symbiosis, recognition is initiated through exchange of signal molecules, generally flavonoids from soybean and lipo-chitooligosaccharides (Nod factors) from the microsymbiont. Application of the Nod factor Nod Bj-V (C 18:1, MeFuc) induced soybean resistance to powdery mildew caused by Microsphaera diffusa. Addition of Nod factor (concentrations ranging from 10-6 to 10-10 M) to soybean root systems led to reductions in disease incidence. The lowest disease incidence was caused by Nod factor treatment at 10-6 M. The effect of Nod factor application on fungal growth and development was measured at 4, 12, 48, and 96 h after inoculation. Colony diameter and number of germ tubes per conidium were decreased by 10 -6 M Nod factor. Phenylalanine ammonia lyase (PAL, EC.4.3.1.1.) is the first enzyme of the phenyl propanoid pathway, and is commonly activated as part of plant responses to disease. Treatment of soybean seedlings with Nod factor, through stem wounds, induced PAL activity; the most rapid increase followed treatment with 10-6 M Nod factor. These data show that soybean plants are able to detect root applied LCO and respond by increased disease resistance. © 2005 Elsevier SAS. All rights reserved.},
   Keywords = {Disease resistance
Nod factor
Phenylalanine ammonia lyase
Soybean},
   Year = {2005} }




@article{
Duzan04,
   Author = {Duzan, H. M. and Zhou, X. and Souleimanov, A. and Smith, D. L.},
   Title = {Perception of Bradyrhizobium japonicum Nod factor by soybean [Glycine max (L.) Merr.] root hairs under abiotic stress conditions},
   Journal = {J Exp Bot},
   Volume = {55},
   Number = {408},
   Pages = {2641-6},
   Abstract = {Suboptimal growth conditions, such as low rhizosphere temperature, high salinity, and low pH can negatively affect the rhizobia-legume symbioses, resulting in poor nodulation and lower amounts of nitrogen fixed. Early stages of the Bradyrhizobium japonicum-soybean [Glycine max (L.) Merr.] symbiosis, such as excretion of genistein (the plant-to-bacteria signal) and infection initiation can be inhibited by abiotic stresses; however, the effect on early events modulated by Nod factors (bacteria-to-plant signalling), particularly root hair deformations is unknown. Thus, the objective of this study was to evaluate the perception of Nod factor by soybean root hairs under three stress conditions: low temperature, low pH, and high salinity. Three experiments were conducted using a 1:1 ratio of Nod Bj-V (C(18:1), MeFuc) and Nod Bj-V (Ac, C(16:0), MeFuc). Nod factor induced four types of root hair deformation (HAD), wiggling, bulging, curling, and branching. Under optimal experimental conditions root hair response to the three levels of Nod factor tested (10(-6), 10(-8), and 10(-10) M) was dose-dependent. The highest frequency of root hair deformations was elicited by the 10(-6) M level. Root hair deformation decreased with temperature (25, 17, and 15 degrees C), low pH, and high salinity. Nod factor concentration did not interact with either low temperature or pH. However, salinity strongly inhibited HAD responses to increases in Nod factor concentration. Thus, the addition of higher levels of Nod factor is able to overcome the effects of low pH and temperature stress, but not salinity.},
      Year = {2004} }




@article{
Eardly90,
   Author = {Eardly, B. D. and Materon, L. A. and Smith, N. H. and Johnson, D. A. and Rumbaugh, M. D. and Selander, R. K.},
   Title = {Genetic structure of natural populations of the nitrogen-fixing bacterium Rhizobium meliloti},
   Journal = {Applied and Environmental Microbiology},
   Pages = {187-194},
   Abstract = {The genetic structure of populations of the symbiotic nitrogen-fixing soil bacterium Rhizobium meliloti was examined by analysis of electrophoretically demonstrable allelic variation in 14 metabolic, presumably chromosomal, enzyme genes. A total of 232 strains were examined, most of which were isolated from southwest Asia, where there is an unsurpassed number of indigenous host species for R. meliloti. The collection consisted of 115 isolates recovered from annual species of Medicago in Syria, Turkey, and Jordan; 85 isolates cultured from two perennial species of Medicago (M. sativa [alfalfa] and M. falcata) in northern Pakistan and Nepal; and 32 isolates collected at various localities in North and South America, Europe, South Africa, New Zealand, and Australia, largely from M. sativa. Fifty distinctive multilocus genotypes (electrophoretic types [ETs]) were identified, and cluster analysis revealed two primary phylogenetic divisions separated at a genetic distance of 0.83. By the criterion of genetic differentiation conventionally applied in defining species limits among members of the family Enterobacteriaceae and certain other bacteria, the two primary divisions of R. meliloti represent distinct evolutionary species. Division A included 35 ETs represented by 209 strains from the eastern Mediterranean basin, northern Pakistan, Nepal, and various other localities worldwide. This division contained the nine commercial alfalfa inoculant strains examined. Division B included 15 ETs represented by 23 isolates, 21 of which were isolated from annual medic species growing in previously uninoculated soils in the eastern Mediterranean basin. The two remaining strains in division B, both representing the same ET, were isolated in the United States and Australia. The common use of certain ETs from both divisions for seed inoculation and for laboratory research accounts for their widespread geographic distribution.},
   Keywords = {gene structure
rhizobium
Soil Microbiology},
   Year = {1990} }




@article{
Eardly05b,
   Author = {Eardly, B. D. and Nour, S. M. and van Berkum, P. and Selander, R. K.},
   Title = {Rhizobial 16S rRNA and dnaK Genes: Mosaicism and the Uncertain Phylogenetic Placement of Rhizobium galegae},
   Journal = {Applied and Environmental Microbiology},
   Volume = {71},
   Number = {3},
   Pages = {1328-1335},
   Abstract = {The phylogenetic relatedness among 12 agriculturally important species in the order Rhizobiales was estimated by comparative 16S rRNA and dnaK sequence analyses. Two groups of related species were identified by neighbor-joining and maximum-parsimony analysis. One group consisted of Mesorhizobium loti and Mesorhizobium ciceri, and the other group consisted of Agrobacterium rhizogenes, Rhizobium tropici, Rhizobium etli, and Rhizobium leguminosarum. Although bootstrap support for the placement of the remaining six species varied, A. tumefaciens, Agrobacterium rubi, and Agrobacterium vitis were consistently associated in the same subcluster. The three other species included Rhizobium galegae, Sinorhizobium meliloti, and Brucella ovis. Among these, the placement of R. galegae was the least consistent, in that it was placed flanking the A. rhizogenes-Rhizobium cluster in the dnaK nucleotide sequence trees, while it was placed with the other three Agrobacterium species in the 16S rRNA and the DnaK amino acid trees. In an effort to explain the inconsistent placement of R. galegae, we examined polymorphic site distribution patterns among the various species. Localized runs of nucleotide sequence similarity were evident between R. galegae and certain other species, suggesting that the R. galegae genes are chimeric. These results provide a tenable explanation for the weak statistical support often associated with the phylogenetic placement of R. galegae, and they also illustrate a potential pitfall in the use of partial sequences for species identification.},
      Year = {2005} }




@article{
Eardly05a,
   Author = {Eardly, B. D. and van Berkum, P.},
   Title = {Use of population genetic structure to define species limits in the Rhizobiaceae},
   Journal = {Symbiosis},
   Volume = {38},
   Number = {2},
   Pages = {109-122},
   Abstract = {Symbiotic bacteria of the family Rhizobiaceae are currently defined using a consensus or polyphasic approach, where emphasis in determining species limits is based on the quantification of overall genotypic and phenotypic similarity. In the first part of this review some of the limitations of this approach are examined. In the second part an alternative population-based approach is considered. The primary assumption underlying this approach is that ecological selection is the dominant force constraining genetic diversity in bacterial populations. Practical methods for assessing the range and extent of this diversity are described, along with an example of how such information has been used to provide evidence for two symbiotic nitrogen-fixing species within the genus Sinorhizobium.},
   Keywords = {Ecotype
Genetic structure
MLST
Phylogeny
Polyphasic
Rhizobiaceae
Species concept
Symbiotic
Systematics},
   Year = {2005} }




@article{
Egelhoff85,
   Author = {Egelhoff, T. T. and Long, S. R.},
   Title = {Rhizobium meliloti nodulation genes: Identification of nodDABC gene products, purification of nodA protein, and expression of nodA in Rhizobium meliloti},
   Journal = {Journal of Bacteriology},
   Volume = {164},
   Number = {2},
   Pages = {591-599},
      Year = {1985} }




@article{
Ehrhardt92,
   Author = {Ehrhardt, D. W. and Atkinson, E. M. and Long, S. R.},
   Title = {Depolarization of alfalfa root hair membrane potential by Rhizobium meliloti nod factors},
   Journal = {Science},
   Volume = {256},
   Number = {5059},
   Pages = {998-1000},
   Abstract = {Although much is known about the bacterial genetics of early nodulation, little is known about the plant cell response. Alfalfa root hair cells were impaled with intracellular microelectrodes to measure a membrane potential depolarizing activity in Rhizobium meliloti cell-free filtrates, a plant response dependent on the bacterial nodulation genes. The depolarization was desensitized by repeated exposure to factors and was not observed in a representative nonlegume. A purified extracellular Nod factor, NodRm-IV(S), caused membrane potential depolarization at nanomolar concentrations. This rapid single-cell assay provides a tool for dissecting the mechanisms of host cell response in early nodulation.},
      Year = {1992} }




@article{
Ehrhardt96,
   Author = {Ehrhardt, D. W. and Wais, R. and Long, S. R.},
   Title = {Calcium spiking in plant root hairs responding to rhizobium modulation signals},
   Journal = {Cell},
   Volume = {85},
   Number = {5},
   Pages = {673-681},
   Abstract = {Rhizobium lipochitooligosaccharide signal molecules stimulate multiple responses in legume host plants, including changes in host gene expression, cell growth, and mitoses leading to root nodule development. The basis for signal transduction in the plant is not known. We examined cytoplasmic free calcium in host root hairs using calcium-sensitive reporter dyes. Image analysis of injected dyes revealed localized periodic spikes in cytoplasmic calcium levels that ensued after a characteristic lag following signal application. Structural features of the signal molecules required to cause nodulation responses in alfalfa are also essential for stimulating calcium spiking. A nonnodulating alfalfa mutant is defective in calcium spiking, consistent with the possibility that this mutant is blocked in an early stage of nodulation signal perception.},
      Year = {1996} }




@article{
Elkan92,
   Author = {Elkan, G. H.},
   Title = {Taxonomy of the Rhizobia},
   Journal = {Canadian Journal of Microbiology},
   Volume = {38},
   Number = {6},
   Pages = {446-450},
   Abstract = {Extensive cross testing on a relatively few legume hosts led initially to a taxonomic characterization of rhizobia based on bacteria-plant cross-inoculation groups. This has gradually become less acceptable, and has been replaced by taxonomic groupings derived from numerical taxonomy, carbohydrate metabolism, antibiotic susceptibilities, serology, and various molecular techniques. It has long been recognized that there are two distinct groups of rhizobia based on growth rate. The fast-growing genus Rhizobium includes R. leguminosarum, R. meliloti, R. loti, R. galegae, R. tropici, and R. huakuii. The slow-growing genus Bradyrhizobium contains only one recognized species, B. japonicum. Two new genera have been recognized: Azorhizobium, with one recognized species (A. caulinadans), and Sinorhizobium, with two species (S. fredii and S. xinjiangensis). Genetic studies of both the fast- and slow-growing groups show unacceptably wide intrageneric and intergeneric diversity. Although there have been some elegant studies of some of the genetic relationships among rhizobia, overall there has (have) not been the comprehensive study(ies) needed to allow a conclusive taxonomic scheme. Because proposals for revision are accelerating, minimum standards have been proposed by the International Subcommittee for the Taxonomy of Rhizobium and Agrobacterium.},
      Year = {1992} }




@article{
Endre02,
   Author = {Endre, G. and Kereszt, A. and Kevei, Z. and Mihacea, S. and Kaló, P. and Kiss, G.B.},
   Title = {A receptor kinase gene regulating symbiotic nodule development},
   Journal = {Nature},
   Volume = {417},
   Number = {6892},
   Pages = {962-966},
   Abstract = {Leguminous plants are able to establish a nitrogen-fixing symbiosis with soil bacteria generally known as rhizobia. Metabolites exuded by the plant root activate the production of a rhizobial signal molecule, the Nod factor, which is essential for symbiotic nodule development. This lipo-chitooligosaccharide signal is active at femtomolar concentrations, and its structure is correlated with host specificity of symbiosis, suggesting the involvement of a cognate perception system in the plant host. Here we describe the cloning of a gene from Medicago sativa that is essential for Nod-factor perception in alfalfa, and by genetic analogy, in the related legumes Medicago truncatula and Pisum sativum. The identified 'nodulation receptor kinase', NORK, is predicted to function in the Nod-factor perception/transduction system (the NORK system) that initiates a signal cascade leading to nodulation. The family of 'NORK extracellular-sequence-like' (NSL) genes is broadly distributed in the plant kingdom, although their biological function has not been previously ascribed. We suggest that during the evolution of symbiosis an ancestral NSL system was co-opted for transduction of an external ligand, the rhizobial Nod factor, leading to development of the symbiotic root nodule.},
      Year = {2002} }




@article{
Esseling04,
   Author = {Esseling, J. J. and Emons, A. M.},
   Title = {Dissection of Nod factor signalling in legumes: cell biology, mutants and pharmacological approaches},
   Journal = {J Microsc},
   Volume = {214},
   Number = {Pt 2},
   Pages = {104-13},
   Abstract = {Nodulation factors (NFs) are lipochito-oligosaccharide signal molecules excreted by soil-living rhizobia. These molecules elicit a range of responses in the legume roots, with which the bacteria can live in symbiosis. In this review we focus on the genetic, pharmacological and cell biological approaches that have been, and are being, undertaken to decipher the signalling pathways that lead to the symbiotic responses in the plant.},
   Keywords = {Actins/metabolism
Cytoskeleton/metabolism
Fabaceae/genetics/*metabolism/microbiology
Gene Expression
Genes, Plant
Ion Transport
Lipopolysaccharides/*metabolism/pharmacology
Mutation
Plant Roots/drug effects/growth \& development/metabolism
Signal Transduction
Support, Non-U.S. Gov't
Symbiosis},
   Year = {2004} }




@article{
Esseling03,
   Author = {Esseling, J. J. and Lhuissier, F. G. and Emons, A. M.},
   Title = {Nod factor-induced root hair curling: continuous polar growth towards the point of nod factor application},
   Journal = {Plant Physiol},
   Volume = {132},
   Number = {4},
   Pages = {1982-8},
   Abstract = {A critical step in establishing a successful nitrogen-fixing symbiosis between rhizobia and legume plants is the entrapment of the bacteria between root hair cell walls, usually in characteristic 180 degrees to 360 degrees curls, shepherd's crooks, which are formed by the host's root hairs. Purified bacterial signal molecules, the nodulation factors (NFs), which are lipochitooligosaccharides, induce root hair deformation in the appropriate host legume and have been proposed to be a key player in eliciting root hair curling. However, for curling to occur, the presence of intact bacteria is thought to be essential. Here, we show that, when spot applied to one side of the growing Medicago truncatula root hair tip, purified NF alone is sufficient to induce reorientation of the root hair growth direction, or a full curl. Using wild-type M. truncatula containing the pMtENOD11::GUS construct, we demonstrate that MtENOD11::GUS is expressed after spot application. The data have been incorporated into a cell biological model, which explains the formation of shepherd's crook curls around NF-secreting rhizobia by continuous tip growth reorientation.},
   Keywords = {Gene Expression Regulation, Plant/drug effects
Lipopolysaccharides/*pharmacology
Medicago/cytology/*drug effects/*growth \& development
Membrane Proteins/genetics/metabolism
Plant Proteins/genetics/metabolism
Plant Roots/cytology/*drug effects/*growth \& development
Support, Non-U.S. Gov't},
   Year = {2003} }




@article{
Estrada01,
   Author = {Estrada-De los Santos, P. and Bustillos-Cristales, R. and Caballero-Mellado, J.},
   Title = {Burkholderia, a genus rich in plant-associated nitrogen fixers with wide environmental and geographic distribution},
   Journal = {Applied and Environmental Microbiology},
   Volume = {67},
   Number = {6},
   Pages = {2790-2798},
   Abstract = {The genus Burkholderia comprises 19 species, including Burkholderia vietnamiensis which is the only known N-2-fixing species of this bacterial genus. The first isolates of B. vietnamiensis were recovered from the rhizosphere of rice plants grown in a phytotron, but its existence in natural environments and its geographic distribution were not reported. In the present study, most N-2-fixing isolates recovered from the environment of field-grown maize and coffee plants cultivated in widely separated regions of Mexico were phenotypically identified as B. cepacia using the API 20NE system. Nevertheless, a number of these isolates recovered from inside of maize roots, as well as from the rhizosphere and rhizoplane of maize and coffee plants, showed similar or identical features to those of B. vietnamiensis TVV75(T). These features include nitrogenase activity with 10 different carbon sources, identical or very similar nifHDK hybridization patterns, very similar protein electrophoregrams, identical amplified 16S rDNA restriction (ARDRA) profiles, and levels of DNA-DNA reassociation higher than 70% with total DNA from strain TVV75(T). Although the ability to fix N-2 is not reported to be a common feature among the known species of the genus Burkholderia, the results obtained show that many diazotrophic Burkholderia isolates analyzed showed phenotypic and genotypic features different from those of the known N-2-fixing species B. vietnamiensis as well as from those of B. kururiensis, a bacterium identified in the present study as a diazotrophic species. DNA-DNA reassociation assays confirmed the existence of N-2-fixing Burkholderia species different from B. vietnamiensis, In addition, this study shows the wide geographic distribution and substantial capability of N-2-fixing Burkholderia spp, for colonizing diverse host plants in distantly separated environments.},
      Year = {2001} }




@article{
Euzeby97,
   Author = {Euz\'eby, J. P.},
   Title = {List of bacterial names with standing in nomenclature: A folder available on the internet},
   Journal = {International Journal of Systematic Bacteriology},
   Volume = {47},
   Number = {2},
   Pages = {590-592},
   Abstract = {The List of Bacterial Names with Standing in Nomenclature includes, alphabetically and chronologically, the official names of bacteria as published or validated in the International Journal of Systematic Bacteriology. It encompasses 5,569 taxa (as of 31 December 1996) and is available on the Internet (URL: ftp://ftp.cict.fr/pub/bacterio/).},
   Keywords = {bacterium
Computer Communication Networks
Terminology},
   Year = {1997} }




@article{
Evans76,
   Author = {Evans, W. R. and Keister, D. L.},
   Title = {Reduction of acetylene by stationary cultures of free-living Rhizobium sp. under atmospheric oxygen levels},
   Journal = {Canadian Journal of Microbiology},
   Volume = {22},
   Number = {7},
   Pages = {949-52},
   Abstract = {The reduction of acetylene to ethylene by stationary (non-shaking) cultures of free-living rhizobia under atmospheric oxygen levels has been demonstrated. Under these conditions the development of the activity is inhibited by 10 mM NH4Cl and about 20% of oxygen is required for maximal activity. When the stationary cultures were shaken, oxygen concentrations of 1% and higher were found to be inhibitory. Specific activities of 20 and 40 nmol of acetylene reduced h-1 mg-1 protein were observed.},
   Keywords = {Acetylene/*metabolism
Ammonium Chloride/metabolism
Atmospheric Pressure
Bacterial Proteins/biosynthesis
Ethylenes/metabolism
Oxidation-Reduction
*Oxygen
Rhizobium/*metabolism},
   Year = {1976} }




@article{
Falla99,
   Author = {Falla, T. J and Chopra, I.},
   Title = {Stabilization of Rhizobium symbiosis plasmids},
   Journal = {Microbiology},
   Volume = {145},
   Number = {3},
   Pages = {515-516},
      Year = {1999} }




@article{
Farrand03,
   Author = {Farrand, Stephen K. and van Berkum, Peter B. and Oger, Philippe},
   Title = {Agrobacterium is a definable genus of the family Rhizobiaceae},
   Journal = {International Journal of Systematic and Evolutionary Microbiology},
   Volume = {53},
   Number = {5},
   Pages = {1681-1687},
   Abstract = {Members of the genus Agrobacterium constitute a diverse group of organisms, all of which, when harbouring the appropriate plasmids, are capable of causing neoplastic growths on susceptible host plants. The agrobacteria, which are members of the family Rhizobiaceae, can be differentiated into at least three biovars, corresponding to species divisions based on differential biochemical and physiological tests. Recently, Young et al. [Int J Syst Evol Microbiol 51 (2003), 89-103] proposed to incorporate all members of the genus Agrobacterium into the genus Rhizobium. We present evidence from classical and molecular comparisons that supports the conclusion that the biovar 1 and biovar 3 agrobacteria are sufficiently different from members of the genus Rhizobium to warrant retention of the genus Agrobacterium. The biovar 2 agrobacteria cluster more closely to the genus Rhizobium, but some studies suggest that these isolates differ from species of Rhizobium with respect to their capacity to interact with plants. We conclude that there is little scientific support for the proposal to group the agrobacteria into the genus Rhizobium and consequently recommend retention of the genus Agrobacterium.},
      Year = {2003} }




@article{
Fath93,
   Author = {Fath, M. J. and Kolter, R.},
   Title = {ABC transporters: Bacterial exporters},
   Journal = {Microbiological Reviews},
   Volume = {57},
   Number = {4},
   Pages = {995-1017},
   Abstract = {The ABC transporters (also called traffic ATPases) make up a large superfamily of proteins which share a common function and a common ATP- binding domain. ABC transporters are classified into three major groups: bacterial importers (the periplasmic permeases), eukaryotic transporters, and bacterial exporters. We present a comprehensive review of the bacterial ABC exporter group, which currently includes over 40 systems. The bacterial ABC exporter systems are functionally subdivided on the basis of the type of substrate that each translocates. We describe three main groups: protein exporters, peptide exporters, and systems that transport nonprotein substrates. Prototype exporters from each group are described in detail to illustrate our current understanding of this protein family. The prototype systems include the alpha-hemolysin, colicin V, and capsular polysaccharide exporters from Escherichia coli, the protease exporter from Erwinia chrysanthemi, and the glucan exporters from Agrobacterium tumefaciens and Rhizobium meliloti. Phylogenetic analysis of the ATP-binding domains from 29 bacterial ABC exporters indicates that the bacterial ABC exporters can be divided into two primary branches. One branch contains the transport systems where the ATP-binding domain and the membrane-spanning domain are present on the same polypeptide, and the other branch contains the systems where these domains are found on separate polypeptides. Differences in substrate specificity do not correlate with evolutionary relatedness. A complete survey of the known and putative bacterial ABC exporters is included at the end of the review.},
      Year = {1993} }




@article{
Felsenstein81,
   Author = {Felsenstein, J.},
   Title = {Evolutionary trees from DNA sequences: A maximum likelihood approach},
   Journal = {Journal of Molecular Evolution},
   Volume = {17},
   Number = {6},
   Pages = {368-376},
   Abstract = {The application of maximum likelihood techniques to the estimation of evolutionary trees from nucleic acid sequence data is discussed. A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available. This method has advantages over the traditional parsimony algorithms, which can give misleading results if rates of evolution differ in different lineages. It also allows the testing of hypotheses about the constancy of evolutionary rates by likelihood ratio tests, and gives rough indication of the error of the estimate of the tree.},
      Year = {1981} }




@article{
Felsenstein85,
   Author = {Felsenstein, J.},
   Title = {Confidence limits on phylogenies: An approach using the bootstrap},
   Journal = {Evolution},
   Volume = {39},
   Pages = {783-791},
      Year = {1985} }




@article{
Felsenstein85b,
   Author = {Felsenstein, J.},
   Title = {Phylogenies and the comparative method.},
   Journal = {American Naturalist},
   Volume = {125},
   Number = {1},
   Pages = {1-15},
   Abstract = {Comparative studies of the relationship between 2 phenotypes, or between a phenotype and an environment, are frequently carried out by invalid statistical methods. Most regression, correlation, and contingency table methods, including nonparametric methods, assume that the points are drawn independently from a common distribution. When species are taken from a branching phylogeny, they are manifestly nonindependent. Use of a statistical method that assumes independence will cause overstatement of the significance in hypothesis tests. Some illustrative examples of these phenomena are given, and limitations of previous proposals of ways to correct for the nonindependence discussed. A method of correcting for the phylogeny is proposed. It requires that we know both the tree topology and the branch lengths, and that we be willing to allow the characters to be modeled by Brownian motion on a linear scale. Given these conditions, the phylogeny specifies a set of contrasts among species, contrasts that are statistically independent and can be used in regression or correlation studies. -from Author},
      Year = {1985} }




@article{
Felsenstein88,
   Author = {Felsenstein, J.},
   Title = {Phylogenies from molecular sequences: inference and reliability},
   Journal = {Annual Review of Genetics},
   Volume = {22},
   Pages = {521-565},
   Keywords = {evolution
genetic model
nucleotide sequence
phylogeny
Base Sequence
Models, Genetic
Models, Statistical
Phylogeny},
   Year = {1988} }




@article{
Felsenstein01a,
   Author = {Felsenstein, J.},
   Title = {Taking variation of evolutionary rates between sites into account in inferring phylogenies},
   Journal = {Journal of Molecular Evolution},
   Volume = {53},
   Number = {4-5},
   Pages = {447-455},
   Abstract = {As methods of molecular phylogeny have become more explicit and more biologically realistic following the pioneering work of Thomas Jukes, they have had to relax their initial assumption that rates of evolution were equal at all sites. Distance matrix and likelihood methods of inferring phylogenies make this assumption; parsimony, when valid, is less limited by it. Nucleotide sequences, including RNA sequences, can show substantial rate variation; protein sequences show rates that vary much more widely. Assuming a prior distribution of rates such as a gamma distribution or lognormal distribution has deservedly been popular, but for likelihood methods it leads to computational difficulties. These can be resolved using hidden Markov model (HMM) methods which approximate the distribution by one with a modest number of discrete rates. Generalized Laguerre quadrature can be used to improve the selection of rates and their probabilities so as to more nearly approach the desired gamma distribution. A model based on population genetics is presented predicting how the rates of evolution might vary from locus to locus. Challenges for the future include allowing rates at a given site to vary along the tree, as in the "covarion" model, and allowing them to have correlations that reflect three-dimensional structure, rather than position in the coding sequence. Markov chain Monte Carlo likelihood methods may be the only practical way to carry out computations for these models.},
      Year = {2001} }




@article{
Felsenstein01b,
   Author = {Felsenstein, J.},
   Title = {The troubled growth of statistical phylogenetics},
   Journal = {Systematic Biology},
   Volume = {50},
   Number = {4},
   Pages = {465-467},
      Year = {2001} }




@article{
Felsenstein93,
   Author = {Felsenstein, J. and Kishino, H.},
   Title = {Is There Something Wrong with the Bootstrap on Phylogenies - a Reply},
   Journal = {Systematic Biology},
   Volume = {42},
   Number = {2},
   Pages = {193-200},
      Year = {1993} }




@article{
Feng03,
   Author = {Feng, J. and Li, Q. and Hu, H.-L. and Chen, X.-C. and Hong, G.-F.},
   Title = {Inactivation of the nod box distal half-site allows tetrameric NodD to activate nodA transcription in an inducer-independent manner},
   Journal = {Nucleic Acids Research},
   Volume = {31},
   Number = {12},
   Pages = {3143-3156},
   Abstract = {In Rhizobium leguminosarum, NodD can activate nodA transcription in response to inducer flavonoids. Here, we show that the inducible nodA promoter contains an intrinsic part through which NodD can activate nodA transcription in an inducer-independent manner. Evidence was provided that NodD binds to target DNA through anchoring the two half-sites of the nod box as a tetramer. An imperfect inverted repeat AT-N<sub>10</sub>-GAT was found in each half-site and is critical for NodD binding. Mutation of the inverted repeat of the nod box distal half-site allowed NodD to activate nodA transcription in an inducer-independent manner in vivo, and to modulate the DNA bending of the NodD-nod box complex in the absence of inducer in vitro.},
   Keywords = {flavonoid
protein NodA
protein nodD
regulator protein
gene expression regulation
regulatory sequence
transactivation
Rhizobium leguminosarum
Gene Expression Regulation, Bacterial
Regulatory Sequences, Nucleic Acid
Trans-Activation (Genetics)},
   Year = {2003} }




@article{
Feng02,
   Author = {Feng, Lu and Roughley, Rodney J. and Copeland, Les},
   Title = {Morphological Changes of Rhizobia in Peat Cultures},
   Journal = {Applied and Environmental Microbiology},
   Volume = {68},
   Number = {3},
   Pages = {1064-1070},
   Abstract = {Morphological changes that take place in peat cultures of several species of rhizobia were examined. These changes seemed to be associated with enhanced survival of cells in peat and after inoculation onto plastic beads, which were used as a model system for seeds. Cell wall changes, in which the periplasmic space appeared to be occluded with electron-dense material, were observed in Rhizobium sp. strain SU343 and Bradyrhizobium lupini WU425 cells after 7 and 14 days in peat, respectively. Nutrient limitation and low O2 concentration in peat are suggested to be factors involved in the induction of the morphological changes. Polyhydroxybutyrate reserves, which were present in broth-cultured cells of both species of rhizobia, were mobilized after transfer into peat but did not appear to influence survival after inoculation onto beads. Enhanced expression of an iron-manganese superoxide dismutase was also observed after the cells were transferred into peat. We conclude that cell wall thickening in rhizobia after transfer from broth cultures into peat is an adaptive response for long-term survival under nutrient-limited conditions in peat. Cells with thickened walls may also be more resistant to other types of stress, such as that encountered on a seed surface.},
      Year = {2002} }




@article{
Fenton94,
   Author = {Fenton, M. and Jarvis, B. D. W.},
   Title = {Expression of the symbiotic plasmid from \emph{Rhizobium leguminosarum} biovar \emph{trifolii} in \emph{Sphingobacterium multivorum}},
   Journal = {Canadian Journal of Microbiology},
   Volume = {40},
   Number = {10},
   Pages = {873-879},
   Abstract = {An inoculant strain of Rhizobium leguminosarum biovar trifolii containing a Tn5 marked symbiotic plasmid transferred this plasmid by conjugation to Sphingobacterium multivorum, an organism that can be found in soil. The transconjugant bacteria nodulated the roots of white clover (Trifolium repens) seedlings but did not fix atmospheric nitrogen. Microscopic examination revealed abnormal nodule structures. Bacteria isolated from the nodules were shown to be closely related to the recipient S. multivolum and Southern blots of genomic digests probed with noda DNA confirmed that the transconjugants contained symbiotic genes. This is the first report of the spontaneous transfer, by conjugation, of a symbiotic plasmid from R. leguminosalum biovar trifolii to S. multivolum.},
   Keywords = {Nod gene transfer
Nodulation
Rhizobium
Spingobacterium
plasmid
rhizobium
symbiosis},
   Year = {1994} }




@article{
Ferguson03,
   Author = {Ferguson, B. J. and Mathesius, U.},
   Title = {Signaling Interactions during Nodule Development},
   Journal = {Journal of Plant Growth Regulation},
   Volume = {22},
   Number = {1},
   Pages = {47-72},
   Abstract = {Nitrogen fixing bacteria, collectively referred to as rhizobia, are able to trigger the organogenesis of a new organ on legumes, the nodule. The morphogenetic trigger is a Rhizobium-produced lipochitin-oligosaccharide called the Nod factor, which is necessary, and in some legumes sufficient, for triggering nodule development in the absence of the bacterium. Because plant development is substantially influenced by plant hormones, it has been hypothesized that plant hormones (mainly the classical hormones abscisic acid, auxin, cytokinins, ethylene and gibberellic acid) regulate nodule development. In recent years, evidence has shown that Nod factors might act in legumes by changing the internal plant hormone balance, thereby orchestrating the nodule developmental program. In addition, many nonclassical hormonal signals have been found to play a role in nodule development, some of them similar to signals involved in animal development. These compounds include peptide hormones, nitric oxide, reactive oxygen species, jasmonic acid, salicylic acid, uridine, flavonoids and Nod factors themselves. Environmental factors, in particular nitrate, also influence nodule development by affecting the plant hormone status. This review summarizes recent findings on the involvement of classical and nonclassical signals during nodule development with the aim of illustrating the multiple interactions existing between these compounds that have made this area so complicated to analyze.},
   Keywords = {Cell division
Defence response
Meristem
Nod factors
Nodulation
Organogenesis
Peptide signals
Plant hormones
Receptor kinase
Systemic acquired resistance},
   Year = {2003} }




@article{
Fernandez89,
   Author = {Fernandez, M. P. and Meugnier, H. and Grimont, P. A. D. and Bardin, R.},
   Title = {Deoxyribonucleic acid relatedness among members of the genus Frankia},
   Journal = {International Journal of Systematic Bacteriology},
   Volume = {39},
   Number = {4},
   Pages = {424-429},
      Year = {1989} }




@article{
Ferreira00,
   Author = {Ferreira, M. C. and De O. Chueire, L. M. and Takemura, S. M. and Hungria, M. and De S. Andrade, D.},
   Title = {Tillage method and crop rotation effects on the population sizes and diversity of bradyrhizobia nodulating soybean},
   Journal = {Soil Biology and Biochemistry},
   Volume = {32},
   Number = {5},
   Pages = {627-637},
   Abstract = {This study was conducted in an area of Brazil cultivated with soybean since the early 1960's but which for the last 17 yr was under different tillage (no-tillage, NT; conventional tillage, CT) and crop rotation (soybean, S/wheat, W/maize, M; S/W; M/W) systems. The area had not received any inoculant for the last 15 yr and our objective was to investigate the effects of tillage and cropping systems on the bradyrhizobia population. The NT system and crop rotations with soybean resulted in high populations of bradyrhizobia, but even in the treatment where soybean had not been cultivated for 17 yr (M/W) the number of viable cells in the soil was high. A total of 142 bradyrhizobia isolated from the different treatments were characterized based on colony morphology, serological reaction, DNA analysis by RAPD, protein and Nod factors profiles. The analyses resulted in grouping of the isolates into 16 DNA, five protein and three Nod factors profiles. A high proportion (37.5%) of the isolates did not react with any known serogroup. Both NT and crop rotations with soybean resulted in a higher bradyrhizobia diversity, with the lowest number of genomic patterns occurring in the CT with M/W rotation. However, there was no relationship between the treatment combinations and genetic relatedness. The evaluation of symbiotic performance under greenhouse conditions showed that the isolates with higher rates of N2 fixation were also isolated from NT with S/W or S/W/M crop rotations. Consequently, the use of agronomic practices such as NT and crop rotation with legumes will not only contribute to agricultural sustainability, but also help to maintain bradyrhizobia population and diversity. (C) 2000 Elsevier Science Ltd.},
   Keywords = {Bacteria diversity
Bradyrhizobium
Crop rotation
Nitrogen fixation
Tillage system},
   Year = {2000} }




@article{
Ferreira02,
   Author = {Ferreira, M. C. and Hungria, M.},
   Title = {Recovery of soybean inoculant strains from uncropped soils in Brazil},
   Journal = {Field Crops Research},
   Volume = {79},
   Number = {2-3},
   Pages = {139-152},
   Abstract = {Soybean (Glycine max (L.) Merrill) and the corresponding bradyrhizobia were introduced in Brazil several decades ago and have been intensively used since then. However, in the past decade the possibility has been raised of native bradyrhizobia strains able to nodulate soybean. To clarify this, a modern cultivar and six unimproved promiscuous genotypes were inoculated with soil dilutions from 14 diverse uncropped soils bearing native vegetation. Isolates of Bradyrhizobium were obtained from seven of the soils, and most proved intolerant of acidity, salinity and high temperature. Thirty-nine of the 40 isolates showed similarity to seven strains that have been, or are, used in commercial inoculants. Characteristics evaluated included: synthesis of indole acetic acid, profiles of protein, lipopolysaccharide and DNA after amplification by PCR with ERIC primer, partial sequence of 16S rRNA and symbiotic properties. From the similarity of these strains to inoculant bradyrhizobia dispersal from soybean-cropped areas seems likely. However, in some strains (as those belonging to serogroup SEMIA 5039), PCR clustering was different from groupings based on serology, profiles of protein and lipopolysaccharide, indicating the presence of indigenous strains with similar properties, or genetic transfer from inoculant strains to indigenous bradyrhizobia, or variability due to the adaptation to different soil conditions. Only one isolate did not fit into the characteristics of known strains and could represent an indigenous soybean Bradyrhizobium, but this isolate showed poor symbiotic performance. © 2002 Elsevier Science B.V. All rights reserved.},
   Keywords = {Bacteria dispersion
Biological nitrogen fixation
Bradyrhizobia ecology
Bradyrhizobium
Competitiveness
Glycine max},
   Year = {2002} }




@article{
Finan02,
   Author = {Finan, T. M.},
   Title = {Evolving insights: symbiosis islands and horizontal gene transfer},
   Journal = {Journal of Bacteriology},
   Volume = {184},
   Number = {11},
   Pages = {2855-6},
   Keywords = {Gene Transfer, Horizontal
Lotus/microbiology
Rhizobium/*genetics/pathogenicity
Soil Microbiology
Support, Non-U.S. Gov't
Symbiosis/*genetics},
   Year = {2002} }




@article{
Finan86,
   Author = {Finan, T. M. and Kunkel, B. and De Vos, G. F. and Signer, E. R.},
   Title = {Second symbiotic megaplasmid in Rhizobium meliloti carrying exopolysaccharide and thiamine synthesis genes},
   Journal = {Journal of Bacteriology},
   Volume = {167},
   Number = {1},
   Pages = {66-72},
      Year = {1986} }




@article{
Finan01,
   Author = {Finan, Turlough M. and Weidner, Stefan and Wong, Kim and Buhrmester, Jens and Chain, Patrick and Vorholter, Frank J. and Hern\'andez-Lucas, Ismael and Becker, Anke and Cowie, Alison and Gouzy, Jerome and Golding, Brian and Puhler, Alfred},
   Title = {The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont \emph{Sinorhizobium meliloti}},
   Journal = {Proceedings of the National Academy of Sciences of the United States of America},
   Volume = {98},
   Number = {17},
   Pages = {9889-9894},
   Abstract = {Analysis of the 1,683,333-nt sequence of the pSymB megaplasmid from the symbiotic N2-fixing bacterium Sinorhizobium meliloti revealed that the replicon has a high gene density with a total of 1,570 protein-coding regions, with few insertion elements and regions duplicated elsewhere in the genome. The only copies of an essential arg-tRNA gene and the minCDE genes are located on pSymB. Almost 20% of the pSymB sequence carries genes encoding solute uptake systems, most of which were of the ATP-binding cassette family. Many previously unsuspected genes involved in polysaccharide biosynthesis were identified and these, together with the two known distinct exopolysaccharide synthesis gene clusters, show that 14% of the pSymB sequence is dedicated to polysaccharide synthesis. Other recognizable gene clusters include many involved in catabolic activities such as protocatechuate utilization and phosphonate degradation. The functions of these genes are consistent with the notion that pSymB plays a major role in the saprophytic competence of the bacteria in the soil environment.},
      Year = {2001} }




@article{
Fischer94,
   Author = {Fischer, H.-M.},
   Title = {Genetic regulation of nitrogen fixation in rhizobia},
   Journal = {Microbiological Reviews},
   Volume = {58},
   Number = {3},
   Pages = {352-386},
   Abstract = {This review presents a comparison between the complex genetic regulatory networks that control nitrogen fixation in three representative rhizobial species, Rhizobium meliloti, Bradyrhizobium japonicum, and Azorhizobium caulinodans. Transcription of nitrogen fixation genes (nif and fix genes) in these bacteria is induced primarily by low-oxygen conditions. Low-oxygen sensing and transmission of this signal to the level of nif and fix gene expression involve at least five regulatory proteins, FixL, FixJ, FixK, NifA, and RpoN (?54). The characteristic features of these proteins and their functions within species-specific regulatory pathways are described. Oxygen interferes with the activities of two transcriptional activators. FixJ and NifA, FixJ activity is modulated via phosphorylation-dephosphorylation by the cognate sensor hemoprotein FixL. In addition to the oxygen responsiveness of the NifA protein, synthesis of NifA is oxygen regulated at the level of transcription. This type of control includes FixLJ in R. meliloti and FixLJ- FixK in A. caulinodans or is brought about by autoregulation in B. japonicum. NifA, in concert with ?54 RNA polymerase, activates transcription from - 24/-12-type promoters associated with nif and fix genes and additional genes that are not directly involved in nitrogen fixation. The FixK proteins constitute a subgroup of the Crp-Fnr family of bacterial regulators. Although the involvement of FixLJ and FixK in nifA regulation is remarkably different in the three rhizobial species discussed here, they constitute a regulatory cascade that uniformly controls the expression of genes (fixNOQP) encoding a distinct cytochrome oxidase complex probably required for bacterial respiration under low-oxygen conditions. In B. japonicum, the FixLJ-FixK cascade also controls genes for nitrate respiration and for one of two ?54 proteins.},
      Year = {1994} }




@article{
Fisher92,
   Author = {Fisher, R.F. and Long, S.R.},
   Title = {Rhizobium-plant signal exchange},
   Journal = {Nature},
   Volume = {357},
   Number = {6380},
   Pages = {655-660},
   Abstract = {Inital stages in the Rhizobium-legume symbiosis can be thought of as a reciprocal molecular conversation: transmission of a gene inducer from legume host to bacterium, with ensuing bacterial synthesis of a morphogen that is transmitted to the plant, switching the developmental fate of the legume root. These signal molecules have a key role in determining bacterium-host specificity and the purified Nod factor compounds provide useful new tools to probe plant cell function.},
      Year = {1992} }




@article{
Fitter96,
   Author = {Fitter, A. H. and Moyersoen, B.},
   Title = {Evolutionary trends in root-microbe symbioses},
   Journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences},
   Volume = {351},
   Number = {1345},
   Pages = {1367-1375},
      Year = {1996} }




@book{
Fletcher-pc,
   Author = {Fletcher, M.},
   Publisher = {Landcare Research, Auckland, New Zealand},
      Year = {personal communication} }




@article{
Flores05,
   Author = {Flores, M. and Morales, L. and Avila, A. and Gonz\'alez, V. and Bustos, P. and García, D. and Mora, Y. and Guo, X. and Collado-Vides, J. and D\'avila, G. and Mora, J. and Palacios, R. and Pi\~nero, D.},
   Title = {Diversification of DNA sequences in the symbiotic genome of Rhizobium etli},
   Journal = {Journal of Bacteriology},
   Volume = {187},
   Number = {21},
   Pages = {7185-7192},
   Abstract = {Bacteria of the genus Rhizobium and related genera establish nitrogen-fixing symbioses with the roots of leguminous plants. The genetic elements that participate in the symbiotic process are usually compartmentalized in the genome, either as independent replicons (symbiotic plasmids) or as symbiotic regions or islands in the chromosome. The complete nucleotide sequence of the symbiotic plasmid of Rhizobium etli model strain CFN42, symbiont of the common bean plant, has been reported. To better understand the basis of DNA sequence diversification of this symbiotic compartment, we analyzed the distribution of single-nucleotide polymorphisms in homologous regions from different Rhizobium etli strains. The distribution of polymorphisms is highly asymmetric in each of the different strains, alternating regions containing very few changes with regions harboring an elevated number of substitutions. The regions showing high polymorphism do not correspond with discrete genetic elements and are not the same in the different strains, indicating that they are not hypervariable regions of functional genes. Most interesting, some highly polymorphic regions share exactly the same nucleotide substitutions in more than one strain. Furthermore, in different regions of the symbiotic compartment, different sets of strains share the same substitutions. The data indicate that the majority of nucleotide substitutions are spread in the population by recombination and that the contribution of new mutations to polymorphism is relatively low. We propose that the horizontal transfer of homologous DNA segments among closely related organisms is a major source of genomic diversification. Copyright © 2005, American Society for Microbiology. All Rights Reserved.},
      Year = {2005} }




@article{
Florindo03,
   Author = {Florindo, F. and Cooper, A. K. and O'Brien, P. E.},
   Title = {Introduction to `Antarctic Cenozoic palaeoenvironments: Geologic record and models'},
   Journal = {Palaeogeography, Palaeoclimatology, Palaeoecology},
   Volume = {198},
   Number = {1-2},
   Pages = {1-9},
      Year = {2003} }




@article{
Fogarty99,
   Author = {Fogarty, G. and Facelli, J. M.},
   Title = {Growth and competition of \emph{Cytisus scoparius}, an invasive shrub, and Australian native shrubs},
   Journal = {Plant Ecology},
   Volume = {144},
   Number = {1},
   Pages = {27-35},
   Abstract = {English broom (Cytisus scoparius) is an aggressive invasive shrub in native sclerophyll forests of South Australia. We studied its relative growth rate (RGR) and competitive ability in soils from invaded and uninvaded woodlands, in comparison to three native species it commonly displaces:Hakea rostrata, Acacia verniciflua, and A. myrtifolia. Hakea was the slowest growing species throughout the year. Both native species had their highest RGR during spring. The RGR of broom was higher than that of both hakea and acacia in the winter and spring. Despite losing its leaves in the summer, the RGR of broom through the year was higher than that of either of the native species. Soil from the invaded stands had higher organic C, N and soluble P than that from uninvaded sites. Broom and acacia grew better in the higher nutrient soil than in the lower nutrient soil. Competition did not decrease the final biomass of any of the species in low nutrient soil. In the higher nutrient soil the biomass of broom was reduced by competition with acacia, but not by competition with hakea. Competition by broom reduced the biomass of hakea but not that of acacia. Broom's earlier and higher RGR, high competitiveness in nutrient rich soils, and probably its ability to change nutrient availability could be important contributors to the mechanisms by which it invades native woodlands.},
      Year = {1999} }




@article{
Foster98,
   Author = {Foster, C. M. and Horner, H. T. and Graves, W. R.},
   Title = {Nodulation response of woody Papilionoid species after inoculation with rhizobia and soil from Hawaii, Asia and North America},
   Journal = {Plant and Soil},
   Volume = {205},
   Number = {2},
   Pages = {103-111},
   Abstract = {Among subfamilies in the Fabaceae, the capacity to form root nodules is most common in the Papilionoideae. Yet nodules have never been observed on species of Cladrastis, and there are conflicting reports of the capacity of species in the genus Styphnolobium to nodulate. Our objectives were to evaluate Styphnolobium japonicum (formerly Sophora japonica) and Cladrastis kentukea for the capacity to nodulate and to characterize any isolated rhizobia. N-deficient plants were inoculated with rhizobia chosen for their low host specificity or for their symbiotic potential with indigenous and introduced trees and shrubs of Sophora species in Hawaii, Japan and China. Soil samples from the root zones of mature S. japonicum, C. kentukea and other woody legumes, introduced or indigenous to Hawaii, Japan, China and the continental USA, also were used as inocula. Inoculation did not elicit nodulation of C. kentukea or S. japonicum, despite that N concentrations of shoots of S. japonicum (1.6%) and C. kentukea (1.5%) fell below the highest shoot N percentage that previously was associated with well-nodulated plants of Maackia amurensis (1.8%). In addition to these analyses, rhizobia were isolated from nodules on the roots of a tree reported to us as S. japonicum. Nine of the 10 isolates selected as representatives of similarity groups were capable of nodulating M. amurensis, which led to the identification of the putative S. japonicum as Maackia floribunda. We also found that broad-range Bradyrhizobium USDA 6, USDA 3384 and USDA 3456 induce nodules on R. pseudoacacia and M, amurensis, which were used as control species during inoculation trials with S. japonicum and C. kentukea. Our conclusion that S. japonicum and C. kentukea lack the capacity to nodulate is based on the most thorough analysis of the nodulation capacity of these species to date. Previous reports of nodulation of S. japonicum may have been due to inaccurate plant or nodule identification.},
      Year = {1998} }




@article{
Foster00,
   Author = {Foster, Carol M. and Horner, Harry T. and Graves, William R.},
   Title = {Accumulation of \emph{ENOD2}-like transcripts in non-nodulating woody Papilionoid legumes},
   Journal = {Plant Physiology},
   Volume = {124},
   Number = {2},
   Pages = {741-750},
   Abstract = {Japanese pagodatree (Styphnolobium japonicum [L.] Schott) and American yellowwood (Cladrastis kentukea Dum.-Cours.) Rudd are the first woody, non-nodulating papilionoid legumes shown to possess putative early nodulin 2 (ENOD2) genes. ENOD2 cDNAs from Japanese pagodatree (807 bp) and American yellowwood (735 bp) have 75% to 79% sequence identity to ENOD2 sequences and encode deduced proteins that possess conserved ENOD2 pentapeptides (PPHEK and PPEYQ). Lower percentages of glucose and higher percentages of histidine and valine suggest that SjENOD2 and CkENOD2 are different from other ENOD2s. Hybridization analyses indicate the clones represent ENOD2 gene families of two to four genes in Japanese pagodatree and American yellowwood genomes, and ENOD2-like transcripts were detected in stems and flowers, as well as roots. Only roots of control species that nodulate, Maackia amurensis Rupr. & Maxim. and alfalfa (Medicago sativa), produced pseudonodules after treatment with zeatin or 2,3,5-triiodobenzoic acid, an auxin transport inhibitor. Accumulation of MaENOD2 transcripts was enhanced during the first 10 d of treatment, but 2,3,5-triiodobenzoic acid and zeatin enhanced transcript accumulation after 30 d in roots of Japanese pagodatree and American yellowwood. Characteristics that distinguish ENOD2 gene families in basal, non-nodulating woody legumes from other ENOD2 genes may provide new information about the function of these genes during symbiotic and non-symbiotic organ development.},
      Year = {2000} }




@article{
Foucher00,
   Author = {Foucher, F. and Kondorosi, E.},
   Title = {Cell cycle regulation in the course of nodule organogenesis in Medicago},
   Journal = {Plant Molecular Biology},
   Volume = {43},
   Number = {5-6},
   Pages = {773-86},
   Abstract = {The molecular mechanisms of de novo meristem formation, cell differentiation and the integration of the cell cycle machinery into appropriate stages of the developmental programmes are still largely unknown in plants. Legume root nodules, which house nitrogen-fixing rhizobia, are unique plant organs and their development may serve as a model for organogenetic processes in plants. Nodules form and are essential for the plant only under limitation of combined nitrogen in the soil. Moreover, their development is triggered by external mitogenic signals produced by their symbiotic partners, the rhizobia. These signals, the lipochitooligosaccharide Nod factors, act as host-specific morphogens and induce the re-entry of root cortical cells into mitotic cycles. Maintenance of cell division activity leads to the formation of a persistent nodule meristem from which cells exit continuously and enter the nodule differentiation programme, involving multiple cycles of endoreduplication and enlargement of nuclear and cell volumes. While the small diploid 2C cells remain uninfected, the large polyploid cells can be invaded and, after completing the differentiation programme, host the nitrogen-fixing bacteroids. This review summarizes the present knowledge on cell cycle reactivation and meristem formation in response to Nod factors and reports on a novel plant cell cycle regulator that can switch mitotic cycles to differentiation programmes.},
   Keywords = {Cell Cycle
Cell Cycle Proteins
metabolism
Cell Differentiation
Cyclins
Growth Substances
Lipopolysaccharides
Medicago sativa
cytology
microbiology
Nitrogen Fixation
Plant Proteins
Plant Roots
Sinorhizobium meliloti
pathogenicity
physiology
Symbiosis},
   Year = {2000} }




@article{
Founoune02a,
   Author = {Founoune, H. and Duponnois, R. and Bâ, A.M.},
   Title = {Ectomycorrhization of Acacia mangium, Willd. and Acacia holosericea, A. Cunn. ex G. Don in Senegal. Impact on plant growth, populations of indigenous symbiotic microorganisms and plant parasitic nematodes},
   Journal = {Journal of Arid Environments},
   Volume = {50},
   Number = {2},
   Pages = {325-332},
   Abstract = {The ectomycorrhization of two Australian Acacia species (A. mangium and A. holosericea) with two basidiomycetes (Pisolithus and Scleroderma) was studied in sterilized and unsterilized soils. The three fungal isolates, two exotic strains (Pisolithus COI 007 and COI 024) and one indigenous (Sclerodermal) enhanced the development of the Acacia species. In the unsterilized soil, the number of nodules per plant of indigenous rhizobia was increased when the plants had associated mycorrhizae. The plant parasitic nematode community was reduced by the fungal strains, especially for H. pararobustus with A. holosericea. The ectomycorrhizal associations of the Australian Acacias, mostly unknown in West Africa, appears to be very promising for use of these trees in afforestation programs. © 2002 Elsevier Science Ltd.},
   Keywords = {Acacia
Mycorrhizae
Plant parasitic nematodes
Reforestation
Rhizobia
Senegal},
   Year = {2002} }




@article{
Founoune02b,
   Author = {Founoune, H. and Duponnois, R. and Meyer, J.M. and Thioulouse, J. and Masse, D. and Chotte, J.L. and Neyra, M.},
   Title = {Interactions between ectomycorrhizal symbiosis and fluorescent pseudomonads on Acacia holosericea: Isolation of mycorrhiza helper bacteria (MHB) from a Soudano-Sahelian soil},
   Journal = {FEMS Microbiology Ecology},
   Volume = {41},
   Number = {1},
   Pages = {37-46},
   Abstract = {Acacia holosericea seedlings were planted in 1-l pots filled with a soil collected from an Australian Acacia plantation in Southern Senegal. After 6 months of culture, mycorrhizosphere soil, roots, galls induced by root-knot nematodes and Rhizobium nodules were sampled from each pot. The diversity of this bacterial group was characterized by siderotyping (pyoverdine IsoElectric Focusing (IEF) analysis) and by restriction fragment length polymorphism (RFLP). The effect of these isolates on the establishment of the ectomycorrhizal symbiosis between an Australian Acacia (A. holosericea) and Pisolithus sp. strain IR100 was studied. In the mycorrhizosphere soil, the population of fluorescent pseudomonads was represented by strains of two different siderovars (groups of bacterial strains presenting an identical pyoverdine-IEF pattern): siderovar 1 (74%) and siderovar 2 (26%). The siderotyping of the isolates around galls of the root-knot nematodes revealed three siderovars (40% from siderovar 1, 40% from siderovar 2 and about 15% from siderovar 3). RFLP of 16S rDNA divided the isolates into four different groups with MspI, two with HhaI and two with HaeIII endonucleases. The establishment of the ectomycorrhizal symbiosis with A. holosericea was promoted by 14 bacterial strains isolated from the mycorrhizosphere soil, three isolates from the roots and four from the galls. Shoot biomass of A. holosericea seedlings was stimulated by eight bacterial isolates from soil, six isolates from galls and seven from roots. These mycorrhiza helper bacteria could have a great ecological importance in tropical areas through the reforestation programs. © 2002 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.},
   Keywords = {Acacia holosericea
Ectomycorrhizal symbiosis
Fluorescent pseudomonad
Pisolithus sp.
Restriction fragment length polymorphism
Siderotyping},
   Year = {2002} }




@article{
Fountain91,
   Author = {Fountain, D. W. and Outred, H. A.},
   Title = {Germination requirements of New Zealand native plants: a review},
   Journal = {New Zealand Journal of Botany},
   Volume = {29},
   Pages = {311-316},
      Year = {1991} }




@article{
Fowler00,
   Author = {Fowler, S. V. and Syrett, P.},
   Title = {Status of broom in New Zealand},
   Journal = {Plant Protection Quarterly},
   Volume = {15},
   Number = {4},
   Pages = {148},
      Year = {2000} }




@article{
Fremont99,
   Author = {Fr\'emont, M. and Pwee, K. H. and Tan, T. K. and Prin, Y. and Diem, H. G. and Chauvi\'ere, M.},
   Title = {A comparison of \emph{Bradyrhizobium} strains using molecular, cultural and field studies},
   Journal = {Plant Science},
   Volume = {141},
   Number = {1},
   Pages = {81-91},
   Abstract = {Acacia mangium is a leguminous tree used in industrial plantations for the production of pulp wood, and for the rehabilitation of degraded soils. Its ability to grow in very poor soils is due to its symbiotic association with nitrogen-fixing Bradyrhizobium. In this study, 33 isolates of Bradyrhizobium and Rhizobium obtained from A. mangium plantations in Sabah, Malaysia, were characterised by PCR amplification of ribosomal DNA and RFLP analysis, host spectrum and antibiotic resistance. The Sabah isolates were also compared with isolates collected from Singapore, Australia, and Africa. The results distinguished two main groups of Bradyrhizobium. Group I strains were prevalent, widely dispersed but genetically closely related. They were also closely related to the Singapore and Australian strains. Strains from Group II were less widely dispersed and more distantly related. Greenhouse and field inoculation trials with A. mangium seedlings showed that the Group I strains were more effective in enhancing plant growth than Group II strains.},
   Keywords = {A. mangium
Bradyrhizobium
Nitrogen-fixing bacteria
Rhizobium},
   Year = {1999} }




@article{
Frank79,
   Author = {Frank, B.},
   Title = {Ueber die Parasiten in den Wurzelanschwillungen der Papilionaceen},
   Journal = {Botanische Zeitung},
   Volume = {37},
   Pages = {376-387, 394-399},
      Year = {1879} }




@article{
Frank89,
   Author = {Frank, B.},
   Title = {Ueber die Pilzsymbiose der Leguminosen},
   Journal = {Berichte der Deutschen Botanischen Gesellschaft},
   Volume = {7},
   Pages = {332-346},
      Year = {1889} }




@article{
Frank92,
   Author = {Frank, S. A.},
   Title = {Models of plant--pathogen coevolution},
   Journal = {Trends in Genetics},
   Volume = {8},
   Number = {6},
   Pages = {213-219},
   Abstract = {Plant populations are often genetically polymorphic for resistance to pathogens. The effectiveness of this resistance is limited because the pathogens are, in turn, polymorphic for virulence genes that can evade plant resistance. Theoretical models and intriguing preliminary data suggest that these plant-pathogen polymorphisms are maintained by continual cycles of coevolution within populations, combined with occasional immigration of new virulence and resistance genes from distant populations.},
      Year = {1992} }




@article{
Fraysse03,
   Author = {Fraysse, N. and Couderc, F. and Poinsot, V.},
   Title = {Surface polysaccharide involvement in establishing the \emph{Rhizobium}--legume symbiosis},
   Journal = {European Journal of Biochemistry},
   Volume = {270},
   Number = {7},
   Pages = {1365-1380},
   Abstract = {When the rhizosphere is nitrogen-starved, legumes and rhizobia (soil bacteria) enter into a symbiosis that enables the fixation of atmospheric dinitrogen. This implies a complex chemical dialogue between partners and drastic changes on both plant roots and bacteria. Several recent works pointed out the importance of rhizobial surface polysaccharides in the establishing of the highly specific symbiosis between symbionts. Exopolysaccharides appear to be essential for the early infection process. Lipopolysaccharides exhibit specific roles in the later stages of the nodulation processes such as the penetration of the infection thread into the cortical cells or the setting up of the nitrogen-fixing phenotype. More generally, even if active at different steps of the establishing of the symbiosis, all the polysaccharide classes seem to be involved in complex processes of plant defense inhibition that allow plant root invasion. Their chemistry is important for structural recognition as well as for physico-chemical properties.},
   Keywords = {Infection
Junction
Polysaccharide
Rhizobium
Role
Symbiosis
lipopolysaccharide
polysaccharide
symbiosis},
   Year = {2003} }




@article{
Freiberg97,
   Author = {Freiberg, C. and Rosenthal, A. and Fellay, R. and Broughton, W. J. and Perret, X. and Bairoch, A.},
   Title = {Molecular basis of symbiosis between Rhizobium and legumes},
   Journal = {Nature},
   Volume = {387},
   Number = {6631},
   Pages = {394-401},
   Abstract = {Access to mineral nitrogen often limits plant growth, and so symbiotic relationships have evolved between plants and a variety of nitrogen-fixing organisms. These associations are responsible for reducing 120 million tonnes of atmospheric nitrogen to ammonia each year. In agriculture, independence from nitrogenous fertilizers expands crop production and minimizes pollution of water tables, lakes and rivers. Here we present the complete nucleotide sequence and gene complement of the plasmid from Rhizobium sp. NGR234 that endows the bacterium with the ability to associate symbiotically with leguminous plants. In conjunction with transcriptional analyses, these data demonstrate the presence of new symbiotic loci and signalling mechanisms. The sequence and organization of genes involved in replication and conjugal transfer are similar to those of Agrobacterium, suggesting a recent lateral transfer of genetic information.},
      Year = {1997} }




@article{
Friedman82,
   Author = {Friedman, A. M. and Long, S. R. and Brown, S. E.},
   Title = {Construction of a broad host range cosmid cloning vector and its use in the genetic analysis of Rhizobium mutants},
   Journal = {Gene},
   Volume = {18},
   Number = {3},
   Pages = {289-296},
      Year = {1982} }




@article{
Frioni98,
   Author = {Frioni, F. and Malates, D. and Irigoyen, I. and Dodera, R.},
   Title = {Promiscuity for nodulation and effectivity in the N2-fixing legume tree Acacia caven in Uruguay},
   Journal = {Applied Soil Ecology},
   Volume = {7},
   Number = {3},
   Abstract = {The leguminous Acacia caven, Erythrina crista-galli, Enterolobium contortisiliquum, Prosopis affinis and P. nigra nodulated with rhizobial strains isolated from other legume trees; therefore they were considered to be promiscuous (poorly specific) for nodulation. Sesbania punicea and Parapiptadenia rigida did not nodulate with the different strains, indicating a significant specificity for nodulation. A. caven was promiscuous for nodulation and nodulated with both fast- and slow-growing strains of rhizobia and our data suggest that the most efficient strains would be fast-growing rhizobia. A. caven was specific for effectivity since the amount of N2 which was fixed markedly depended on the strain. The relative efficiency (RE) of 6 out of the 11 strains used was higher than 0.80, suggesting they had an active hydrogenase. Ac5, a strain isolated from A. caven, exhibited the highest N2-fixing ability and highest NE (nodule efficiency) when inoculated on its host and also had the highest RE. Shoot dry weight and acetylene reducing activity (ARA) were significantly correlated with the amount of N2 fixed (determined by the total nitrogen difference method), indicating that any of these methods could be used for screening the strains according to their ability to fix N2. The relative efficiency was not correlated with any of these parameters.},
      Year = {1998} }




@article{
Frioni01,
   Author = {Frioni, L. and Rodriguez, A. and Meerhoff, M.},
   Title = {Differentiation of rhizobia isolated from native legume trees in Uruguay},
   Journal = {Applied Soil Ecology},
   Volume = {16},
   Number = {3},
   Pages = {275-282},
   Abstract = {Legume trees are symbiotically associated with rhizobia and mycorrhizal fungi, microorganisms that improve their growth. The objective of this work was to characterize 61 rhizobial isolates from eight species of native legume trees: Acacia caven, Inga uruguensis, Lonchocarpus nitidus, Prosopis nigra, Sesbania virgata, Peltophorum dubium, Enterolobium contortisiliquum and Erythrina crista-galli. The strains were isolated from nodules with high nitrogenase activity and their growth rate, antibiotic, salinity and acidity resistances were determined. Their relationships were analyzed building a matrix with the resistance characteristics. Most of the isolates were fast growers and acid-producing with high level of exopolysaccharides. In general, isolates were erythromycin resistant but sensitive to rifampicin. All the isolates grew well at pH 5.5 while 75% did so at pH 4.4. More than 60% of the isolates grew in 2% of NaCl but this declined to 21% of the isolates in 3% NaCl. This population showed high antibiotic, salinity and pH resistance, suggesting adaptability to major ecological environment stresses, and great saprohytic competence within soil environments. Isolates from the same host showed high homology between them. (C) 2001 Elsevier Science B.V. All rights reserved.},
      Year = {2001} }




@article{
Fuchs80,
   Author = {Fuchs, R. L. and Keister, D. L.},
   Title = {Identification of two glutamine synthetases in Agrobacterium},
   Journal = {Journal of Bacteriology},
   Volume = {141},
   Number = {2},
   Pages = {996-8},
   Abstract = {Two distinct glutamine synthetases have been identified in Agrobacterium and in the fast-growing rhizobia. A limited survey indicates that GSII may be found only in the Rhizobiaceae family.},
   Keywords = {Cell-Free System
Glutamate-Ammonia Ligase/*analysis/metabolism
Isoenzymes/*analysis/metabolism
Molecular Weight
Peptides/analysis
Phenylmethylsulfonyl Fluoride/pharmacology
Rhizobium/*enzymology
Species Specificity
Support, U.S. Gov't, Non-P.H.S.
gamma-Glutamyltransferase/metabolism},
   Year = {1980} }




@article{
Fukuda05,
   Author = {Fukuda, T. and Nakamura, T. and Song, I.-J. and Ito, T. and Kanno, A. and Kameya, T. and Yokoyama, J. and Maki, M. and Ochiai, T.},
   Title = {Molecular phylogeny and evolution of alcohol dehydrogenase (Adh) genes in legumes},
   Journal = {BMC Plant Biology},
   Volume = {5},
   Abstract = {Background: Nuclear genes determine the vast range of phenotypes that are responsible for the adaptive abilities of organisms in nature. Nevertheless, the evolutionary processes that generate the structures and functions of nuclear genes are only now be coming understood. The aim of our study is to isolate the alcohol dehydrogenase (Adh) genes in two distantly related legumes, and use these sequences to examine the molecular evolutionary history of this nuclear gene. Results: We isolated the expressed Adh genes from two species of legumes, Sophora flavescens Ait. and Wisteria floribunda DC., by a RT-PCR based approach and found a new Adh locus in addition to homologues of the Adh genes found previously in legumes. To examine the evolution of these genes, we compared the species and gene trees and found gene duplication of the Adh loci in the legumes occurred as an ancient event. Conclusion: This is the first report revealing that some legume species have at least two Adh gene loci belonging to separate clades. Phylogenetic analyses suggest that these genes resulted from relatively ancient duplication events. © 2005 Fukuda et al; licensee BioMed Central Ltd.},
      Year = {2005} }




@article{
Gadgil01,
   Author = {Gadgil, R.L. and Douglas, G.B. and Ede, F.J. and Beeser, H.F. and Foote, A.G.},
   Title = {Establishment of nitrogen-fixing plants from seed on partially stabilised coastal sand},
   Journal = {New Zealand Journal of Forestry Science},
   Volume = {31},
   Number = {3},
   Pages = {339-346},
   Abstract = {Seeds of eight nitrogen-fixing species (Acacia saligna H. Wendl., Acacia sophorae (Labill.) C. Martius. Astragalus cicer L., Chamaecytisus palmensis (Christ) Bisby et K. Nicholls, Doryenium hirsutum (L.) Ser., Lathyrus latifolius L., Lotus pedunculatus Schk., Teline stenopetala Webb et Berth.) which tolerate the coastal sand dune environment when introduced as healthy plants, were broadcast-sown in 1995 at two sites on sand dunes which had been partially stabilised by planting marram grass (Ammophila arenaria L.). Establishment rates of 0-1% of viable seed sown after 6 months and 0-9% after 10 months, were considered to be unsatisfactory for sand revegetation purposes. Other trials at the two sites commenced in 1996 and compared the effects of three sowing methods on establishment rates of Lathyrus latifolius and Lotus pedunculatus. Lupinus arboreus Sims, once successful in this habitat but now attacked by a fungal disease before reaching full maturity, was included as a benchmark species. Sand accretion resulted in establishment failure at one site but at the other site L. arboreus provided satisfactory vegetation cover within 6 months (84-99% where seed had been partially or completely buried; 31% where seed had been broadcast-sown). Plot coverage by the other two species did not exceed 4%. Results of these trials do not explain why establishment rates were low in species other than Lupinus arboreus, but indicate that direct seeding is unlikely to be a satisfactory technique for establishing most nitrogen-fixing species on sand partially stabilised by the planting of a sand-binding grass. Enhancement of the chronically low nitrogen status of coastal sand in order to promote effective vegetation cover continues to depend on either frequent fertiliser application or the introduction of nursery-raised, nitrogen-fixing plants.},
   Keywords = {Coastal sand
Establishment
Legumes
New Zealand
Nitrogen
Revegetation
Species performance
Biodiversity
Diseases
Nitrogen fixation
Sand
Seed
Vegetation
Coastal sands
Plants (botany)
dune
habitat creation
nitrogen fixation
seeding
seedling establishment
stabilization
New Zealand
Acacia saligna
Acacia sophorae
Ammophila arenaria
Astragalus cicer
Chamaecytisus palmensis
Dorycnium hirsutum
Lathyrus latifolius
Lotus pedunculatus
Lupinus arboreus
Teline stenopetala},
   Year = {2001} }




@article{
Gadgil99,
   Author = {Gadgil, R. L. and Lowe, A. T. and Sandberg, A. M.},
   Title = {Two seedling rooting media and subsequent growth of nitrogen-fixing plants in a New Zealand coastal sand-dune environment},
   Journal = {New Zealand Journal of Forestry Science},
   Volume = {29},
   Number = {2},
   Pages = {195-202},
   Abstract = {Continuous vegetation cover preventing erosion of coastal sand dunes is essential for the protection and development of productive forestry, farming, and other activities in their vicinity. Use of symbiotic nitrogen fixation to enhance the nutritional status (and thus the vigour) of sand dune vegetation currently depends on the introduction of nursery-raised plants. Local sand and a standard nursery potting compost were seen as possible alternatives for seedling rooting media, but their relative effects on plant performance after transfer to exposed dune sites were unknown. Three nitrogen-fixing species representing a range of tolerance to dune conditions in the north of the North Island (Acacia sophorae (Labill.) C. Martius, Chamaecytisus palmensis (Christ) Bisby et K. Nicholls, and Lotus uliginosus Schk.) were used as the basis for comparison. A slight overall plant size advantage was associated with potting compost during the first year after transplanting, but this was not maintained during the second and third years. Long-term plant survival was not influenced by seedling rooting medium, although mortality of C. palmensis (the least tolerant species) was twice as great in compost-raised plants as in sand-raised plants during the first 6 months. There was no evidence of any consistent effect of seedling rooting medium on relative nitrogenase activity. It was concluded that choice of medium for raising seedlings in the nursery is likely to have only a minor and transitory effect on the performance of nitrogen-fixing plants in sand-dune revegetation projects and species-screening trials.},
   Keywords = {Coastal sand
Nitrogen fixation
Revegetation
Rooting media
Seedling production
plant growth
rooting medium
seedling
dune
growth
nitrogen fixation
nutritional status
productivity
revegetation
New Zealand
Acacia sophorae
Chamaecytisus palmensis
Lotus uliginosus},
   Year = {1999} }




@article{
Gage04,
   Author = {Gage, D. J.},
   Title = {Infection and invasion of roots by symbiotic, nitrogen-fixing rhizobia during nodulation of temperate legumes},
   Journal = {Microbiology and Molecular Biology Reviews},
   Volume = {68},
   Number = {2},
   Pages = {280-300},
   Abstract = {Bacteria belonging to the genera Rhizobium, Mesorhizobium, Sinorhizobium, Bradyrhizobium, and Azorhizobium (collectively referred to as rhizobia) grow in the soil as free-living organisms but can also live as nitrogen-fixing symbionts inside root nodule cells of legume plants. The interactions between several rhizobial species and their host plants have become models for this type of nitrogen-fixing symbiosis. Temperate legumes such as alfalfa, pea, and vetch form indeterminate nodules that arise from root inner and middle cortical cells and grow out from the root via a persistent meristem. During the formation of functional indeterminate nodules, symbiotic bacteria must gain access to the interior of the host root. To get from the outside to the inside, rhizobia grow and divide in tubules called infection threads, which are composite structures derived from the two symbiotic partners. This review focuses on symbiotic infection and invasion during the formation of indeterminate nodules. It summarizes root hair growth, how root hair growth is influenced by rhizobial signaling molecules, infection of root hairs, infection thread extension down root hairs, infection thread growth into root tissue, and the plant and bacterial contributions necessary for infection thread formation and growth. The review also summarizes recent advances concerning the growth dynamics of rhizobial populations in infection threads.},
      Year = {2004} }




@article{
Gage96,
   Author = {Gage, D. J. and Bobo, T. and Long, S. R.},
   Title = {Use of green fluorescent protein to visualize the early events of symbiosis between Rhizobium meliloti and alfalfa (Medicago sativa)},
   Journal = {Journal of Bacteriology},
   Volume = {178},
   Number = {24},
   Pages = {7159-7166},
   Abstract = {A gene encoding a variant of green fluorescent protein (GFP) of Aequorea victoria was put under the control of a promoter which is constitutive in Rhizobium meliloti. The heterologous GFP gene was expressed at high levels during all stages of symbiosis, allowing R. meliloti cells to be visualized as they grew in the rhizosphere, on the root surface, and inside infection threads. In addition, nodules that were infected with bacteria which were synthesizing GFP fluoresced when illuminated with blue light. GFP-tagged bacteria could be seen inside infection threads, providing the opportunity to measure the growth rate and determine the patterns of growth of R. meliloti residing inside its host plant.},
      Year = {1996} }




@article{
Gage00,
   Author = {Gage, D. J. and Margolin, W.},
   Title = {Hanging by a thread: invasion of legume plants by rhizobia},
   Journal = {Current Opinion in Microbiology},
   Volume = {3},
   Number = {6},
   Pages = {613-7},
   Abstract = {Nitrogen-fixing nodules on plants such as alfalfa, pea and vetch arise from the root inner cortex and grow via a persistent meristem. Thus, these nodules are defined as indeterminate. The formation of functional indeterminate nodules requires that symbiotic bacteria, collectively called rhizobia, gain access to the interior of roots and root nodules via infection threads. Recent work has begun to elucidate the important functions of the root cell cytoskeleton in infection thread formation. It has also recently become apparent that rhizobial Nod factors and rhizobial exopolysaccharides play key roles in the initiation and elongation of infection threads.},
   Keywords = {Calcium-Binding Proteins
physiology
Fabaceae
microbiology
Genes
Bacterial
Plant Roots
Plants
Medicinal
Polysaccharides
Rhizobium
pathogenicity
Support
Non-U.S.Gov't
U.S.Gov't
Non-P.H.S.
P.H.S.},
   Year = {2000} }




@article{
Galibert01,
   Author = {Galibert, Francis and Finan, Turlough M. and Long, Sharon R. and Puhler, Alfred and Abola, Pia and Ampe, Frederic and Barloy-Hubler, Frederique and Barnett, Melanie J. and Becker, Anke and Boistard, Pierre and Bothe, Gordana and Boutry, Marc and Bowser, Leah and Buhrmester, Jens and Cadieu, Edouard and Capela, Delphine and Chain, Patrick and Cowie, Alison and Davis, Ronald W. and Dreano, Stephane and Federspiel, Nancy A. and Fisher, Robert F. and Gloux, Stephanie and Godrie, Therese and Goffeau, Andre and Golding, Brian and Gouzy, Jerome and Gurjal, Mani and Hernandez-Lucas, Ismael and Hong, Andrea and Huizar, Lucas and Hyman, Richard W. and Jones, Ted and Kahn, Daniel and Kahn, Michael L. and Kalman, Sue and Keating, David H. and Kiss, Erno and Komp, Caridad and Lelaure, Valerie and Masuy, David and Palm, Curtis and Peck, Melicent C. and Pohl, Thomas M and Portetelle, Daniel and Purnelle, Benedicte and Ramsperger, Uwe and Surzycki, Raymond and Thebault, Patricia and Vandenbol, Micheline and Vorholter, Frank-J. and Weidner, Stefan and Wells, Derek H. and Wong, Kim and Yeh, Kuo-Chen and Batut, Jacques},
   Title = {The composite genome of the legume symbiont \emph{Sinorhizobium meliloti}},
   Journal = {Science},
   Volume = {293},
   Number = {5530},
   Pages = {668-672},
      Year = {2001} }




@article{
Galli03,
   Author = {Galli-Terasawa, L. V. and Glienke-Blanco, C. and Hungria, M.},
   Title = {Diversity of a soybean rhizobial population adapted to a Cerrados soil},
   Journal = {World Journal of Microbiology and Biotechnology},
   Volume = {19},
   Number = {9},
   Pages = {933-939},
   Abstract = {One hundred isolates were trapped by soybean (Glycine max) plants inoculated with a soil from the Cerrados, the main producing area in Brazil. The soil was originally void of rhizobia able to nodulate soybean, and 15 years before received inoculant containing Bradyrhizobium elkanii strains SEMIA 587 and SEMIA 5019; the area has been annually cropped with soybean since then, but with no further inoculation for the past 7 years. Enormous diversity was observed among the isolates, with thirteen serologically distinct groups, twelve protein and seven lipopolysaccharide profiles; no more than five isolates shared similar characteristics. An unexpected feature was that 48% of the isolates showed multiple reactions with the antisera to the serogroups established in the soils. Also 40% of the isolates reacted with the antiserum to B. japonicum strain SEMIA 566, that has never been introduced into the soil, probably due to dispersion from other cropping areas, associated with its high saprophytic competence; 13% of the isolates did not react with any of the antisera. Nodulation and N2 fixation capacity also varied considerably among the isolates. Although one third of the isolates were fast growers with an acid reaction in vitro, and many formed pseudo-nodules on common bean (Phaseolus vulgaris), they shared several properties with the Bradyrhizobium inoculant strains. A high level of genetic diversity was confirmed when the DNAs were amplified with BOX and RPO1 primers, and several isolates were positioned in far different clusters in the analysis of interspersed repetitive or nif-directed sequences. Moreover, serological properties showed higher correlation with BOX than with RPO1 products. The high diversity could be attributed both to lateral transfer of genetic material between inoculant and indigenous strains and to genomic rearrangements during the adaptation to the Cerrados, and may play an important role as a biological buffer, avoiding the dominance of a particular strain.},
      Year = {2003} }




@article{
Gao01,
   Author = {Gao, J. and Terefework, Z. and Chen, W. and Lindstr\"om, K.},
   Title = {Genetic diversity of rhizobia isolated from \emph{Astragalus adsurgens} growing in different geographical regions of China},
   Journal = {Journal of Biotechnology},
   Volume = {91},
   Number = {2-3},
   Pages = {155-168},
   Abstract = {The genetic diversity among 95 isolates from Astragalus adsurgens was investigated using molecular biological methods. All of the isolates and 24 reference strains could be differentiated by AFLP, REP-, ERIC- and BOX-PCR fingerprinting analysis. By cluster analysis of the data, 31 AFLP and 38 Rep-PCR genomic groups were delineated, indicating considerable genetic diversity among the isolates. Fifty-four representative strains were further analyzed by RFLP of PCR-amplified 16S and 23S rDNA, revealing 26 rDNA genotypes among the isolates. The phylogenetic relationship of the isolates was determined by partial sequencing of 16S rRNA genes of 16 strains. The results suggest that the A. adsurgens rhizobia belong to the genera Agrobacterium, Mesorhizobium, Rhizobium and Sinorhizobium. © 2001 Elsevier Science B.V. All rights reserved.},
   Keywords = {Astragalus adsurgens
Diversity
PCR fingerprinting
Phylogeny
Rhizobia
DNA
Genes
Geographical regions
RNA
Genetic diversity
Genetic engineering
argobacterium
biodiversity
Mesorhizobium
Rhizobium
Sinorhizobium
Variation (Genetics)
Agrobacterium
Astragalus adsurgens
Mesorhizobium
Rhizobium
Sinorhizobium},
   Year = {2001} }




@article{
Gao94,
   Author = {Gao, J. L. and Sun, J. G. and Li, Y. and Wang, E. T. and Chen, W. X.},
   Title = {Numerical taxonomy and DNA relatedness of tropical rhizobia isolated from Hainan Province, China},
   Journal = {International Journal of Systematic Bacteriology},
   Volume = {44},
   Number = {1},
   Pages = {151-158},
   Abstract = {A total of 63 strains of rhizobia isolated from Hainan Province, a tropical region of the People's Republic of China, and 27 representative strains belonging to the genera Rhizobium, Bradyrhizobium, and Agrobacterium were compared by performing numerical taxonomy, DNA hybridization, and DNA base composition analysis to determine the relationships among these rhizobia. The results indicated that the strains isolated from Hainan Province fell into two distinct phena, the slowly growing rhizobia and the fast-growing rhizobia. The slowly growing rhizobia, which formed three subphena that seemed to be three subspecies, are Bradyrhizobium japonicum strains. The fast-growing strains belong to the genus Rhizobium and might be further divided into three specific groups. Sometimes both slowly growing rhizobia and fast-growing rhizobia were isolated from host plants belonging to the same genus or species or even from the same nodule. There was no correlation between hosts and the distribution of rhizobia in the subphena. Isolates obtained from members of the same host genus or species fell into different groups or subgroups.},
   Keywords = {agrobacterium
rhizobium
rhizobium japonicum},
   Year = {1994} }




@article{
Gao04b,
   Author = {Gao, Jun-Lian and Turner, Sarah Lea and Kan, Feng Ling and Wang, En Tao and Tan, Zhi Yuan and Qiu, Yu Hui and Gu, Jun and Terefework, Zewdu and Young, J. Peter W. and Lindstr\"om, Kristina and Chen, Wen Xin},
   Title = {\emph{Mesorhizobium septentrionale} sp. nov. and \emph{Mesorhizobium temperatum} sp. nov., isolated from \emph{Astragalus adsurgens} growing in the northern regions of China},
   Journal = {International Journal of Systematic and Evolutionary Microbiology},
   Volume = {54},
   Number = {6},
   Pages = {2003-2012},
   Abstract = {Ninety-five rhizobial strains isolated from Astragalus adsurgens growing in the northern regions of China were classified into three main groups, candidate species I, II and III, based on a polyphasic approach. Comparative analysis of full-length 16S rRNA gene sequences of representative strains showed that candidate species I and II were Mesorhizobium, while candidate species III, which consisted of non-nodulating strains, was closely related to Agrobacterium tumefaciens. The phylogenetic relationships of the three candidate species and some related strains were also confirmed by the sequencing of glnA genes, which were used as an alternative chromosomal marker. The DNA-DNA relatedness was between 11{middle dot}3 and 47{middle dot}1 % among representative strains of candidate species I and II and the type strains of defined Mesorhizobium species. Candidate III had DNA relatedness of between 4{middle dot}3 and 25{middle dot}2 % with type strains of Agrobacterium tumefaciens and Agrobacterium rubi. Two novel species are proposed to accommodate candidate species I and II, Mesorhizobium septentrionale sp. nov. (type strain, SDW014T=CCBAU 11014T=HAMBI 2582T) and Mesorhizobium temperatum sp. nov. (type strain, SDW018T=CCBAU 11018T=HAMBI 2583T), respectively. At least two distinct nodA sequences were identified among the strains. The numerically dominant nodA sequence type was most similar to that from the Mesorhizobium tianshanense type strain and was identified in strains belonging to the two novel species as well as other, as yet, undefined genome types. Host range studies indicate that the different nodA sequences correlate with different host ranges. Further comparative studies with the defined Agrobacterium species are needed to clarify the taxonomic identity of candidate species III.},
      Year = {2004} }




@article{
Gao04a,
   Author = {Gao, L. and Deng, X. and Wang, H. and Hu, Z.},
   Title = {Diversity and resistance of rhizobia isolated from \emph{Caragana intermedia} in Maowusu sandland},
   Journal = {Ying Yong Sheng Tai Xue Bao},
   Volume = {15},
   Number = {1},
   Pages = {44-8. In Chinese, English summary},
   Abstract = {Fifteen rhizobia strains were isolated from wild shrubby legume Caragana intermedia in Maowusu sandland. A dendrogram was constructed based on esterase profiles, showing a rich diversity of these rhizobia. Many biochemical characteristics were detected, including acid or alkali production, catalase activity, utilization of sole carbon sources, and resistance to salt, acid-alkali and temperature variation. The results indicated that all the rhizobia strains isolated from Caragana intermedia could excrete H+ on YMA agar and produce catalase. 73.3% strains could tolerate NaCl stress at 3% concentration, and 80% strains could grow at 50 degrees C. Except the difference in lactose and starch utilization, rhizobia strains had no bias on the rest carbon sources. However, the difference in resistance to stress existed among strains, which might be related to the adaptation of rhizobia to diverse landscapes in Maowusu sandland. It was revealed that rhizobia nodulating Caragana intermedia could be used as a new germplasm to fix nitrogen under severe environment.},
   Keywords = {Caragana/*microbiology
Culture Media
English Abstract
Hydrogen-Ion Concentration
Rhizobium/*isolation \& purification
Sodium Chloride/pharmacology
Support, Non-U.S. Gov't
Temperature},
   Year = {2004} }




@article{
Garnock98,
   Author = {Garnock-Jones, P. J. and Breitwieser, I.},
   Title = {New Zealand floras and systematic botany: Progress and prospects},
   Journal = {Australian Systematic Botany},
   Volume = {11},
   Number = {2},
   Pages = {175-184},
   Abstract = {Botanists have produced vascular plant Floras of New Zealand at regular intervals since 1775. The current tracheophyte Flora series is nearing completion, but early volumes already need major revision. There are few Flora treatments covering algae and fungi. Moss and liverwort Floras are in early stages, while the Lichen Flora is now under revision. Current research attention is focused on revisions of critical groups, phylogenetic studies to investigate generic circumscriptions or family placements, and provision of new tools for plant identification. Plans are under way to produce an Excursion Flora.},
      Year = {1998} }




@book{
Bergeys-outline,
   Author = {Garrity, G. M. and Bell, J. A. and Lilburn, T. G.},
   Title = {Taxonomic outline of the prokaryotes, Bergey's Manual of Systematic Bacteriology, second edition,  Release 5.0 May 2004},
   Publisher = {Bergey's Manual Trust},
      Year = {2004} }




@article{
Gaude04,
   Author = {Gaude, N. and Tippmann, H. and Udvardi, M. and Dörmann, P. and Flemetakis, E. and Katinakis, P.},
   Title = {The galactolipid digalactosyldiacylglycerol accumulates in the peribacteroid membrane of nitrogen-fixing nodules of soybean and Lotus},
   Journal = {Journal of Biological Chemistry},
   Volume = {279},
   Number = {33},
   Pages = {34624-34630},
   Abstract = {The peribacteroid membrane (PBM) surrounding nitrogen fixing rhizobia in the nodules of legumes is crucial for the exchange of ammonium and nutrients between the bacteria and the host cell. Digalactosyldiacylglycerol (DGDG), a galactolipid abundant in chloroplasts, was detected in the PBM of soybean (Glycine max) and Lotus japonicus. Analyses of membrane marker proteins and of fatty acid composition confirmed that DGDG represents an authentic PBM lipid of plant origin and is not derived from the bacteria or from plastid contamination. In Arabidopsis, DGDG is known to accumulate in extraplastidic membranes during phosphate deprivation. However, the presence of DGDG in soybean PBM was not restricted to phosphate limiting conditions. Complementary DNA sequences corresponding to the two DGDG synthases, DGD1 and DGD2 from Arabidopsis, were isolated from soybean and Lotus. The two genes were expressed during later stages of nodule development in infected cells and in cortical tissue. Because nodule development depends on the presence of high amounts of phosphate in the growth medium, the accumulation of the non-phosphorus galactolipid DGDG in the PBM might be important to save phosphate for other essential processes, i.e. nucleic acid synthesis in bacteroids and host cells.},
      Year = {2004} }




@article{
Gaunt01,
   Author = {Gaunt, M. W. and Turner, S. L. and Rigottier-Gois, L. and Lloyd-Macgilp, S. A. and Young, J. P.},
   Title = {Phylogenies of \emph{atpD} and \emph{recA} support the small subunit rRNA-based classification of rhizobia},
   Journal = {International Journal of Systematic and Evolutionary Microbiology},
   Volume = {51},
   Number = {6},
   Pages = {2037-2048},
   Abstract = {The current classification of the rhizobia (root-nodule symbionts) assigns them to six genera. It is strongly influenced by the small subunit (16S, SSU) rRNA molecular phylogeny, but such single-gene phylogenies may not reflect the evolution of the genome as a whole. To test this, parts of the atpD and recA genes have been sequenced for 25 type strains within the alpha-Proteobacteria, representing species in Rhizobium, Sinorhizobium, Mesorhizobium, Bradyrhizobium, Azorhizobium, Agrobacterium, Phyllobacterium, Mycoplana and Brevundimonas. The current genera Sinorhizobium and Mesorhizobium are well supported by these genes, each forming a distinct phylogenetic clade with unequivocal bootstrap support. There is good support for a Rhizobium clade that includes Agrobacterium tumefaciens, and the very close relationship between Agrobacterium rhizogenes and Rhizobium tropici is confirmed. There is evidence for recombination within the genera Mesorhizobium and Sinorhizobium, but the congruence of the phylogenies at higher levels indicates that the genera are genetically isolated. rRNA provides a reliable distinction between genera, but genetic relationships within a genus may be disturbed by recombination.},
      Year = {2001} }




@article{
Geiger02,
   Author = {Geiger, O. and Lopez-Lara, I. M.},
   Title = {Rhizobial acyl carrier proteins and their roles in the formation of bacterial cell-surface components that are required for the development of nitrogen-fixing root nodules on legume hosts},
   Journal = {FEMS Microbiology Letters},
   Volume = {208},
   Number = {2},
   Pages = {153-62},
   Abstract = {Acyl carrier protein (ACP) of Escherichia coli is a small acidic protein which functions as carrier of growing acyl chains during their biosynthesis and as donor of acyl chains during transfer to target molecules. This unique ACP of E. coli is expressed constitutively. In more complex bacteria, multiple ACPs are present, indicating a channeling of pools of multi-carbon units into different biosynthetic routes. In rhizobia, for example, besides the constitutive ACP (AcpP) involved in the biosynthesis and transfer of common fatty acids, three specialized ACPs have been reported: (1) the flavonoid-inducible nodulation protein NodF, (2) AcpXL that transfers 27-hydroxyoctacosanoic acid to a sugar backbone during lipid A biosynthesis, and (3) the RkpF protein which is required for the biosynthesis of rhizobial capsular polysaccharides. All three of those specialized rhizobial ACPs are required for the biosynthesis of cell-surface molecules that play a role in establishing the symbiotic relationship between rhizobia and their legume hosts. Surprisingly, the recently sequenced genomes from Mesorhizobium loti and Sinorhizobium meliloti suggest even more candidates for ACPs in rhizobia.},
      Year = {2002} }




@article{
Genkai99,
   Author = {Genkai-Kato, M. and Yamamura, N.},
   Title = {Evolution of mutualistic symbiosis without vertical transmission},
   Journal = {Theor Popul Biol},
   Volume = {55},
   Number = {3},
   Pages = {309-23},
   Abstract = {Mutualistic symbioses are considered to evolve from parasitic relationships. Vertical transmission, defined as the direct transfer of infection from a parent organism to its progeny, has been suggested as a key factor causing reduction of symbiont virulence and evolution of mutualism. On the other hand, there are several mutualistic associations without vertical transmission, such as those between plants and mycorrhizal fungi, legumes and rhizobia, and some corals and dinoflagellates. It is expected that all mutualisms evolve perfect vertical transmission if the relationship is really mutualistic, because hosts may fail to acquire symbionts if they do not transmit the symbionts by vertical transmission. We have developed a mathematical model to clarify the conditions under which mutualistic symbiosis without vertical transmission should evolve. The evolution may occur when and only when (i) vertical transmission involves some costs in the host, (ii) the symbiont suffers direct negative effects if it exploits the host too intensively, (iii) the host establishes the ability to make use of waste products from the symbiont, and (iv) the mechanism of vertical transmission is controlled by the host. We also clarify the conditions under which mutualistic symbiosis with vertical transmission evolves.},
   Keywords = {Animals
*Ecosystem
*Evolution
*Models, Genetic
Plants/*genetics
Reproducibility of Results
Reproduction/*genetics
*Selection (Genetics)
Support, Non-U.S. Gov't
Symbiosis/*genetics},
   Year = {1999} }




@article{
Gest03,
   Author = {Gest, Howard},
   Title = {Names of bacteria and their evolutionary relationships},
   Journal = {Microbiology},
   Volume = {149},
   Number = {8},
   Pages = {1956-1958},
      Year = {2003} }




@article{
Geurts05,
   Author = {Geurts, R. and Fedorova, E. and Bisseling, T.},
   Title = {Nod factor signaling genes and their function in the early stages of Rhizobium infection},
   Journal = {Current Opinion in Plant Biology},
   Volume = {8},
   Number = {4},
   Pages = {346-352},
   Abstract = {A lipochitosaccharide-based signal molecule that is secreted by Rhizobium, named Nod factor (NF), induces root nodule formation in legumes. This molecule is also essential for the establishment of bacterial infection. Genetic analyses in the legume species Lotus japonicus and Medicago truncatula have led to the identification of many components of the NF signaling cascade. At least three of these genes do not function exclusively in the Rhizobium symbiosis but are also essential for the formation of mycorrhiza, an endosymbiosis found in many higher plant species. Recent studies have advanced our understanding of the functions of NF signaling genes in the Rhizobium infection process and the extent to which these genes are unique to legumes. © 2005 Elsevier Ltd. All rights reserved.},
      Year = {2005} }




@article{
Gosh06,
   Author = {Ghosh, Wriddhiman and Roy, Pradosh},
   Title = {\emph{Mesorhizobium thiogangeticum} sp. nov., a novel sulfur-oxidizing chemolithoautotroph from rhizosphere soil of an Indian tropical leguminous plant},
   Journal = {International Journal of Systematic and Evolutionary Microbiology},
   Volume = {56},
   Number = {1},
   Pages = {91-97},
   Abstract = {The bacterial strain SJTT, along with 15 other mesophilic, neutrophilic and facultatively sulfur-oxidizing chemolithotrophic isolates, was isolated by enrichment on reduced sulfur compounds as the sole energy and electron source from soils immediately adjacent to the roots of Clitoria ternatea, a slender leguminous herb of the Lower Gangetic plains of India. Strain SJTT was able to oxidize thiosulfate and elemental sulfur for chemolithoautotrophic growth. 16S rRNA and recA gene sequence-based phylogenetic analyses showed that the Gram-negative rod-shaped bacterium belonged to the genus Mesorhizobium and was most closely related to Mesorhizobium loti, Mesorhizobium plurifarium, Mesorhizobium amorphae and Mesorhizobium chacoense. Unequivocally low 16S rRNA (<97 %) and recA ([&lt;=]88 %) gene sequence similarities to all existing species of the most closely related genera, a unique fatty acid profile, a distinct G+C content (59{middle dot}6 mol%) and phenotypic characteristics all suggested that strain SJTT represents a novel species. DNA-DNA hybridization and SDS-PAGE analysis of whole-cell proteins also confirmed the taxonomic uniqueness of SJTT. It is therefore proposed that isolate SJTT (=LMG 22697T=MTCC 7001T) be classified as the type strain of a novel species, Mesorhizobium thiogangeticum sp. nov.},
      Year = {2006} }




@article{
Gibson80,
   Author = {Gibson, A. H.},
   Title = {Methods for legumes in glasshouses and controlled environment cabinets},
   Journal = {Methods for Evaluating Biological Nitrogen Fixation},
   Pages = {139-184},
      Year = {1980} }




@article{
Gilles-Gonzalez91,
   Author = {Gilles-Gonzalez, M. A. and Ditta, G. S. and Helinski, D. R.},
   Title = {A haemoprotein with kinase activity encoded by the oxygen sensor of Rhizobium meliloti},
   Journal = {Nature},
   Volume = {350},
   Number = {6314},
   Pages = {170-172},
   Abstract = {The expression of the nitrogen-fixation genes of Rhizobium meliloti is controlled by oxygen. These genes are induced when the free oxygen concentration is reduced to microaerobic levels. Two regulator proteins, FixL and FixJ, initiate the oxygen response cascade, and the genes that encode them have been cloned. The fixL product seems to be a transmembrane sensor that modulates the activity of the fixJ product, a cytoplasmic regulator. FixL and FixJ are homologous to a family of bacterial two-component regulators, for which the mode of signal transduction is phosphorylation. We report here the purification of both FixJ and a soluble truncated FixL (FixL*), overproduced from a single plasmid construct. FixL* catalyses its own phosphorylation and the transfer of the ?-phosphate of ATP to FixJ. The resulting FixJ-phosphate linkage is sensitive to base, as are the aspartyl phosphates of homologous systems. Visible spectra of purified FixL* show that it is an oxygen-binding haemoprotein. We propose that FixL senses oxygen through its haem moiety and transduces this signal by controlling the phosphorylation of FixJ.},
      Year = {1991} }




@article{
Gilles-Gonzalez94,
   Author = {Gilles-Gonzalez, M. A. and Gonzalez, G. and Perutz, M. F.},
   Title = {Heme-based sensors, exemplified by the kinase FixL, are a new class of heme protein with distinctive ligand binding and autoxidation},
   Journal = {Biochemistry},
   Volume = {33},
   Number = {26},
   Pages = {8067-8073},
   Abstract = {FixL's are chimeric heme protein kinases from symbiotic nitrogen-fixing Rhizobia. We have overexpressed three FixL variants in Escherichia coli. Bradyrhizobium japonicum FixL, a soluble dimeric protein, is the first full- length FixL to be purified. The other two proteins are soluble truncations of Rhizobium meliloti FixL, which is a membrane protein. One contains both heme and kinase domains and is dimeric: the other has only the heme domain and is monomeric. We find that all the FixL's bind oxygen and carbon monoxide non- cooperatively, with very low affinities due entirely to slow association rates. FixL P50's for oxygen are 17-76 mmHg. FixL's may sense nitric oxide and carbon monoxide in addition to oxygen, especially at the low oxygen pressures encountered in vivo. Autoxidation rates are about 50 times faster than that of sperm whale myoglobin. The carbon monoxide affinity of FixL's is about 300 times lower than that of myoglobin, resulting in the unusually low values of 7.5-17 for the partition constant, M = P50(O2)/P50(CO), between carbon monoxide and oxygen. Met-FixL's have their Soret absorption maximum at 395 nm instead of the typical 408 nm and a steep hydroxymet transition at pH ? 9.3; these properties indicate a pentacoordinated high- spin ferric heme and suggest a sterically hindered hydrophobic heme pocket lacking a distal (E7) histidine. FixL is the first member of a new class of heme proteins, the heme-based sensors, distinct from the oxygen carriers and electron transporters. We expect that some of the novel properties of FixL will be characteristic of the class.},
      Year = {1994} }




@incollection{
Gillis05,
   Author = {Gillis, M. and Vandamme, P. and De Vos, P. and Swings, J. and Kersters, K.},
   Title = {Polyphasic taxonomy},
   BookTitle = {Part A, Introductory essays, Bergey's Manual of Systematic Bacteriology},
   Editor = {Brenner, D. J. and Krieg, R. K. and Staley, J. T. and Garrity, G. M.},
   Publisher = {Springer},
   Address = {New York},
   Volume = {2},
   Edition = {2nd},
   Pages = {43-48},
      Year = {2005} }




@article{
Giuntini05,
   Author = {Giuntini, E. and Mengoni, A. and Bazzicalupo, M. and De Filippo, C. and Cavalieri, D. and Aubin-Horth, N. and Landry, C. R. and Becker, A.},
   Title = {Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of Sinorhizobium meliloti natural strains},
   Journal = {BMC Genomics},
   Volume = {6},
   Abstract = {Background: Sinorhizobium meliloti is a soil bacterium that forms nitrogen-fixing nodules on the roots of leguminous plants such as alfalfa (Medicago sativa). This species occupies different ecological niches, being present as a free-living soil bacterium and as a symbiont of plant root nodules. The genome of the type strain Rm 1021 contains one chromosome and two megaplasmids for a total genome size of 6 Mb. We applied comparative genomic hybridisation (CGH) on an oligonucleotide microarrays to estimate genetic variation at the genomic level in four natural strains, two isolated from Italian agricultural soil and two from desert soil in the Aral Sea region. Results: From 4.6 to 5.7 percent of the genes showed a pattern of hybridisation concordant with deletion, nucleotide divergence or ORF duplication when compared to the type strain Rm 1021. A large number of these polymorphisms were confirmed by sequencing and Southern blot. A statistically significant fraction of these variable genes was found on the pSymA megaplasmid and grouped in clusters. These variable genes were found to be mainly transposases or genes with unknown function. Conclusions: The obtained results allow to conclude that the symbiosis-required megaplasmid pSymA can be considered the major hot-spot for intra-specific differentiation in S. meliloti. © 2005 Giuntini et al., licensee BioMed Central Ltd.},
      Year = {2005} }




@article{
Godley75,
   Author = {Godley, E. J.},
   Title = {Kowhais},
   Journal = {New Zealand Nature Heritage},
   Volume = {65},
   Pages = {1804-1806},
      Year = {1975} }




@article{
Godley89,
   Author = {Godley, E. J.},
   Title = {The supposed Easter Island Sophora in Christchurch, New Zealand},
   Journal = {Botanic Gardens Conservation News},
   Volume = {1},
   Pages = {37-38},
      Year = {1989} }




@article{
Goldblatt81,
   Author = {Goldblatt, P.},
   Title = {Cytology and the phylogeny of Leguminosae},
   Journal = {Advances in Legume Systematics},
   Number = {2 PART},
   Pages = {427-463},
      Year = {1981} }




@article{
Golebiowska62,
   Author = {Golebiowska, J. and Sypniewska, U.},
   Title = {The effect of the plant and of ecological conditions on development of symbiosis between Lupine and Rhizobium lupini},
   Journal = {Acta Microbiologica Polonica},
   Volume = {11},
   Pages = {319-328},
      Year = {1962} }




@article{
Gonzalez03,
   Author = {Gonzalez, J. E. and Marketon, M. M.},
   Title = {Quorum sensing in nitrogen-fixing rhizobia},
   Journal = {Microbiol Mol Biol Rev},
   Volume = {67},
   Number = {4},
   Pages = {574-92},
   Abstract = {Members of the rhizobia are distinguished for their ability to establish a nitrogen-fixing symbiosis with leguminous plants. While many details of this relationship remain a mystery, much effort has gone into elucidating the mechanisms governing bacterium-host recognition and the events leading to symbiosis. Several signal molecules, including plant-produced flavonoids and bacterially produced nodulation factors and exopolysaccharides, are known to function in the molecular conversation between the host and the symbiont. Work by several laboratories has shown that an additional mode of regulation, quorum sensing, intercedes in the signal exchange process and perhaps plays a major role in preparing and coordinating the nitrogen-fixing rhizobia during the establishment of the symbiosis. Rhizobium leguminosarum, for example, carries a multitiered quorum-sensing system that represents one of the most complex regulatory networks identified for this form of gene regulation. This review focuses on the recent stream of information regarding quorum sensing in the nitrogen-fixing rhizobia. Seminal work on the quorum-sensing systems of R. leguminosarum bv. viciae, R. etli, Rhizobium sp. strain NGR234, Sinorhizobium meliloti, and Bradyrhizobium japonicum is presented and discussed. The latest work shows that quorum sensing can be linked to various symbiotic phenomena including nodulation efficiency, symbiosome development, exopolysaccharide production, and nitrogen fixation, all of which are important for the establishment of a successful symbiosis. Many questions remain to be answered, but the knowledge obtained so far provides a firm foundation for future studies on the role of quorum-sensing mediated gene regulation in host-bacterium interactions.},
   Keywords = {Nitrogen Fixation/*physiology
Rhizobium/genetics/growth \& development/metabolism/*physiology
Soil Microbiology
Support, Non-U.S. Gov't
Support, U.S. Gov't, Non-P.H.S.
Symbiosis},
   Year = {2003} }




@article{
Goormachtig04,
   Author = {Goormachtig, S. and Capoen, W. and James, E. K. and Holsters, M.},
   Title = {Switch from intracellular to intercellular invasion during water stress-tolerant legume nodulation},
   Journal = {Proceedings of the National Academy of Sciences of the United States of America},
   Volume = {101},
   Number = {16},
   Pages = {6303-8},
   Abstract = {Rhizobia colonize their legume hosts by different modes of entry while initiating symbiotic nitrogen fixation. Most legumes are invaded via growing root hairs by the root hair-curl mechanism, which involves epidermal cell responses. However, invasion of a number of tropical legumes happens through fissures at lateral root bases by cortical, intercellular crack entry. In the semiaquatic Sesbania rostrata, the bacteria entered via root hair curls under nonflooding conditions. Upon flooding, root hair growth was prevented, invasion on accessible root hairs was inhibited, and intercellular invasion was recruited. The plant hormone ethylene was involved in these processes. The occurrence of both invasion pathways on the same host plant enabled a comparison to be made of the structural requirements for the perception of nodulation factors, which were more stringent for the epidermal root hair invasion than for the cortical intercellular invasion at lateral root bases.},
   Keywords = {Ethylenes/metabolism
Fabaceae/microbiology/*physiology
Nitrogen Fixation/*physiology
Plant Roots/microbiology
Research Support, Non-U.S. Gov't
Rhizobium/*physiology
*Water},
   Year = {2004} }




@article{
Gottfert01,
   Author = {Gottfert, M. and Rothlisberger, S. and Kundig, C. and Beck, C. and Marty, R. and Hennecke, H.},
   Title = {Potential symbiosis-specific genes uncovered by sequencing a 410-kilobase DNA region of the Bradyrhizobium japonicum chromosome},
   Journal = {Journal of Bacteriology},
   Volume = {183},
   Number = {4},
   Pages = {1405-12},
   Abstract = {The physical and genetic map of the Bradyrhizobium japonicum chromosome revealed that nitrogen fixation and nodulation genes are clustered. Because of the complex interactions between the bacterium and the plant, we expected this chromosomal sector to contain additional genes that are involved in the maintenance of an efficient symbiosis. Therefore, we determined the nucleotide sequence of a 410-kb region. The overall G+C nucleotide content was 59.1%. Using a minimum gene length of 150 nucleotides, 388 open reading frames (ORFs) were selected as coding regions. Thirty-five percent of the predicted proteins showed similarity to proteins of rhizobia. Sixteen percent were similar only to proteins of other bacteria. No database match was found for 29%. Repetitive DNA sequence-derived ORFs accounted for the rest. The sequenced region contained all nitrogen fixation genes and, apart from nodM, all nodulation genes that were known to exist in B. japonicum. We found several genes that seem to encode transport systems for ferric citrate, molybdate, or carbon sources. Some of them are preceded by -24/-12 promoter elements. A number of putative outer membrane proteins and cell wall-modifying enzymes as well as a type III secretion system might be involved in the interaction with the host.},
   Keywords = {Acyltransferases
genetics
Amidohydrolases
Bacterial Outer Membrane Proteins
Bacterial Proteins
secretion
Bradyrhizobium
Cations
metabolism
Cell Wall
Chromosomes
Bacterial
DNA
Ferredoxins
Genes
Glucuronidase
Metals
Models
Genetic
Molecular Sequence Data
N-Acetylglucosaminyltransferases
Nitrogen Fixation
Open Reading Frames
Peptide Synthases
Propanolamines
Recombination
Sequence Analysis
standards
Support
Non-U.S.Gov't
Symbiosis},
   Year = {2001} }




@article{
Graff03,
   Author = {Graff, A. and Stubner, S.},
   Title = {Isolation and molecular characterization of thiosulfate-oxidizing bacteria from an Italian rice field soil},
   Journal = {Systematic and Applied Microbiology},
   Volume = {26},
   Number = {3},
   Pages = {445-452},
   Abstract = {In rice paddy soils an active cycling of sulfur compounds takes place. To elucidate the diversity of thiosulfate-oxidizing bacteria these organisms were enriched from bulk soil and rice roots by the most probable number method in liquid medium. From the MPN enrichment cultures 21 bacterial strains were isolated on solid mineral medium, and could be further shown to produce sulfate from thiosulfate. These strains were characterized by 16S rDNA analyses. The isolates were affiliated to seven different phylogenetic groups within the ?- and ?-subclass of Proteobacteria. Two of these phylotypes were already described as S-oxidizers in this environment (Xanthobacter sp. and Bosea sp. related strains), but five groups represented new S-oxidizers in rice field soil. These isolates were closely related to Mesorhizobium loti, to Hydrogenophaga sp., to Delftia sp., to Pandoraea sp. or showed sequence similarity to a strain of Achromobacter sp.},
   Keywords = {16S rDNA
Phylogenetic analysis
RFLP
Rice field soil
S-oxidizing bacteria},
   Year = {2003} }




@article{
Graham91,
   Author = {Graham, P. H. and Sadowsky, M. J. and Keyser, H. H. and Barnet, Y. M. and Bradley, R. S. and Cooper, J. E. and Deley, D. J. and Jarvis, B. D. W. and Roslycky, E. B. and Strijdom, B. W. and Young, J. P. W.},
   Title = {Proposed minimal standards for the description of  new  genera and  species of  root- nodulating and  stem- nodulating  bacteria},
   Journal = {International Journal of Systematic Bacteriology},
   Volume = {41},
   Number = {4},
   Pages = {582-587},
   Abstract = {Since the first volume of Bergey's Manual of Systematic Bacteriology was published, in 1984, two additional genera and several new species of stem- and root-nodulating bacteria have been proposed; further changes to the taxonomy of this group of organisms appear likely. This paper briefly reviews the current status of "Rhizobium" taxonomy and proposes minimal standards for the description of future genera and species belonging to this group of organisms.},
      Year = {1991} }




@article{
Gram84,
   Author = {Gram, H. C.},
   Title = {\"Uber die isolierte F\"arbung der Schizomyceten in Schnitt- und Trockenpr\"aparaten},
   Journal = {Fortschritte der Medizin},
   Volume = {2},
   Pages = {185-189},
      Year = {1884} }




@article{
Gray96,
   Author = {Gray, K. M. and Pearson, J. P. and Greenberg, E. P. and Downie, J. A. and Boboye, B. E. A.},
   Title = {Cell-to-cell signaling in the symbiotic nitrogen-fixing bacterium Rhizobium leguminosarum: Autoinduction of a stationary phase and rhizosphere-expressed genes},
   Journal = {Journal of Bacteriology},
   Volume = {178},
   Number = {2},
   Pages = {372-376},
   Abstract = {The Sym plasmid pRL1JI encodes functions for the formation of nitrogen-fixing pea root nodules by Rhizobium leguminosarum. Some of the nodulation genes are involved in recognition of chemical signals produced by the plant root, and others are required for production of chemical signals recognized by the plant. pRL1JI also contains a regulatory gene, rhiR, that is homologous to luxR, the transcriptional activator of luminescence genes in Vibrio fischeri. LuxR requires a signal compound, an autoinducer, for its activity. We have identified an R. leguminosarum autoinducer that, together with RhiR, is required to activate both the rhizosphere-expressed rhiABC operon and a growth-inhibiting function encoded by pRL1JI. This intercellular signal is an N-acylated homoserine lactone structurally related to the V. fischeri and other autoinducers. These findings indicate a new level of intercellular communication in root nodule formation.},
      Year = {1996} }




@article{
Graybeal98,
   Author = {Graybeal, A.},
   Title = {Is It Better to Add Taxa or Characters to a Difficult Phylogenetic Problem?},
   Journal = {Systematic Biology},
   Volume = {47},
   Number = {1},
   Pages = {9-17},
   Abstract = {The effects on phylogenetic accuracy of adding characters and/or taxa were explored using data generated by computer simulation. The conditions of this study were constrained but allowed for systematic investigation of certain parameters. The starting point for the study was a four-taxon tree in the "Felsenstein zone," representing a difficult phylogenetic problem with an extreme situation of long branch attraction. Taxa were added sequentially to this tree in a manner specifically designed to break up the long branches, and for each tree data matrices of different sizes were simulated. Phylogenetic trees were reconstructed from these data using the criteria of parsimony and maximum likelihood. Phylogenetic accuracy was measured in three ways: (1) proportion of trees that are completely correct, (2) proportion of correctly reconstructed branches in all trees, and (3) proportion of trees in which the original four-taxon statement is correctly reconstructed. Accuracy improved dramatically with the addition of taxa and much more slowly with the addition of characters. If taxa can be added to break up long branches, it is much more preferable to add taxa than characters.},
   Keywords = {Long branch attraction
Parsimony
Phylogenetic reconstruction
Simulation
Taxon sampling},
   Year = {1998} }




@article{
Green94,
   Author = {Green, P.S.},
   Title = {Norfolk Island and Lord Howe Island},
   Journal = {Flora of Australia},
   Volume = {49},
   Pages = {1-26},
      Year = {1994} }




@article{
Greenwood69,
   Author = {Greenwood, R. M.},
   Title = {\emph{Rhizobium} studies in New Zealand soils},
   Journal = {New Zealand Soil News},
   Volume = {2},
   Pages = {45-48},
   Abstract = {acid producers, see norris 1965
nodulalted by clover rhizobia
mentioned close relationship between carmichaelia, clianthus and sophora strains
explains amino acid patterns},
      Year = {1969} }




@inproceedings{
Greenwood77,
   Author = {Greenwood, R. M.},
   Title = {The \emph{Rhizobium} component of the nitrogen-fixing symbiosis},
   BookTitle = {Proceedings of the New Zealand Grassland Association},
   Address= {Nelson},
   Volume = {38},
   Pages = {167-174},
   Abstract = {clover, lucerne and lupins, some on gorse and brooms, sainfoin and carm},
      Year = {1977} }




@inproceedings{
Greenwood78a,
   Author = {Greenwood, R. M.},
   Title = {Rhizobia associated with indigenous legumes of New Zealand and Lord Howe Island},
   BookTitle = {Microbial Ecology},
   Editor = {Loutit, M. W. and Miles, J. A. R.},
   Series= {Proceedings in Life Sciences},
   Address= {Dunedin},
   Publisher = {Springer-Verlag},
   Pages = {402-403},
   Abstract = {similarity between carmichaelia, clianthus and sophora strains
cross innoc},
      Year = {1978} }




@article{
Greenwood92,
   Author = {Greenwood, R. M.},
   Title = {Some Differences between Plants of the Chatham Islands and the New-Zealand Mainland},
   Journal = {New Zealand Journal of Ecology},
   Volume = {16},
   Number = {1},
   Pages = {51-52},
   Abstract = {A number of Chatham Island plants show morphological differences from related plants on mainland New Zealand. These differences could have arisen as a result of freedom from moa browsing on the Chatham Islands. A possible test for this hypothesis is suggested.},
      Year = {1992} }




@article{
Greenwood78b,
   Author = {Greenwood, R. M. and Bathurst, N. O.},
   Title = {Effect of rhizobial strain and host on the amino acid patterns in legume root nodules},
   Journal = {New Zealand Journal of Science},
   Volume = {21},
   Pages = {107-120},
      Year = {1978} }




@article{
Grobbelaar74,
   Author = {Grobbelaar, N. and Clarke, B.},
   Title = {A qualitative study of the nodulating ability of legume species: List 4},
   Journal = {Agroplantae},
   Volume = {6},
   Pages = {59-64},
      Year = {1974} }




@article{
Gruner01,
   Author = {Gruner, I. and Heenan, P. B.},
   Title = {Viability and germination of seeds of Carmichaelia (Fabaceae) after prolonged storage},
   Journal = {New Zealand Journal of Botany},
   Volume = {39},
   Number = {1},
   Abstract = {Eleven species of Carmichaelia retained high seed viability for up to 24 years, linked with sustained impermeability of the seed testa. Viable seeds germinated rapidly after scarification and showed no specific light requirements. Shrub and dwarf shrub species retained high viability after prolonged storage, whereas seeds of tree species had reduced viability in older seeds. Long-term seed storage would be a suitable ex situ conservation tool for shrub and dwarf shrub species.},
      Year = {2001} }




@article{
Gualtieri00,
   Author = {Gualtieri, G. and Bisseling, T.},
   Title = {The evolution of nodulation},
   Journal = {Plant Molecular Biology},
   Volume = {42},
   Number = {1},
   Pages = {181-194},
   Abstract = {In this review we will first describe the different steps leading to nodule formation, and these will be compared with processes of non-symbiotic plant development and growth. In general, aspects of both actinorhizal as well as rhizobial symbiosis are described, but in several cases, the emphasis will be on the Rhizobium-legume symbiosis because more knowledge of this system is available. Subsequently, the phylogeny of nodulating plants is described and a comparison is made between several aspects of legume and actinorhizal nodulation. At the end of this paper the relationship between nodule symbiosis and endomycorrhizal symbiosis is described, and it is discussed to what extent the development of root nodules involves unique properties, or whether processes and genes have been recruited from common plant development and the endomycorrhizal symbiosis.},
   Keywords = {Actinorhiza
Endomycorrhizae
Evolution
Frankia
Haemoglobins
Nod factors
Nodulation
Phylogeny
Rhizobia},
   Year = {2000} }




@article{
Guindon03,
   Author = {Guindon, S. and Gascuel, O.},
   Title = {A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood},
   Journal = {Systematic Biology},
   Volume = {52},
   Number = {5},
   Pages = {696-704},
   Abstract = {The increase in the number of large data sets and the complexity of current probabilistic sequence evolution models necessitates fast and reliable phylogeny reconstruction methods. We describe a new approach, based on the maximum-likelihood principle, which clearly satisfies these requirements. The core of this method is a simple hill-climbing algorithm that adjusts tree topology and branch lengths simultaneously. This algorithm starts from an initial tree built by a fast distance-based method and modifies this tree to improve its likelihood at each iteration. Due to this simultaneous adjustment of the topology and branch lengths, only a few iterations are sufficient to reach an optimum. We used extensive and realistic computer simulations to show that the topological accuracy of this new method is at least as high as that of the existing maximum-likelihood programs and much higher than the performance of distance-based and parsimony approaches. The reduction of computing time is dramatic in comparison with other maximum-likelihood packages, while the likelihood maximization ability tends to be higher. For example, only 12 min were required on a standard personal computer to analyze a data set consisting of 500 rbcL sequences with 1,428 base pairs from plant plastids, thus reaching a speed of the same order as some popular distance-based and parsimony algorithms. This new method is implemented in the PHYML program, which is freely available on our web page: http://www.lirmm.fr/w3ifa/MAAS/.},
   Keywords = {Algorithm
Computer simulations
Maximum likelihood
Phylogeny
rbcL
RDPII project},
   Year = {2003} }




@article{
Gulash84,
   Author = {Gulash, M. and Ames, P. and Larosiliere, R. C. and Bergman, K.},
   Title = {Rhizobia are attracted to localized sites on legume roots},
   Journal = {Applied and Environmental Microbiology},
   Volume = {48},
   Number = {1},
   Pages = {149-52},
   Abstract = {Clouds of Rhizobium meliloti were attracted to localized sites on the surface of the infectible region of alfalfa roots. This behavior, which required active motility and chemotaxis, was not species specific. Correlation between the behavior of various mutants and their competitiveness for nodulation suggests that cloud formation has a role in the infection of host legume roots by rhizobia.},
   Keywords = {Chemotaxis
Fabaceae/*microbiology
Medicago sativa/*microbiology
Mutation
*Plants, Medicinal
Rhizobium/*isolation \& purification
Soil Microbiology
Support, U.S. Gov't, Non-P.H.S.
Support, U.S. Gov't, P.H.S.},
   Year = {1984} }




@article{
Hogberg97,
   Author = {H\"ogberg, P.},
   Title = {Tansley review no. 95 natural abundance in soil-plant systems},
   Journal = {New Phytologist},
   Volume = {137},
   Number = {2},
   Pages = {179-203},
   Abstract = {Equilibrium and kinetic isotope fractionations during incomplete reactions result in minute differences in the ratio between the two stable N isotopes, 15SN and 14N, in various N pools. In ecosystems such variations (usually expressed in per rail [?15N]deviations from the standard atmospheric N2) depend on isotopic signatures of inputs and outputs, the input-output balance, N transformations and their specific isotope effects, and compartmentation of N within the system. Products along a sequence of reactions, e.g. the N mineralization-N uptake pathway, should, if fractionation factors were equal for the different reactions, become progressively depleted. However, fractionation factors vary. For example, because nitrification discriminates against 15N in the substrate more than does N mineralization, NH4+ can become isotopically heavier than the organic N from which it is derived. Levels of isotopic enrichment depend dynamically on the stoichiometry of reactions, as well as on specific abiotic and biotic conditions. Thus, the ?15N of a specific N pool is not a constant, and ?15N of a N compound added to the system is not a conservative, unchanging tracer. This fact, together with analytical problems of measuring ?15N in small and dynamic pools of N in the soil-plant system, and the complexity of the N cycle itself (for instance the abundance of reversible reactions), limit the possibilities of making inferences based on observations of 15N abundance in one or a few pools of N in a system. Nevertheless, measurements of ?15N might offer the advantage of giving insights into the N cycle without disturbing the system by adding 15N tracer. Such attempts require, however, that the complex factors affecting ?15N in plants be taken into account, viz. (i) the source(s) of N (soil, precipitation, NO(x), NH3, N2-fixation), (ii) the depth(s) in soil from which N is taken up, (iii) the form(s) of soil-N used (organic N, NH4+, No8-), (iv) influences of mycorrhizal symbioses and fractionations during and after N uptake by plants, and (v) interactions between these factors and plant phenology. Because of this complexity, data on ?15N can only be used alone when certain requirements are met, e.g. when a clearly discrete N source in terms of amount and isotopic signature is studied. For example, it is recommended that N in non-N2-fixing species should differ more than 5? from N derived by N2-fixation, and that several non-N2-fixing references are used, when data on ?15N are used to estimate N2-fixation in poorly described ecosystems. As well as giving information on N source effects, ?15N can give insights into N cycle rates. For example, high levels of N deposition onto previously N-limited systems leads to increased nitrification, which produces 15N-enriched NH4+ and 15N-depleted NO3-. As many forest plants prefer NH4+ they become enriched in 15N in such circumstances. This change in plant ?15N will subsequently also occur in the soil surface horizon after litter-fall, and might be a useful indicator of N saturation, especially since there is usually an increase in ?15N with depth in soils of N-limited forests. Generally, interpretation of 15N measurements requires additional independent data and modelling, and benefits from a controlled experimental setting. Modelling will be greatly assisted by the development of methods to measure the ?15N of small dynamic pools of N in soils. Direct comparisons with parallel low tracer level 15N studies will be necessary to further develop the interpretation of variations in ?15N in soil-plant systems. Another promising approach is to study ratios of 15N:14N together with other pairs of stable isotopes, e.g. 13C:12C or 18O: 16O, in the same ion or molecules. This approach can help to tackle the challenge of distinguishing isotopic source effects from fractionations within the system studied.},
   Keywords = {15N abundance
Nitrogen
Plants
Soils},
   Year = {1997} }




@article{
Hafeez04,
   Author = {Hafeez, F. Y. and Safdar, M. E. and Malik, K. A. and Chaudhry, A. U.},
   Title = {Rhizobial inoculation improves seedling emergence, nutrient uptake and growth of cotton},
   Journal = {Australian Journal of Experimental Agriculture},
   Volume = {44},
   Number = {6},
   Pages = {617-622},
   Abstract = {Experiments were conducted to determine the growth promoting activities of various rhizobia in cotton (Gossypium hirsutum L.) under growth room conditions. Seeds of 4 cotton cultivars were inoculated with 4-indole-3-acetic acid producing selected (Brady) rhizobium strains and Azotobacter plant growth promoting rhizobacteria strains, included as a positive control. Growth responses to inoculation exhibited bacterial strain-cotton cultivar specificity and also included increase in rate of seedling emergence by 3-9%. Shoot dry weight, biomass and N uptake were increased by 48, 75 and 57%, respectively, due to inoculation with both the Rhizobium leguminosarum bv. trifolii E11 and Azotobacter sp. S8, whereas, strain E11 also increased root dry weight, root length and area by 248, 332 and 283%, respectively. K+ and Ca 2+ uptake was also increased by 2-21% and 9-14%, respectively, due to rhizobial inoculation. The results also showed that (Brady) rhizobium strains promoted cotton growth through efficient nutrient uptake, which was mainly related to increased root growth due to the effect of IAA produced by these strains. However, growth promotion by Azotobacter sp. S8, in addition to 4-indole-3-acetic acid production, might also involve biological N2 fixation by this rhizobacterial strain at some stage during its growth.},
   Keywords = {(Brady)rhizobium
Biomass
BNF
PGPR
Rhizobium
Root growth},
   Year = {2004} }




@article{
Hahn66,
   Author = {Hahn, N. J.},
   Title = {The Congo red reaction in bacteria and its usefulness in the identification of rhizobia},
   Journal = {Canadian Journal of Microbiology},
   Volume = {12},
   Number = {4},
   Pages = {725-33},
   Keywords = {*Congo Red
Culture Media
Ions/pharmacology
Magnesium/pharmacology
Nitrates/pharmacology
Rhizobium/*isolation \& purification
Temperature},
   Year = {1966} }




@article{
Hamdi74,
   Author = {Hamdi, Y. A.},
   Title = {Vertical movement of rhizobia in soil},
   Journal = {Zentralbl Bakteriol Parasitenkd Infektionskr Hyg},
   Volume = {129},
   Number = {3-4},
   Pages = {373-7},
   Keywords = {Cell Movement
Particle Size
Rhizobium/*physiology
*Soil Microbiology
Water},
   Year = {1974} }




@article{
Hamdi77,
   Author = {Hamdi, Y. A.},
   Title = {Certain environmental factors affecting rhizobia and symbiotic systems},
   Journal = {Zentralbl Bakteriol Parasitenkd Infektionskr Hyg},
   Volume = {132},
   Number = {4},
   Pages = {350-60},
   Abstract = {The interrelation between rhizobia and certain fungi, bacteria, actinomycetes, nematodes, and seed-coat diffusates of Phaseolus vulgaris were investigated. The effect of pesticides, i.e. fungicides, herbicides, and nematocides on growth of rhizobia, and the symbiotic systems between rhizobia and their respective host is reported. Degradation of certain herbicides and insecticides is shown. The movement of rhizobia in soil as affected by water tension, tolerance of salts, and soil temperatures are discussed. Environmental factors may affect the successful establishment of an effective symbiosis between rhizobia and their hosts at any or all the three stages. They may 1) affect occurrence, growth, and survival of root nodule bacteria, 2) modify nodule formation, or 3) affect the function of the formed nodules (VINCENT 1962). The environmental aspect considered here include the antagonistic factors against rhizobia, the pesticides, and some ecological aspects of rhizobia in soil, e.g., the movement and salts and heat tolerance. These aspects were investigated by Egyptian workers over the period 1948-1972. Comprehensive reviews on the effect of environmental factors on rhizobia were reported by VINCENT (1962) and NUTMAN (1972).},
   Keywords = {Actinomycetales/growth \& development
Animals
Antibiosis
Bacteria/growth \& development
Ecology
Fungi/growth \& development
Nematoda/growth \& development
Pesticides/pharmacology
Plants/growth \& development/*microbiology
Rhizobium/drug effects/*growth \& development
Soil
*Soil Microbiology
*Symbiosis
Temperature
Water},
   Year = {1977} }




@book{
Hamilton90,
   Author = {Hamilton, H. R.},
   Title = {Seasonality in Gorse},
   Publisher = {Oxford Polytechnic},
   Address = {Oxford, UK},
   Series = {Unpublished Dissertation},
      Year = {1990} }




@article{
Han05,
   Author = {Han, S.-Z. and Wang, E.-T. and Chen, W.-X. and Han, S.-Z.},
   Title = {Diverse bacteria isolated from root nodules of \emph{Phaseolus vulgaris} and species within the genera \emph{Campylotropis} and \emph{Cassia} grown in China},
   Journal = {Systematic and Applied Microbiology},
   Volume = {28},
   Number = {3},
   Pages = {265-276},
   Abstract = {Eighty bacterial isolates from root nodules of the leguminous plants Phaseolus vulgaris, Campylotropis spp. and Cassia spp. grown in China were classified into five groups by phenotypic analyses, SDS-PAGE of whole-cell proteins, PCR-based 16S rRNA gene restriction-fragment-length-polymorphism and sequencing. Thirty-three isolates from the three plant genera were identified as Agrobacterium tumefaciens because they are closely related to the type strain of A. tumefaciens. Fourteen isolates from P. vulgaris grown in Yunnan and Inner Mongolia were classified as R. leguminosarum bv. phaseoli based on their close relationship with the type strain in numerical taxonomy and in 16S rDNA phylogeny. Twenty-seven isolates from Campylotropis delavayi, P. vulgaris and four species of Cassia grown in the central zones of China were classified into three groups within the genus Bradyrhizobium. One of these three groups could be defined as Bradyrhizobium japonicum. Our results demonstrated that P. vulgaris and the species of Campylotropis and Cassia could form nodules with diverse rhizobia in Chinese soils, including novel lineages associated with P. vulgaris. These results also offered information about the convergent evolution between rhizobia and legumes since the rhizobial populations associated with P. vulgaris in Chinese soils were completely different from those in Mexico, the original cite of this plant. Some rhizobial species could be found in all of the three leguminous genera. © 2004 Published by Elsevier GmbH.},
   Keywords = {Campylotropis
Cassia
Diversity
Phaseolus vulgaris
Rhizobia},
   Year = {2005} }




@article{
Hanin97,
   Author = {Hanin, M. and Jabbouri, S. and QuesadaVincens, D. and Freiberg, C. and Perret, X. and Prome, J. C. and Broughton, W. J. and Fellay, R.},
   Title = {Sulphation of Rhizobium sp. NGR234 Nod factors is dependent on noeE, a new host-specificity gene},
   Journal = {Molecular Microbiology},
   Volume = {24},
   Number = {6},
   Pages = {1119-1129},
   Abstract = {Rhizobia secrete specific lipo-chitooligosaccharide signals (LCOs) called Nod factors that are required for infection and nodulation of legumes. In Rhizobium sp. NGR234, the reducing N-acetyl-D-glucosamine of LCOs is substituted at C-6 with 2-O-methyl-L-fucose which can be acetylated or sulphated. We identified a flavonoid-inducible locus on the symbiotic plasmid pNGR234a that contains a new nodulation gene, noeE, which is required for the sulphation of NGR234 Nod factors (NodNGR). noeE was identified by conjugation into the closely related Rhizobium fredii strain USDA257, which produces fucosylated but non-sulphated Nod factors (NodUSDA). R. fredii transconjugants producing sulphated LCOs acquire the capacity to nodulate Calopogonium caeruleum. Furthermore, mutation of noeE (NGR Delta noeE) abolishes the production of sulphated LCOs and prevents nodulation of Pachyrhizus tuberosus. The sulphotransferase activity linked to NoeE is specific for fucose. In contrast, the sulphotransferase NodH of Rhizobium meliloti seems to be less specific than NoeE, because its introduction into NGR Delta noeE leads to the production of a mixture of LCOs that are sulphated on C-6 Of the reducing terminus and sulphated on the P-O-methylfucose residue. Together, these findings show that noeE is a host-specificity gene which probably encodes a fucose-specific sulphotransferase.},
      Year = {1997} }




@article{
Hao04,
   Author = {Hao, W. and Golding, G. B.},
   Title = {Patterns of bacterial gene movement},
   Journal = {Mol Biol Evol},
   Volume = {21},
   Number = {7},
   Pages = {1294-307},
   Abstract = {Lateral gene transfer has emerged as an important force in bacterial evolution. A substantial number of genes can be inserted into or deleted from genomes through the process of lateral transfer. In this study, we looked for atypical occurrence of genes among related organisms to detect laterally transferred genes. We have analyzed 50 bacterial complete genomes from nine groups. For each group we use a 16s rRNA phylogeny and a comparison of protein similarity to map gene insertions/deletions onto their species phylogeny. The results reveal that there is poor correlation of genes inserted, deleted, and duplicated with evolutionary branch length. In addition, the numbers of genes inserted, deleted, or duplicated within the same branch are not always correlated with each other. Nor is there any similarity within groups. For example, in the Rhizobiales group, the ratio of insertions to deletions in the evolutionary branch leading to Agrobacterium tumefaciens str. C58 (Cereon) is 0.52, but it is 39.52 for Mesorhizobium loti. Most strikingly, the number of insertions of foreign genes is much larger in the external branches of the trees. These insertions also greatly outnumber the occurrence of deletions, and yet the genome sizes of these bacteria remain roughly constant. This indicates that many of the insertions are specific to each organism and are lost before related species can evolve. Simulations of the process of insertion and deletion, tailored to each phylogeny, support this conclusion.},
      Year = {2004} }




@article{
Harris02,
   Author = {Harris, Jeanne},
   Title = {Shedding light on an underground problem},
   Journal = {Proceedings of the National Academy of Sciences of the United States of America},
   Volume = {99},
   Number = {23},
   Pages = {14616-14618},
      Year = {2002} }




@article{
Harris03,
   Author = {Harris, J. M. and Wais, R. and Long, S. R.},
   Title = {Rhizobium-induced calcium spiking in Lotus japonicus},
   Journal = {Molecular Plant-Microbe Interactions},
   Volume = {16},
   Number = {4},
   Pages = {335-341},
   Abstract = {Legumes and rhizobium bacteria form a symbiosis that results in the development of nitrogen-fixing nodules on the root of the host plant. The earliest plant developmental changes are triggered by bacterially produced nodulation (Nod) factors. Within minutes of exposure to Nod factors, sharp oscillations in cytoplasmic calcium levels (calcium spiking) occur in epidermal cells of several closely related legumes. We found that Lotus japonicus, a legume that follows an alternate developmental pathway, responds to both its bacterial partner and to the purified bacterial signal with calcium spiking. Thus, calcium spiking is not restricted to a particular pathway of nodule development and may be a general component of the response of host legumes to their bacterial partner. Using Nod factor-induced calcium spiking as a tool to identify mutants blocked early in the response to Nod factor, we show that the L. japonicus Ljsym22-1 mutant but not the Ljsym30 mutant fails to respond to Nod factor with calcium spiking.},
      Year = {2003} }




@article{
Harrison99,
   Author = {Harrison, M. J.},
   Title = {Molecular and cellular aspects of the arbuscular mycorrhizal symbiosis},
   Journal = {Annual Review of Plant Physiology and Plant Molecular Biology},
   Volume = {50},
   Pages = {361-389},
   Abstract = {Arbuscular mycorrhizae are symbiotic associations formed between a wide range of plant species including angiosperms, gymnosperms, pteridophytes, and some bryophytes, and a limited range of fungi belonging to a single order, the Glomales. The symbiosis develops in the plant roots where the fungus colonizes the apoplast and cells of the cortex to access carbon supplied by the plant. The fungal contribution to the symbiosis is complex, but a major aspect includes the transfer of mineral nutrients, particularly phosphate from the soil to the plant. Development of this highly compatible association requires the coordinate molecular and cellular differentiation of both symbionts to form specialized interfaces over which bi-directional nutrient transfer occurs. Recent insights into the molecular events underlying these aspects of the symbiosis are discussed.},
   Keywords = {Fungus
Phosphate transport
Plant-microbe interaction
Rhizobium-legume symbiosis
Root},
   Year = {1999} }




@article{
HKY85,
   Author = {Hasegawa, M. and Kishino, H. and Yano, T.},
   Title = {Dating of the human-ape splitting by a molecular clock of mitochondrial DNA},
   Journal = {Journal of Molecular Evolution},
   Volume = {22},
   Number = {2},
   Pages = {160-174},
   Abstract = {A new statistical method for estimating divergence dates of species from DNA sequence data by a molecular clock approach is developed. This method takes into account effectively the information contained in a set of DNA sequence data. The molecular clock of mitochondrial DNA (mtDNA) was calibrated by setting the date of divergence between primates and ungulates at the Cretaceous-Tertiary boundary (65 million years ago), when the extinction of dinosaurs occurred. A generalized least-squares method was applied in fitting a model to mtDNA sequence data, and the clock gave dates of 92.3 ± 11.7, 13.3 ± 1.5, 10.9 ± 1.2, 3.7 ± 0.6, and 2.7 ± 0.6 million years ago (where the second of each pair of numbers is the standard deviation) for separation of mouse, gibbon, orangutan, gorilla, and champanzee, respectively, from the line leading to humans. Although there is some uncertainty in the clock, this dating may pose a problem for the widely believed hypothesis that the bipedal creature Australopithecus afarensis, which lived some 3.7 million years ago at Laetoli in Tanzania and at Hadar in Ethiopia, was ancestral to man and evolved after the human-ape splitting. Another likelier possibility is that mtDNA was transferred through hybridization between a proto-human and a protochimpanzee after the former had developed bipedalism.},
      Year = {1985} }




@book{
Hastings66,
   Author = {Hastings, A and Greenwood, R. M. and Proctor, M. H.},
   Title = {Legume inoculation in New Zealand},
   Publisher = {Department of Scientific and Industrial Research},
   Address = {Wellington},
   Series = {New Zealand. Department of Scientific and Industrial Research. Information series; No. 58},
   Abstract = {mostly good for saying that innoclation has been goin on in nz},
      Year = {1966} }




@article{
Haukka98,
   Author = {Haukka, K. and Lindstr\"om, K. and Young, J. P. W.},
   Title = {Three phylogenetic groups of \emph{nodA} and \emph{nifH} genes in \emph{Sinorhizobium} and \emph{Mesorhizobium} isolates from leguminous trees growing in Africa and Latin America},
   Journal = {Applied and Environmental Microbiology},
   Volume = {64},
   Number = {2},
   Pages = {419-426},
   Abstract = {The diversity and phylogeny of nodA and nifH genes were studied by using 52 rhizobial isolates from Acacia senegal, Prosopis chilensis, and related leguminous trees growing in Africa and Latin America. All of the strains had similar host ranges and belonged to the genera Sinorhizobium and Mesorhizobium, as previously determined by 16S rRNA gene sequence analysis. The restriction patterns and a sequence analysis of the nodA and nifH genes divided the strains into the following three distinct groups: sinorhizobia from Africa, sinorhizobia from Latin America, and mesorhizobia from both regions. In a phylogenetic tree also containing previously published sequences, the nodA genes of our rhizobia formed a branch of their own, but within the branch no correlation between symbiotic genes and host trees was apparent. Within the large group of African sinorhizobia, similar symbiotic gene types were found in different chromosomal backgrounds, suggesting that transfer of symbiotic genes has occurred across species boundaries. Most strains had plasmids, and the presence of plasmid-borne nifH was demonstrated by hybridization for some examples. The nodA and nifH genes of Sinorhizobium teranga ORS1009(T) grouped with the nodA and nifH genes of the other African sinorhizobia, but Sinorhizobium saheli ORS609(T) had a totally different nodA sequence, although it was closely related based on the 16S rRNA gene and nifH data. This might be because this S. saheli strain was originally isolated from Sesbania sp., which belongs to a different cross-nodulation group than Acacia and Prosopis spp. The factors that appear to have influenced the evolution of rhizobial symbiotic genes vary in importance at different taxonomic levels.},
      Year = {1998} }




@article{
Haukka96,
   Author = {Haukka, K. and Young, J. P. W. and Lindstr\"om, K.},
   Title = {Diversity of partial 16S rRNA sequences among and within strains of African rhizobia isolated from \emph{Acacia} and \emph{Prosopis}},
   Journal = {Systematic and Applied Microbiology},
   Volume = {19},
   Number = {3},
   Pages = {352-359},
   Abstract = {To assess the phylogenetic diversity of fast-growing rhizobium strains isolated from root nodules of Acacia senegal and Prosopis chilensis trees growing in Sudan and Kenya, a 230-nucleotide segment of the 16S ribosomal RNA gene was sequenced from each of thirty strains. Twelve different sequences were found: four were identical to those of previously described species, eight were novel. Sequence comparisons indicated that one strain belonged to the Rhizobium huakuii phylogenetic branch, while tile rest were Sinorhizobium, as they were close to S. (Rhizobium) meliloti, S. fredii, S. teranga and S. saheli. Isolates from Acacia and from Prosopis often had the same sequence, but the sequence type was not very well correlated with the phenotypic characteristics determined previously for these strains. One isolate had two 16S rRNA sequences, differing at six positions, in approximately equal copy number. The type strain of S. saheli was also shown to have two different sequences.},
   Keywords = {16S rRNA
Acacia
Diversity
Prosopis
Rhizobium
Sequence microheterogeneity
Sinorhizobium
bacterial rna
rna 16s
bacterial gene
phylogeny
rhizobium
rna sequence},
   Year = {1996} }




@article{
Heenan95b,
   Author = {Heenan, P. B.},
   Title = {A taxonomic revision of \emph{Carmichaelia} (Fabaceae -- Galegeae) in New Zealand. (part I)},
   Journal = {New Zealand Journal of Botany},
   Volume = {33},
   Number = {4},
   Pages = {455-475},
   Abstract = {Nine species are recognised in the first part of a revision of Carmichaelia. These are C. astonii, C. compacta, C. corrugata, C. curta, C. juncea, C. monroi, C. nana, C. uniflora, and C. vexillata. C. juncea and C. nana have priority over several later names, and C. vexillata is a new spe cies segregated from C. monroi. Synonymy, descriptions, distribution maps, habitat, variation, and illustrations are presented for all taxa. Conservation status is discussed for C. astonii, C. compacta, C. curta, and C. juncea.},
      Year = {1995} }




@article{
Heenan95c,
   Author = {Heenan, P. B.},
   Title = {The typification of \emph{Clianthus puniceus} (Fabaceae -- Galegeae)},
   Journal = {New Zealand Journal of Botany},
   Volume = {33},
   Number = {4},
   Pages = {561-562},
   Abstract = {A lectotype for Clianthus puniceus (G.Don) Sol. ex Lindl. is selected from the A. B. Lambert herbarium at the British Museum.},
      Year = {1995} }




@article{
Heenan95a,
   Author = {Heenan, P. B.},
   Title = {Typification of names in \emph{Carmichaelia}, \emph{Chordospartium}, \emph{Corallospartium}, and \emph{Notospartium} (Fabaceae-Galegeae) from New Zealand},
   Journal = {New Zealand Journal of Botany},
   Volume = {33},
   Number = {4},
   Pages = {439-454},
   Abstract = {All names of New Zealand species and varieties in Carmichaelia, Chordospartium, Corallospartium, and Notospartium are typified as background to a revision of these genera.},
      Year = {1995} }




@article{
Heenan96a,
   Author = {Heenan, P. B.},
   Title = {Identification and distribution of the Marlborough pink brooms, \emph{Notospartium carmichaeliae} and \emph{N. glabrescens} (Fabaceae - Galegeae), in New Zealand},
   Journal = {New Zealand Journal of Botany},
   Volume = {34},
   Number = {3},
   Abstract = {Notospartium is accepted as comprising three species, N. carmichaeliae, N. glabrescens, and N. torulosum. However, in the recent literature, N. carmichaeliae and N. glabrescens have been confused or one treated as a synonym of the other. These two species are allopatric, growing on riparian bluffs, cliffs, and alluvium in western and eastern Marlborough respectively; they are separated by the Awatere Fault, which runs parallel to the Awatere River. The southern limit of N. glabrescens and the northern limit of N. torulosum fall on either side of the Hope Fault. N. glabrescens is a calcicole, occurring on soils derived from base-rich limestone, sandstone, mudstone, and siltstone parent materials. N. carmichaeliae occurs on well-indurated greywackes of the Torlesse Supergroup which are base-poor. The pods, a key diagnostic feature of both species, are illustrated and conservation status is reassessed.},
      Year = {1996} }




@article{
Heenan96b,
   Author = {Heenan, P. B.},
   Title = {A taxonomic revision of \emph{Carmichaelia} (Fabaceae -- Galegeae) in New Zealand. (Part II)},
   Journal = {New Zealand Journal of Botany},
   Volume = {34},
   Number = {2},
   Pages = {157-177},
   Abstract = {Eight species are recognised in the second part of a revision of Carmichaelia. These are C. appressa, C. arborea, C. australis, C. hollowayi, C. kirkii, C. odorata, C. petriei, and C. williamsii. Carmichaelia arborea is the earliest name for plants previously known as C. grandiflora. Carmichaelia odorata includes C. angustata and C. glabrata in synonymy, and C. australis is the earliest name for the widespread shrubby broom which previous authors have segregated into numerous species, including C. aligera, C. flagelliformis, C. ovata, and C. robusta. Synonymy, descriptions, distribution maps, habitats, variation, and illustrations are presented. Conservation status is discussed for C. appressa, C. hollowayi, C. kirkii, and C. williamsii.},
      Year = {1996} }




@article{
Heenan97c,
   Author = {Heenan, P. B.},
   Title = {Fruit anatomy of \emph{Clianthus puniceus} and \emph{Swainsona novae-zelandiae} (Fabaceae - Galegeae)},
   Journal = {New Zealand Journal of Botany},
   Volume = {35},
   Number = {1},
   Pages = {119-123},
   Abstract = {The anatomy of the fruit of Clianthus puniceus and Swainsona novae-zelandiae is described. Distinctive features of C. puniceus include a thick mesocarp with 30-36 layers of parenchymatous cells, a layer of fibres 4-12 cells high, and the fibres of an average length of 0.86 mm and oriented transverse to the longitudinal axis of the fruit. S. novae-zelandiae has a thin mesocarp with 10-14 layers of parenchymatous cells, and two layers of fibres in which each layer is 1-2 cells high and the layers are crossed and oriented diagonal to the longitudinal axis of the fruit. The fibres are an average length of 0.51 mm. The dehiscence mechanisms differ, the fruit of S. novae-zelandiae having an abscission layer through the median vascular system and dehiscence promoted by differential shrinkage of the crossing fibres. The follicle of C, puniceus is likely to dehisce by differential shrinkage of different cell layers.},
      Year = {1997} }




@article{
Heenan97d,
   Author = {Heenan, P. B.},
   Title = {Heteroblasty in \emph{Carmichaelia}, \emph{Chordospartium}, \emph{Corallospartium}, and \emph{Notospartium} (Fabaceae - Galegeae) from New Zealand},
   Journal = {New Zealand Journal of Botany},
   Volume = {35},
   Number = {2},
   Pages = {243-249},
   Abstract = {Habit-heteroblasty is described for Chordospartium, Corallospartium, Notospartium, and most species of Carmichaelia. Transition from the juvenile to the adult occurs in the first year after seed germination and is marked by an abrupt change in stem habit and morphology and in leafiness. Carmichaelia astonii, C. monroi, C. nana, and C. williamsii pass from the juvenile to the adult without change. Leaf-heteroblasty occurs in Chordospartium, Corallospartium, and Notospartium, whereas the leaves of Carmichaelia are usually of similar shape on juvenile and adult plants. The orientation of the juvenile stems can be correlated with ecological preferences. The patterns of heteroblastic development described are not well correlated with the generic boundaries of the Carmichaelia complex.},
   Keywords = {Carmichaelia
Chordospartium
Corallospartium
Fabaceae
Galegeae
Habit-heteroblasty
Ju venility
Leaf-heteroblasty
New Zealand flora
Notospartium
Carmichaelia
Chordospartium
Corallospartium
Notospartium
Carmichaelia astonii
Carmichaelia monroi
Carmichaelia nana
Carmichaelia williamsii
Fabaceae
growth habit
heteroblasty
leafiness
morphology
New Zealand},
   Year = {1997} }




@article{
Heenan97a,
   Author = {Heenan, P. B.},
   Title = {Wood anatomy of the \emph{Carmichaelia} (Fabaceae) complex in New Zealand},
   Journal = {New Zealand Journal of Botany},
   Volume = {35},
   Number = {3},
   Pages = {395-415},
   Abstract = {Wood anatomy of Carmichaelia australis, Ca. compacta, Ca. corrugata, Ca. monroi, Ca. nana, Ca. odorata, Ca. petriei, Ca. williamsii, Chordospartium muritai, Ch. stevensonii, Corallospartium crassicaule, Notospartium carmichaeliae, N. glabrescens, and N. torulosum is described. These species share vessels with helical thickening and simple perforations; vessels, axial parenchyma, and short rays arranged in storied structure; predominantly fusiform parenchyma; and rays 1-20 cells wide. The ray cells of Carmichaelia and Corallospartium are procumbent, square, or upright, and those of Chordospartium and Notospartium procumbent. The wood of the Carmichaelia complex has well developed xeromorphic features that include narrow diameter and short vessel elements, high numbers of vessels per mm(2), and the vessels usually arranged in pronounced diagonal aggregations. Vulnerability and mesomorphy indices are calculated and these support the relationship between species wood anatomy and the xeric habitats they occupy.},
      Year = {1997} }




@article{
Heenan98c,
   Author = {Heenan, P. B.},
   Title = {An emended circumscription of \emph{Carmichaelia}, with new combinations, a key, and notes on hybrids},
   Journal = {New Zealand Journal of Botany},
   Volume = {36},
   Number = {1},
   Pages = {53-63},
   Abstract = {The circumscription of Carmichaelia is emended to accommodate Chordospartium, Corallospartium and Notospartium following the recommendations made in a recent phylogenetic study of the group. Accordingly, Carmichaelia crassicaule is reinstated and the following new combinations are made: Carmichaelia carmichaeliae, Carmichaelia glabrescens, Carmichaelia muritai, Carmichaelia stevensonii, and Carmichaelia torulosa. A dichotomous key is presented to the 23 species of Carmichaelia that are indigenous to New Zealand. Natural and garden-originated interspecific hybrids of Carmichaelia are also listed and briefly described.},
      Year = {1998} }




@article{
Heenan98d,
   Author = {Heenan, P. B.},
   Title = {\emph{Montigena} (Fabaceae), a new genus endemic to New Zealand},
   Journal = {New Zealand Journal of Botany},
   Volume = {36},
   Number = {1},
   Pages = {41-51},
   Abstract = {Montigena, a new monotypic genus, is distinguished from Swainsona by a strongly rhizomatous habit, terminal innovation shoots, stems with persistent pith, vessel elements with helical thickenings, well developed ray parenchyma, and slender and flexuose phloem fibres. A new combination Montigena novae-zelandiae replaces Swainsona novae-zelandiae as the name for this legume that is endemic to the dry eastern mountains of the South Island of New Zealand, where it grows on partially stable screes. A botanical description is presented, followed by detailed notes on growth habit, rhizome anatomy, leaf anatomy, distribution, and habitats, with an assessment of conservation status.},
      Year = {1998} }




@article{
Heenan98a,
   Author = {Heenan, P. B.},
   Title = {Phylogenetic anaylsis of the \emph{Carmichaelia} complex, \emph{Clianthus}, and \emph{Swainsona} (Fabaceae), from Australia and New Zealand},
   Journal = {New Zealand Journal of Botany},
   Volume = {36},
   Number = {1},
   Pages = {21-40},
   Abstract = {A phylogenetic analysis of Carmichaelia, Chordospartium, Corallospartium, Notospartium, Clianthus, and Swainsona was undertaken to test the monophyly of each genus and to examine relationships among species. The data matrix included 42 terminal taxa and 47 mainly morphological and anatomical characters. PAUP analyses resulted in two islands of equally parsimonious trees of 175 steps. Strict consensus trees identify a monophyletic New Zealand clade and a monophyletic Australian clade, and the phylogenetic analysis infers a single dispersal event to New Zealand. The taxa in the New Zealand clade are characterised by being woody shrubs or subshrubs, having terminal innovation shoots, persistent pith, wide ray parenchyma, vessel elements with helical thickenings, and slender and flexuose phloem fibres. Swainsona is polyphyletic if S. novae-zelandiae is included, and Carmichaelia is paraphyletic if Chordospartium, Corallospartium, and Notospartium are excluded. Recommendations are made for a revised generic classification with recognition of four monophyletic genera: Clianthus, Australian Swainsona, segregation of Swainsona novae-zelandiae from Swainsona, and enlargement of Carmichaelia to include Chordospartium, Corallospartium, and Notospartium. The inclusion of five quantitative characters and reweighting of all characters by the rescaled consistency index assisted in resolving polytomies within the Carmichaelia clade.},
      Year = {1998} }




@article{
Heenan98e,
   Author = {Heenan, P. B.},
   Title = {The pollination system and stigmatic cuticle of \emph{Clianthus puniceus} (Fabaceae)},
   Journal = {New Zealand Journal of Botany},
   Volume = {36},
   Number = {2},
   Pages = {311-314},
   Abstract = {Clianthus puniceus and C. puniceus var. maximus have a protective cuticle covering the stigma. When intact this cuticle prevents pollination, but when it is ruptured pollination can occur. At flower senescence the cuticle on C. puniceus ruptures allowing self-pollination to occur, whereas on C. puniceus var. maximus it usually remains intact. An absence of pollinators for C. puniceus var. maximus is likely to limit seed set in wild populations.},
   Keywords = {Clianthus puniceus
Clianthus puniceus var. maximus
New Zealand flora
Pollination
Stigma
Stigmatic cuticle
Threatened species
cuticle
mating system
plant development
pollination
pollination
reproductive strategy
Clianthus puniceus},
   Year = {1998} }




@article{
Heenan98b,
   Author = {Heenan, P. B.},
   Title = {Reinstatement of \emph{Sophora longicarinata} (Fabaceae -- Sophoreae) from northern South Island, New Zealand, and typification of \emph{S. microphylla}},
   Journal = {New Zealand Journal of Botany},
   Volume = {36},
   Number = {3},
   Pages = {369-379},
   Abstract = {Sophora longicarinata is reinstated at species rank, having recently been placed as a variety of S. microphylla. Sophora longicarinata is recognised by a suite of characters, including its lack of a juvenile growth phase, its shrubby, slender growth habit, sometimes producing several main stems from below ground level, and often suckering, its small, dark green, and numerous leaflets, and often twisted pedicels and flowers that are inverted in bud. Sophora longicarinata is restricted to marble and other limestone areas in northern Nelson and western Marlborough, is sparsely distributed, has few plants at each locality, and is considered to be a local endemic.

A lectotype for S. microphylla is selected from the Banks and Solander herbarium at the Natural History Museum, London.},
      Year = {1998} }




@article{
Heenan00,
   Author = {Heenan, P. B.},
   Title = {\emph{Clianthus} (Fabaceae) in New Zealand: a reappraisal of Colenso's taxonomy},
   Journal = {New Zealand Journal of Botany},
   Volume = {38},
   Number = {3},
   Pages = {361-371},
   Abstract = {Two species of Clianthus are accepted as endemic to New Zealand. Clianthus puniceus refers to plants with matte, grey-green, and narrow leaves, and light salmon-red or salmon-pink flowers. Clianthus maximus, described by W. Colenso in 1885, is reinstated at species rank. Clianthus maximus is distinguished from C. puniceus by its leaves, which are glossy, green, and broad, and its flower which is significantly larger and a dark salmon-red, red, or orange-red colour. The glossiness of C. maximus leaves results from a thick layer of epicuticular waxes; in C. puniceus the matte surface results from the cuticle which is ornamented with a reticulum of buttressed ridges. The two species are considered to be threatened, with C. maximus having a rank of vulnerable, whereas C. puniceus is critically endangered.},
      Year = {2000} }




@article{
Heenan01a,
   Author = {Heenan, P. B.},
   Title = {The correct name for Chilean pelu (Fabaceae): the identity of \emph{Edwardsia macnabiana} and the reinstatement of \emph{Sophora cassioides}},
   Journal = {New Zealand Journal of Botany},
   Volume = {39},
   Number = {1},
   Pages = {167-170},
   Abstract = {The earliest available legitimate name for the Chilean tree legume, pelu, is Sophora cassioides. This is reinstated and a type specimen selected from the herbarium of F. Philippi. Pelu has previously been known as S. microphylla, a name now considered to belong to a New Zealand endemic and also as S. macnabiana and S. microphylla subsp. macnabiana. Type material of Edwardsia macnabiana, the basionym of S. macnabiana and S. microphylla subsp. macnabiana, has not been found in the Robert Graham herbarium and there was insufficient information in the protologue to allow the selection of a suitable neotype. The name E. macnabiana, and its nomenclatural synonyms, were therefore abandoned. It was also shown that the combination Sophora macnabiana, which has been attributed to Skottsberg, was not validly published.},
      Year = {2001} }




@article{
Heenan01b,
   Author = {Heenan, P. B.},
   Title = {Relationships of Streblorrhiza (Fabaceae), an extinct monotypic genus from Phillip Island, South Pacific Ocean},
   Journal = {New Zealand Journal of Botany},
   Volume = {39},
   Number = {1},
   Pages = {9-15},
   Abstract = {Aspects of the stem, fruit, and leaf anatomy and morphology are described for the extinct Streblorrhiza speciosa. The stems of Streblorrhiza have persistent pith, upright ray parenchyma cells, and the vessels are solitary or in radial multiples, with single perforations, no helical thickenings, their pits are alternate and vestured, and they sometimes have grooves interconnecting pit apertures. An important fruit character of Streblorrhiza is the orientation of the fibres in a single direction, a character shared with the New Zealand Clianthus and Carmichaelia.},
      Year = {2001} }




@article{
Heenan04,
   Author = {Heenan, P. B. and Dawson, M. I. and Wagstaff, S. J.},
   Title = {The relationship of \emph{Sophora} sect.~\emph{Edwardsia} (Fabaceae) to \emph{Sophora tomentosa}, the type species of the genus \emph{Sophora}, observed from DNA sequence data and morphological characters},
   Journal = {Botanical Journal of the Linnean Society},
   Volume = {146},
   Number = {4},
   Pages = {439-446},
   Abstract = {Sophora tomentosa, the type species of the genus Sophora, is shown by phylogenetic analyses of rbcL and ITS sequence data to be sister to Sophora sect. Edwardsia. S. tomentosa and most of the species from sect. Edwardsia share hypogeal germination, exstipulate leaves, and terete filaments. These species have buoyant seeds, and are distributed by ocean currents throughout the pantropics (S. tomentosa) and around southern temperate oceanic islands (sect. Edwardsia). S. tomentosa differs from the species of sect. Edwardsia by its frutescent growth habit, terminal elongate inflorescence and smooth-walled legume. S. macrocarpa is unusual in sect. Edwardsia as its leaves have stipules, the filaments are winged, and the legume is smooth-walled. © 2004 The Linnean Society of London.},
   Keywords = {ITS
New Zealand flora
Phylogeny
rbcL
Sophora macrocarpa
Sophora tomentosa},
   Year = {2004} }




@article{
Heenan99,
   Author = {Heenan, P. B. and de Lange, P. J.},
   Title = {Reproductive biology, ecology and conservation of \emph{Carmichaelia williamsii} (Fabaceae), a vulnerable legume from New Zealand},
   Journal = {Pacific Conservation Biology},
   Volume = {5},
   Number = {3},
   Pages = {179-190},
   Abstract = {Carmichaelia williamsii is a threatened leguminous shrub that is most common on the Poor Knights Islands and Aldermen Islands, northern New Zealand. Flower morphology and structure of C. williamsii is suited to a bird pollination syndrome as the floral parts are stout, the petals yellow, the nectar source is distant from the stigma, and the flowers lack scent. The stigma is covered by a protective cuticle that prevents pollination until it is ruptured, which would usually be by foraging birds. Experimental self- and cross-pollinations demonstrated that if the cuticle is not ruptured fertilization will not occur, and that the species is self-compatible. Field observations on Aorangi Island, Poor Knights Islands, confirmed that C. williamsii is probably bird pollinated as plants in full flower were being systematically worked by the native passerine honeyeater the Bellbird (Anthornis melanura; Meliphagidae). C. williamsii mainly grows in seral habitats, and populations often comprise plants of a similar height class. Introduced rats and the loss of pollinating birds could pose conservation and management problems for the species.},
   Keywords = {Carmichaelia williamsii
Ecology
Management and New Zealand
Pollination
conservation status
legume
pollination
reproductive biology
zoochory
New Zealand
Carmichaelia williamsii},
   Year = {1999} }




@article{
Heenan01c,
   Author = {Heenan, P. B. and de Lange, P. J. and Wilton, A. D.},
   Title = {\emph{Sophora} (Fabaceae) in New Zealand: taxonomy, distribution, and biogeography},
   Journal = {New Zealand Journal of Botany},
   Volume = {39},
   Number = {1},
   Pages = {17-53},
   Abstract = {A taxonomic treatment is provided for the Sophora microphylla complex in New Zealand. Sophora microphylla sensu stricto is endemic to New Zealand and includes those plants with a distinct divaricating and/or strongly flexuose juvenile phase, orange-brown to yellow-brown juvenile stems and distant leaflets. S. chathamica is reinstated at species rank, S. fulvida is a new combination provided for the taxon previously known as S. microphylla var. fulvida, and S. godleyi and S. molloyi are described as new species. S. chathamica, S. fulvida, S. godleyi and S. molloyi lacked a divaricating and/or strongly flexuose juvenile phase and were each distinguished by a number of leaf characters. S. fulvida and S. godleyi have distinctive leaf hairs. S. chathamica is a predominant coastal species in Northland, Auckland, Waikato, Wellington and the Chatham Islands. S. fulvida occurs in Northland and North Auckland on volcanic rock outcrops, S. godleyi occurs on calcareous mudstone and sandstone in eastern Taranaki, King Country, Wanganui and Manawatu and S. molloyi is restricted to extremely dry and exposed bluffs and rock outcrops of southern North Island headlands, Kapiti Island and several islands in Cook Strait. Cluster analyses of 11 leaf and 4 growth habit characters provided additional support for the revised classification, and variation in 7 leaf characters was evaluated with box plots. A key was provided to Sophora in New Zealand, hybridism is discussed, an assessment of each species' conservation status is made, and biogeography is reconsidered in view of the new taxonomic treatment.},
      Year = {2001} }




@article{
Helal84,
   Author = {Helal, H. M. and Sauerbeck, D. R.},
   Title = {Influence of plant roots on C and P metabolism in soil.},
   Journal = {Plant and Soil},
   Volume = {76},
   Number = {1-3},
   Pages = {175-182},
   Abstract = {Soil zones differently affected by plant roots can be separated for subsequent analysis. The C released from maize Zea mays roots to soil was 13% of the total assimilated C. The remaining root- derived C in soil was relatively small (15%). Maize roots induced a decrease in organic soil C and in both total and isotopically exchangeable soil P. On the other hand they increased the microbial biomass C, phosphatase activity, bicarbonate extractable organic P and phospholipid P and enhanced the incorporation of 32P into organic P fractions. Both root C and root influences were detectable outside the immediate root zone. Results demonstrate an intensive C turnover and P mobilization in the rhizosphere soil, including some organic P fractions. -from Authors},
      Year = {1984} }




@article{
Henikoff88,
   Author = {Henikoff, S. and Haughn, G. W. and Calvo, J. M. and Wallace, J. C.},
   Title = {A large family of bacterial activator proteins},
   Journal = {Proceedings of the National Academy of Sciences of the United States of America},
   Volume = {85},
   Number = {18},
   Pages = {6602-6606},
   Abstract = {At least nine different bacterial proteins belong to the LysR family. The gene sequence for one of these proteins is presented here. Six others (Escherichia coli LysR, IlvY, CysB; Salmonella typhimurium MetR; Rhizobium NodD; and Enterobacter cloacae AmpR) are known to activate other genes. Based on sequence alignments, each member of this family is predicted to have a helix-turn-helix DNA binding motif near its amino terminus. The combined evidence indicates that all nine proteins are related by common ancestry, are similarly folded, and are not detectably related to other known bacterial regulatory proteins. The DNA database searching procedure and other methods used in this study should be useful in detecting other groups of related proteins.},
      Year = {1988} }




@article{
Hennecke85,
   Author = {Hennecke, H. and Kaluza, K. and Th\"ony, B and Fuhrmann, M. and Ludwig, W. and Stackebrandt, E},
   Title = {Concurrent evolution of nitrogenase genes and 16S rRNA in Rhizobium species and  other nitrogen fixing bacteria.},
   Journal = {Archives of Microbiology},
   Volume = {142},
   Pages = {342-348},
      Year = {1985} }




@article{
Henz05,
   Author = {Henz, S. R. and Huson, D. H. and Auch, A. F. and Nieselt-Struwe, K. and Schuster, S. C.},
   Title = {Whole-genome prokaryotic phylogeny},
   Journal = {Bioinformatics},
   Volume = {21},
   Number = {10},
   Pages = {2329-2335},
   Abstract = {Current understanding of the phylogeny of prokaryotes is based on the comparison of the highly conserved small ssu-rRNA subunit and similar regions. Although such molecules have proved to be very useful phylogenetic markers, mutational saturation is a problem, due to their restricted lengths. Now, a growing number of complete prokaryotic genomes are available. This paper addresses the problem of determining a prokaryotic phylogeny utilizing the comparison of complete genomes. We introduce a new strategy, GBDP, 'genome blast distance phylogeny', and show that different variants of this approach robustly produce phylogenies that are biologically sound, when applied to 91 prokaryotic genomes. In this approach, first Blast is used to compare genomes, then a distance matrix is computed, and finally a tree- or network-reconstruction method such as UPGMA, Neighbor-Joining, BioNJ or Neighbor-Net is applied. © The Author 2004. Published by Oxford University Press. All rights reserved.},
      Year = {2005} }




@article{
Hernandez95b,
   Author = {Hern\'andez-Lucas, I. and Pardo, M. A. and Segovia, L. and Miranda, J. and Mart\'inez-Romero, E.},
   Title = {Rhizobium tropici chromosomal citrate synthase gene},
   Journal = {Applied and Environmental Microbiology},
   Volume = {61},
   Number = {11},
   Pages = {3992-3997},
   Abstract = {Two genes encoding citrate synthase, a key enzyme in the Krebs cycle, have been found in Rhizobium tropici. One of them is in the bacterial chromosome, while the other is in the symbiotic plasmid. We sequenced the chromosomal gene and found that it is very similar to the previously reported plasmidic gene sequence in its structural region but not in its regulatory region. The chromosomal gene is able to complement an Escherichia coli titrate synthase mutant. In R. tropici, a mutant in the chromosomal citrate synthase gene has a diminished citrate synthase activity (in free-living bacteria), a diminished nodulation capacity, and forms nitrogen-fixing nodules. In contrast, the citrate synthase double mutant forms ineffective nodules devoid of bacteroids and forms less nodules than the single chromosomal mutant. It is inferred that both genes are functional and required during the nodulation process in R. tropici.},
   Keywords = {citrate synthase
rhizobium
Genes, Bacterial},
   Year = {1995} }




@article{
Hernandez04,
   Author = {Hern\'andez-Lucas, I. and Rogel-Hern\'andez, M. A. and Mart\'inez-Romero, E. and Segovia, L. and Rojas-Jim\'enez, K.},
   Title = {Phylogenetic relationships of rhizobia based on citrate synthase gene sequences},
   Journal = {Systematic and Applied Microbiology},
   Volume = {27},
   Number = {6},
   Pages = {703-706},
   Abstract = {Partial nucleotide sequences of the citrate synthase (gltA) gene from different rhizobia genera were determined. Tree topologies based on this housekeeping gene were similar to that obtained using 16S rRNA sequences. However gltA appeared to be more reliable at determining phylogenetic relationships of closely related taxa. We propose gltA sequences as an additional tool to be used in molecular phylogenetic studies.},
   Keywords = {16S rRNA
gltA
Phylogeny},
   Year = {2004} }




@article{
Hernandez95a,
   Author = {Hern\'andez-Lucas, I. and Segovia, L. and Mart\'inez-Romero, E. and Pueppke, S. G.},
   Title = {Phylogenetic relationships and host range of Rhizobium spp. that nodulate Phaseolus vulgaris L.},
   Journal = {Applied and Environmental Microbiology},
   Volume = {61},
   Number = {7},
   Pages = {2775-2779},
   Abstract = {We determined the nucleotide sequences of 16S rRNA gene segments from five Rhizobium strains that have been isolated from tropical legume species. All share the capacity to nodulate Phaseolus vulgaris L., the common bean. Phylogenetic analysis confirmed that these strains are of two different chromosomal lineages. We defined the host ranges of two strains of Rhizobium etli and three strains of R. tropici, comparing them with those of the two most divergently related new strains. Twenty-two of the 43 tested legume species were nodulated by three or more of these strains. All seven strains have broad host ranges that include woody species such as Albizia lebbeck, Gliricidia maculata, and Leucaena leucocephala.},
   Keywords = {rna 16s
rhizobium
Plants, Medicinal
Phaseolus vulgaris},
   Year = {1995} }




@article{
Herrera99,
   Author = {Herrera-Cervera, J. A. and Caballero-Mellado, J. and Laguerre, G. and Tichy, H. V. and Requena, N. and Amarger, N. and Mart\'inez-Romero, E. and Olivares, J. and Sanjuan, J.},
   Title = {At least five rhizobial species nodulate Phaseolus vulgaris in a Spanish soil},
   Journal = {FEMS Microbiology Ecology},
   Volume = {30},
   Number = {1},
   Pages = {87-97},
   Abstract = {The genetic relationships among bacteria nodulating Phaseolus vulgaris in a soil of Granada, Spain, were investigated by multilocus enzyme electrophoresis, restriction fragment length polymorphism and partial sequencing of the 16S rRNA genes and restriction fragment length polymorphisms of symbiotic genes. Multilocus enzyme electrophoresis analysis of 39 isolates determined 11 different electrophoretic types, clustered into three main genetic groups. Genetic distances between groups were above 0.8. Five different 16S rRNA gene alleles were identified in this population, corresponding to previously described rhizobial species, Rhizobium etli, Rhizobium fredii, Rhizobium gallicum, Rhizobium giardinii and Rhizobium leguminosarum. Using R. etli strain CFN42 nifH and nodB genes as hybridization probes, identical restriction fragment length polymorphism profiles were found among isolates belonging to four different 16S rRNA gene species, indicative of interspecific gene transfer. Most of the bean-nodulating strains carried three copies of nifH and strongly hybridized to the nodB gene of R. etli CFN42, suggesting that their symbiotic plasmid genes are organized similarly. Combined data from multilocus enzyme electrophoresis and 16S allele characterization indicate that more than five bacterial species compose this rhizobial population, as almost identical 16S rDNA alleles were identified in isolates belonging to deeply divergent multilocus enzyme electrophoresis lineages. (C) 1999 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.},
      Year = {1999} }




@article{
Herrera98,
   Author = {Herrera-Cervera, J. A. and Sanjuan-Pinilla, J. M. and Olivares, J. and Sanjuan, J.},
   Title = {Cloning and identification of conjugative transfer origins in the Rhizobium meliloti genome},
   Journal = {Journal of Bacteriology},
   Volume = {180},
   Number = {17},
   Pages = {4583-4590},
   Abstract = {A simple approach was used to identify Rhizobium meliloti DNA regions with the ability to convert a nontransmissible vector into a mobilizable plasmid, i.e., to contain origins of conjugative transfer (oriT, mob). RecA- defective R. meliloti merodiploid populations, where each individual contained a hybrid cosmid from an R. meliloti GR4 gene library, were used as donors en masse in conjugation with another R. meliloti recipient strain, selecting transconjugants for vector-encoded antibiotic resistance. Restriction analysis of cosmids isolated from individual transconjugants resulted in the identification of 11 nonoverlapping DNA regions containing potential oriTs. Individual hybrid cosmids were confirmed to be mobilized from the Original recA donors at frequencies ranging from 10-2 to 10-5 per recipient cell. DNA hybridization experiments showed that seven mob DNA regions correspond to plasmid replicons: four on symbiotic megaplasmid 1 (pSym1), one on pSym2, and another two on each of the two cryptic plasmids harbored by R. meliloti GR4. Another three mob clones could not be located to any plasmid and were therefore preliminarily assigned to the chromosome. With this strategy, we were able to characterize the oriT of the conjugative plasmid pRmeGR4a, which confirmed the reliability of the approach to select for oriTs. Moreover, transfer of the 11 mob cosmids from R. meliloti into Escherichia coli occurred at frequencies as high as 10-1, demonstrating the R. meliloti gene transfer capacity is not limited to the family Rhizobiaceae. Our results show that the R. meliloti genome contains multiple oriTs that allow efficient DNA mobilization to rhizobia as well as to phylogenetically distant gram-negative bacteria.},
      Year = {1998} }




@article{
Herrick97,
   Author = {Herrick, J. B. and Stuart-Keil, K. G. and Ghiorse, W. C. and Madsen, E. L.},
   Title = {Natural horizontal transfer of a naphthalene dioxygenase gene between bacteria native to a coal tar-contaminated field site},
   Journal = {Applied and Environmental Microbiology},
   Volume = {63},
   Number = {6},
   Pages = {2330-2337},
   Abstract = {Horizontal transfer of genes responsible for pollutant biodegradation may play a key role in the evolution of bacterial populations and the adaptation of microbial communities to environmental contaminants. However, held evidence fur horizontal gene transfer between microorganisms has traditionally been very difficult to obtain. In this study, the sequences of the 16S rRNA and naphthalene dioxygenase iron-sulfur protein (nahAc) genes of nine naphthalene-degrading bacteria isolated from a coal tar waste- contaminated site, as well as a naphthalene-degrading bacterium from a contaminated site in Washington state and two archetypal naphthalene- degrading strains, were compared. Seven strains from the study site had a single nahAc allele, whereas the 16S rRNA gene sequences of the strains differed by as much as 7.9%. No nahAc alleles from the site were identical to those of the archetypal strains, although the predominant allele was closely related to that of Pseudomonas putida NCIB 9816-4, isolated in the British Isles. However, one site-derived nahAc allele was identical to that of the Washington state strain. Lack of phylogenetic congruence of the nahAc and 16S rRNA genes indicates that relatively recent in situ horizontal transfer of the nahAc gene has occurred, possibly as a direct or indirect consequence of pollutant contamination. Alkaline lysis plasmid preparations and pulsed- field gel electrophoresis have revealed the presence of plasmids ranging in size from 70 to 88 kb in all site isolates. Southern hybridizations with a 417-bp nahAc probe have suggested that the nahAc gene is plasmid borne in all the site isolates but one, a strain isolated from subsurface sediment 400 m upstream from the source of the other site isolates. In this strain and in the naphthalene-degrading strain from Washington state, nahAc appears to be chromosomally located. In addition, one site isolate may carry nahAc on both chromosome and plasmid. Within the group of bacteria with identical nahAc sequences, the Southern hybridizations showed that the gene was distributed between plasmids of different sizes and a chromosome. This suggests that plasmid modification after transfer may have been effected by transposons. Horizontal transfer of catabolic genes may play a significant role in the acclimation of microbial communities to pollutants.},
      Year = {1997} }




@article{
Hicks01,
   Author = {Hicks, D. L. and Campbell, D. J. and Atkinson, I. A. E.},
   Title = {Options for managing the Kaimaumau Wetland, Northland, New Zealand},
   Journal = {Science for Conservation},
   Volume = {155},
   Pages = {5-75},
   Abstract = {This report details results of a scoping study made during the 1996/97 summer to identify possible management responses to the major problems affecting the Kaimaumau wetland. The perceived drying out of the wetland is found to be real but is a consequence of a run of lower-than-normal annual rainfalls rather than effects of drainage in and around the wetland. A feature of wetlands on sand country is that seasonally inundated margins surround a permanent wet zone. During a run of dry years, water table rise is less and shorter in duration. Recommendations are made concerning management of water levels in the wetland. Invasion of the wetland system by woody weeds, particularly Sydney golden wattle, is the most serious management problem. Trials for developing methods of replacing wattle with native trees are recommended. Trials are also needed to clarify the relationship between fires and the distribution and abundance of rare plants in the wetland. Systematic monitoring of some populations of these plants is necessary to identify the threats affecting them and thus the remedial actions needed. The difficulty of managing fire-adapted native vegetation against incursions by fire-adapted introduced weeds is discussed. Several recommendations are made for inclusion in a fire contingency plan. Use of large-scale controlled burning as a method of reducing the fuel load and thus the fire hazard is not recommended because of the risks of accelerating the spread of woody weeds and initiating persistent peat fires. Small-scale tightly controlled and carefully timed burns could be used to create habitats for some threatened plants. Suggestions are made for rationalising the boundaries of the Scientific Reserve. Inclusion of Lake Waikaramu within the Scientific Reserve is recommended, as comparable habitats within Lake Ohia have been lost. It is recommended that more opportunities are made for involving the local community in the management of the Kaimaumau wetland.},
   Keywords = {Acacia longifolia
Aupouri Ecological district
Drainage management
Fire hazard control
Fireadapted weeds
Kaimaumau wetland
Lake Waikaramu
Sand dunes
Scientific reserve
Threatened plants
Wetlands
conservation management
habitat management
hydrology
wetland management
New Zealand},
   Year = {2001} }




@article{
Higgins86,
   Author = {Higgins, C. F. and Hiles, I. D. and Salmond, G. P. C.},
   Title = {A family of related ATP-binding subunits coupled to many distinct biological processes in bacteria},
   Journal = {Nature},
   Volume = {323},
   Number = {6087},
   Pages = {448-450},
   Abstract = {Many biological processes are coupled to ATP hydrolysis. We describe here a class of closely related ATP-binding proteins, from several bacterial species, which are associated with a variety of cellular functions including membrane transport, cell division, nodulation in Rhizobium and haemolysin export. These proteins comprise a family of structurally and functionally related subunits which share a common evolutionary origin, bind ATP and probably serve to couple ATP hydrolysis to each of these biological processes. This finding suggests a specific role for ATP in cell division, nodulation during nitrogen fixation and protein export, and allows us to assign a probable function to one of the protein components from each of these systems.},
      Year = {1986} }




@article{
Hilario04,
   Author = {Hilario, E. and Buckley, T. R. and Young, J. M.},
   Title = {Improved resolution on the phylogenetic relationships among \emph{Pseudomonas} by the combined analysis of \emph{atpD}, \emph{carA}, \emph{recA} and 16S rDNA},
   Journal = {Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology},
   Volume = {86},
   Number = {1},
   Pages = {51-64},
   Abstract = {A study of representatives of the bacterial genus Pseudomonas, analysing a combined data set of four molecular sequences with completely different properties and evolutionary constraints, is reported. The best evolutionary model was obtained with a hierarchical hypothesis testing program to describe each data set and the combined data set is presented and analysed under the likelihood criterion. The resolution among Pseudomonas taxa based on the combined data set analysis of the different lineages increased due to a synergistic effect of the individual data sets. The unresolved fluorescens lineage, as well as other weakly supported lineages in the single data set trees, should be revised in detail at the biochemical and molecular level. The taxonomic status of biovars of P. putida is discussed.},
      Year = {2004} }




@article{
Hilario93,
   Author = {Hilario, E. and Gogarten, J. P.},
   Title = {Horizontal transfer of ATPase genes--the tree of life becomes a net of life},
   Journal = {Biosystems},
   Volume = {31},
   Number = {2-3},
   Pages = {111-9},
   Abstract = {An ancient gene duplication gave rise to the catalytic and non-catalytic subunits of each of the three types of proton pumping ATPases: vacuolar, archaebacterial and eubacterial. Previously, this gene duplication has been used to root the universal tree of life. However, recent findings of archaebacterial type ATPases in eubacteria and of eubacterial type in an archaebacterium suggested that both types of ATPases may have been already present in the last common ancestor. Here we show that a phylogenetic analysis of these ATPase subunits indicates that this conclusion is premature. We suggest that horizontal gene transfer can explain the data. In addition, we show that the analysis of glutamate dehydrogenases data neither affirm nor contradict any particular placement of the last common ancestor in the universal tree of life. The prevalence and the mode of horizontal gene transfer is discussed.},
   Keywords = {Adenosinetriphosphatase/*genetics
Archaea/classification/enzymology/genetics
Enterococcus/enzymology/genetics
Eukaryotic Cells/enzymology
*Evolution
*Genes, Bacterial
Glutamate Dehydrogenase/genetics
Multigene Family
Phylogeny
Support, Non-U.S. Gov't
Support, U.S. Gov't, Non-P.H.S.
Thermus thermophilus/enzymology/genetics},
   Year = {1993} }




@article{
Hill02,
   Author = {Hill, R. L. and Gourlay, A. H.},
   Title = {Host-range testing, introduction, and establishment of Cydia succedana (Lepidoptera: Tortricidae) for biological control of gorse, Ulex europaeus L., in New Zealand},
   Journal = {Biological Control},
   Volume = {25},
   Number = {2},
   Pages = {173-186},
   Abstract = {Cydia succedana Denis and Schifferm\"uller (Lepidoptera: Tortricidae) has been introduced to New Zealand as a biological control agent to attack the seeds of gorse (Ulex europaeus; Fabaceae). Gorse is a major weed in New Zealand and in other temperate parts of the world including Oregon and California (USA), at high elevations in Hawaii (USA), Chile, and Australia. This paper describes the host-range tests conducted to assess the risk that C. succedana posed to nontarget plants, and to gain approval for the introduction of this moth into New Zealand. The release and establishment of C. succedana are recorded. First-instar larvae transferred onto excised pods of 39 leguminous test plants completed development on gorse controls (40.0%), Pisum sativum (7.2 and 8.0%), and the rare native species Clianthus puniceus (10.0%). Larvae also fed on pods of Lens culinaris and Sophora spp. but none completed development. Excised shoots bearing flowers and pods of 33 leguminous plants were exposed to female moths in small cages. No eggs were laid on 17 species. Oviposition on the other 16 plants never exceeded 10% of that on controls. Eggs were laid on C. puniceus and Sophora microphylla, but not on P. sativum or L. culinaris. Tests were conducted in larger cages outdoors using whole plants of 17 leguminous species. Moths were more selective in this arena. No eggs were laid on C. puniceus, but occasional eggs were laid on S. microphylla in both "choice" and "no-choice" tests. Behavioral observations suggested that larvae tend to actively seek out gorse pods in preference to pods of S. microphylla. It was concluded that C. succedana posed no significant threat to Sophora spp., or to any other plants with economic or environmental value in New Zealand. C. succedana was released in 1992, and since then has been distributed at 134 sites in New Zealand. It has established at 78% of the sites that have been adequately assessed. There appears to be no geographic establishment pattern, and this species may establish wherever gorse occurs. The potential effect of C. succedana on the population dynamics of gorse in New Zealand is discussed. Introduction of this species to Hawaii and Australia is being considered. © 2002 Elsevier Science (USA). All rights reserved.},
   Keywords = {Biological control
Cydia succedana
Gorse
Gorse pod moth
Host-range testing
New Zealand
Ulex europaeus
Weeds
biological pest control
weed control
Clianthus puniceus
Cydia succedana
Lens culinaris
Pisum sativum
Sophora microphylla
Ulex europaeus},
   Year = {2002} }




@article{
Hill01,
   Author = {Hill, R. L.  and Gourlay, A. H.  and Barker, R. J.},
   Title = {Survival of \emph{Ulex europaeus} seeds in the soil at three sites in New Zealand},
   Journal = {New Zealand Journal of Botany},
   Volume = {39},
   Number = {2},
   Pages = {235-244},
   Abstract = {Seed banks are a major factor in the persistence of perennial, woody, leguminous weed species. The longevity of seeds of Ulex europaeus, (gorse) in the soil at three sites was determined, and the implications of these results for the selection of biological control agents for the weed are discussed. Locally collected seeds were buried in bags at depths ranging from 2.5 cm to 15 cm at three climatically distinct sites. Seeds were recovered and germinated over a 10-year period to estimate the dormancy characteristics and viability of U. europaeus seed banks at the three sites. The decline in the seed bank conformed to a linear model using an exponential transformation. Seeds survived longer when buried deeper, but this influence was weak. The main determinant of seed survival was the time elapsed since burial. Results indicate that the dynamics of the seed bank vary from site to site. Thus, the view that U. europaeus seeds last almost indefinitely in the seed bank may be exaggerated, at least in some sites. At two sites, the number of viable seeds buried at a depth of 5 cm declined to 10% of the original number within 10 years of burial and to 1% within 20 years. By contrast, data from the third site suggested that in some places seed could survive many decades in the seed bank. Almost all seeds recovered from the soil were viable, and losses from the seed bank were probably due to germination. Local climatic conditions or local genotype may explain the variation in seed longevity between sites, although this study could not examine the relative importance of these factors. Seed-feeding biological control agents reduce U. europaeus seed rain, and these may influence the population dynamics of the weed within several decades in areas where the rate of seed decline in the soil is rapid.},
      Year = {2001} }




@inproceedings{
Hill86,
   Author = {Hill, R. L. and Sandrey, R. A.},
   Title = {The costs and benefits of gorse},
   BookTitle = {Proceedings of the 39th New Zealand Weed and Pest Control Conference},
   Publisher = {New Zealand Plant Protection Society},
   Pages = {70-73},
      Year = {1986} }




@article{
Hirsch99,
   Author = {Hirsch, A. M.},
   Title = {Role of lectins (and rhizobial exopolysaccharides) in legume nodulation},
   Journal = {Current Opinion in Plant Biology},
   Volume = {2},
   Number = {4},
   Pages = {320-326},
      Year = {1999} }




@article{
Hirsch04,
   Author = {Hirsch, A. M.},
   Title = {Plant-microbe symbioses: A continuum from commensalism to parasitism},
   Journal = {Symbiosis},
   Volume = {37},
   Number = {1-3},
   Pages = {345-363},
   Abstract = {Photosynthetic organisms establish symbioses with a wide range of microorganisms. This review examines the diversity of symbiotic interactions, and proposes that there is a continuum from commensalism to mutualism to pathogenesis/parasitism in plant-microbe associations. The advantage of considering commensalism, mutualism, and pathogenesis/parasitism as a continuum rather than as discrete relationships between hosts and microbes, as they have been considered in the past, is that it will motivate us to focus more on common molecular mechanisms.},
   Keywords = {Commensalism
Mutualism
Parasitism
Symbiosis},
   Year = {2004} }




@article{
Hirsch97,
   Author = {Hirsch, A. M. and LaRue, T. A.},
   Title = {Is the legume nodule a modified root or stem or an Organ sui generis?},
   Journal = {Critical Reviews in Plant Sciences},
   Volume = {16},
   Number = {4},
   Pages = {361-392},
   Abstract = {The legume nodule, which houses nitrogen-fixing rhizobia, is a unique plant organ. Its homology with lateral roots has been inferred by a comparison with other nitrogen-fixing nodules, especially those formed on actinorhizal plants in response to Frankia inoculation or on Parasponia roots following inoculation with Bradyrhizobium species. These nodules are clearly modified lateral roots in terms of their structure and development. However, legume nodules differ from lateral roots and these other nodules in their developmental origin, anatomy, and patterns of gene expression, and, consequently, several other evolutionary derivations, including from stems, wound or defense responses, or the more ancient vesicular-arbuscular mycorrhizal symbiosis, have been postulated for the legume nodule. In this review, we first present a broad view of the legume family showing the diversity of nodulation occurrence and types in the different subfamilies and particularly within the subfamily Papilionoideae. We then define the typological and molecular criteria used to discriminate the basic organs - root, stem, leaf - of the plant. Finally, we discuss the possible origins of the legume nodule in terms of these typological and molecular bases.},
      Year = {1997} }




@article{
Hirsch01,
   Author = {Hirsch, A. M. and Lum, M. R. and Downie, J. A.},
   Title = {What makes the rhizobia-legume symbiosis so special?},
   Journal = {Plant Physiology},
   Volume = {127},
   Number = {4},
   Pages = {1484-1492},
      Year = {2001} }




@article{
Hirsch00,
   Author = {Hirsch, A. M. and McFall-Ngai, M. J.},
   Title = {Fundamental concepts in symbiotic interactions: Light and dark, day and night, squid and legume},
   Journal = {Journal of Plant Growth Regulation},
   Volume = {19},
   Number = {2},
   Pages = {113-130},
   Abstract = {The legume-Rhizobium symbiosis and that between Euprymna scolopes and Vibrio fischeri show some surprising physiological similarities as well as differences. Both interactions rely on exchange of signal molecules, some of which are derived from bacterial cell surface molecules. Although the legume-Rhizobium symbiosis is nutritionally based as are many animal-microbe symbioses, it is not obligate because the plant initiates nodule formation only when the soil is deficient in nitrogen. In contrast, the squid-Vibrio symbiosis is obligate for the squid but is not nutritionally based. Rather, the bacteria produce light, which enables the animal to evade predators. These similarities and differences are described and discussed in term of the overall question of whether or not these two symbiotic relationships have evolved from commensal or pathogenic/parasitic interactions between prokaryotes and eukaryotes.},
   Keywords = {Euprymna scolopes
Legume
Rhizobium
Sepiolid
Symbiosis
Vibrio fischeri},
   Year = {2000} }




@article{
Hirsch84,
   Author = {Hirsch, A. M. and Wilson, K. J. and Jones, J. D. G.},
   Title = {Rhizobium meliloti nodulation genes allow Agrobacterium tumefaciens and Escherichia coli to form pseudonodules on alfalfa},
   Journal = {Journal of Bacteriology},
   Volume = {158},
   Number = {3},
   Pages = {1133-1143},
      Year = {1984} }




@article{
Hirsch96,
   Author = {Hirsch, P. R.},
   Title = {Population dynamics of indigenous and genetically modified rhizobia in the field},
   Journal = {New Phytologist},
   Volume = {133},
   Number = {1},
   Pages = {159-171},
   Abstract = {Many factors have been shown to affect rhizobial populations in soil. These include: soil fertility; physical properties such as pH and clay content; biotic factors such as distribution of the host plant and the prevalence of predators; and climatic effects including temperature and rainfall. Extremes of soil pH, temperature and moisture are not favourable to rhizobia. In certain circumstances, some rhizobial species seem to survive as part of the saprophytic soil microflora, whereas others cannot be detected unless their leguminous plant host is present. There have been numerous reports over the past century on factors which influence rhizobial survival, reflecting the importance of rhizobial inoculants in agriculture. Many of these results appear to be contradictory, presumably because of the complexity of the interactions between different influences, which this review of the literature attempts to clarify. Results from monitoring population dynamics of different rhizobial species and biovars under various crops at Rothamsted demonstrate that populations of Rhizobium leguminosarum biovars survive in the absence of their host plants at c. 104-105 nodulating cells g-1 soil, and increase only about threefold following cultivation of the host. In contrast, Sinorhizobium meliloti could not be detected before its host was grown, but increased to 106 nodulating cells g-1 soil when lucerne was cultivated. The behaviour of a genetically modified R. leguminosarum bv. viciae strain, RSM2004, following field release as an inoculant, was similar to that of the indigenous population, numbers remaining stable in the absence of the host following an initial decline, with a small but significant numerical advantage being conferred by the presence of the host in the subsequent years. A second genetically modified R. leguminosarum bv. viciae inoculant, CT0370, was found to survive in numbers similar to those of the indigenous population.},
   Keywords = {Bacteria-plant interactions
GMO survival
Microbial population dynamics
Rhizobium leguminosarum
Sinorhizobium meliloti},
   Year = {1996} }




@article{
Hirsch05,
   Author = {Hirsch, P. R.},
   Title = {Release of transgenic bacterial inoculants - Rhizobia as a case study},
   Journal = {Plant and Soil},
   Volume = {266},
   Number = {1-2},
   Pages = {1-10},
   Abstract = {The current debate on the release of genetically modified organisms to the environment must be informed by scientific data obtained from field studies. Many of the microorganisms that have potential applications outside the laboratory, especially in agriculture and horticulture, could be improved by genetic modification. Rhizobia, the bacteria that form N<sub>2</sub>-fixing symbioses with leguminous plants, have a long history of safe use as seed inoculants, their biology is relatively well known, and they represent a relevant model system. There have been several field releases of genetically modified (GM) rhizobia in the USA and Europe, which provide information on various aspects of their ecology and efficacy. This review summarises the rationale for each release, details of the methods used for monitoring, and the results. Novel properties of rhizobia did not always have the predicted effects. Most studies revealed that rhizobial numbers dropped rapidly after application to soil or seeds but then numbers stabilised for months or years. The monitoring of survival and spread of rhizobia was greatly improved by the presence of novel marker genes. Tagging of rhizobia with marker genes provided more accurate information compared to the use of conventional strains, illustrating an important application of genetic modification, for tracking bacteria in the environment. © 2004 Kluwer Academic Publishers.},
   Keywords = {Bradyrhizobium
Field release
Genetic modification
Monitoring survival
Rhizobium
Sinorhizobium},
   Year = {2005} }




@article{
Hodisan77,
   Author = {Hodisan, V. and Tamas, M.},
   Title = {Sarothamnus scoparius (L) Wimm. in the Padurea Neagra spa (Bihor district)},
   Journal = {Farmacia},
   Volume = {25},
   Number = {3},
   Pages = {143-148},
   Keywords = {alkaloid
sparteine
drug determination
drug identification
drug industry
drug isolation
plant
thin layer chromatography},
   Year = {1977} }




@article{
Holben88,
   Author = {Holben, W. E. and Jansson, J. K. and Chelm, B. K. and Tiedje, J. M.},
   Title = {DNA probe method for the detection of specific microorganisms in the soil bacterial community},
   Journal = {Applied and Environmental Microbiology},
   Volume = {54},
   Number = {3},
   Pages = {703-711},
   Abstract = {We developed a protocol which yields purified bacterial DNA from the soil bacterial community. The bacteria were first dispersed and separated from soil particles in the presence of polyvinylpolypyrrolidone, which removes humic acid contaminants by adsorption to this insoluble polymer. The soil bacteria were then collected by centrifugation and lysed by using a comprehensive protocol designed to maximize disruption of the various types of bacteria present. Total bacterial DNA was purified from the cell lysate and remaining soil contaminants by using equilibrium density gradients. The isolated DNA was essentially pure as determined by UV spectral analysis, was at least 48 kilobases long, and was not subject to degradation, which indicated that there was no contaminating nuclease activity. The isolated DNA was readily digested by exogenously added restriction endonucleases and successfully analyzed by slot blot and Southern blot hybridizations. Using single-stranded, 32P-labeled DNA probes, we could detect and quantitate the presence of a specific microbial population in the natural soil community on the basis of the presence of a DNA sequence unique to that organism. The sensitivity of our methodology was sufficient to detect Bradyrhizobium japonicum at densities as low as 4.3 x 104 cells per g (dry weight) of soil, which corresponds to about 0.2 pg of hybridizable DNA in a 1-?g DNA sample.},
      Year = {1988} }




@article{
Hong87,
   Author = {Hong, G. F. and Burn, J. E. and Johnston, A. W.},
   Title = {Evidence that DNA involved in the expression of nodulation (nod) genes in Rhizobium binds to the product of the regulatory gene nodD.},
   Journal = {Nucleic acids research},
   Volume = {15},
   Number = {23},
   Pages = {9677-9690},
   Abstract = {In Rhizobium leguminosarum biovar viciae, the regulatory nodulation nodD gene has at least two functions. It constitutively represses its own transcription and in the presence of inducer flavonoid molecules, it activates the expression of two other nod gene transcriptional units, nodABCIJ and nodFE. Upstream of nodA and nodF is a conserved sequence, the nod box, which has been implicated in nodD-mediated transcriptional activation of these genes. DNA fragments spanning the nod boxes that precede nodA and nodF were end-labelled and were exposed to cell-free extracts obtained from strains of Rhizobium. Using the gel retardation technique, it was shown that a complex between protein and these DNA fragments was formed, but only if the extract contained a functional nodD gene. Evidence that the protein that binds to the regulatory sequences is the nodD gene product came from the observation that a complex was formed between the nod box preceding nodA and protein from a cell-free extract isolated from Escherichia coli containing the cloned nodD gene. Extracts from Rhizobium strains containing mutant forms of nodD which were specifically affected in autoregulation or in flavonoid-dependent activation formed either no protein DNA complex or formed a complex with altered mobility compared to that obtained with extracts from wild-type strains.},
      Year = {1987} }




@book{
Hooker53,
   Author = {Hooker, J. D.},
   Title = {Flora Novae-Zelandiae},
   Publisher = {Reeve},
   Address = {London},
   Volume = {I: Flowering plants},
      Year = {1853} }




@article{
Hooykaas81,
   Author = {Hooykaas, P.J. J. and Van Brussel, A. A. N. and Den Dulk-Ras, H.},
   Title = {Sym plasmid of \emph{Rhizobium trifolii} expressed in different rhizobial species and \emph{Agrobacterium tumefaciens}},
   Journal = {Nature},
   Volume = {291},
   Number = {5813},
   Pages = {351-353},
      Year = {1981} }




@article{
Horiuchi05,
   Author = {Horiuchi, Jun-ichiro and Prithiviraj, Balakrishnan and Bais, Harsh P. and Kimball, Bruce A. and Vivanco, Jorge M.},
   Title = {Soil nematodes mediate positive interactions between legume plants and rhizobium bacteria},
   Journal = {Planta},
   Number = {e-pub},
   Pages = {1-10},
   Abstract = {Symbiosis between legume species and rhizobia results in the sequestration of atmospheric nitrogen into ammonium, and the early mechanisms involved in this symbiosis have become a model for plant-microbe interactions and thus highly amenable for agricultural applications. The working model for this interaction states that the symbiosis is the outcome of a chemical/molecular dialogue initiated by flavonoids produced by the roots of legumes and released into the soil as exudates, which specifically induce the synthesis of nodulation factors in rhizobia that initiate the nodulation process. Here, we argue that other organisms, such as the soil nematode Caenorhabditis elegans, also mediate the interaction between roots and rhizobia in a positive way, leading to nodulation. We report that C. elegans transfers the rhizobium species Sinorhizobium meliloti to the roots of the legume Medicago truncatula in response to plant-released volatiles that attract the nematode. These findings reveal a biologically-relevant and largely unknown interaction in the rhizosphere that is multitrophic and may control the initiation of the symbiosis. © Springer-Verlag 2005.},
      Year = {2005} }




@article{
Horner03,
   Author = {Horner, D. and Martin, W. and Blankenship, R. and Cavalier-Smith, T. and Nisbet, E.},
   Title = {On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells - Discussion},
   Journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences},
   Volume = {358},
   Number = {1429},
   Pages = {83-85},
      Year = {2003} }




@article{
Howieson04,
   Author = {Howieson, J. and Ballard, R.},
   Title = {Optimising the legume symbiosis in stressful and competitive environments within southern Australia - Some contemporary thoughts},
   Journal = {Soil Biology and Biochemistry},
   Volume = {36},
   Number = {8},
   Pages = {1261-1273},
   Abstract = {In the managed agricultural ecosystems of southern Australia, if an edaphic environment is not stressful to root-nodule bacteria (hereafter rhizobia), it is likely to become a competitive environment for nodulation (although not always detrimentally so) soon after the introduction of an inoculated legume. We suggest that stressful environments limit rhizobial communities to less than 100 cells g-1 soil at some time during the season. This overview puts forward the hypothesis that in perturbed ecosystems (i.e. those that are intensively managed) such as in the 25 millionha of the southern Australian grain and grazing belts, the rhizobial community is still substantially immature in an evolutionary sense. The rhizobial community is representative of only a few species, primarily those of Mediterranean origin that were accidentally introduced, or have been fostered by legume development programs, or remnants of the populations associated with native legumes. We consider there is little inter-specific competition for substrates because of this relative immaturity, but suggest that intra-specific competition for nodulation is commonplace wherever abiotic stress is absent. We nominate two primary abiotic stresses that are permanently present that have limited rhizobial colonization or legume nodulation for some species in southern Australia and four secondary (temporary) abiotic stresses. We believe that selection of adapted symbioses, or where warranted adapted elite rhizobial strains or legume host genotypes, can overcome these stress factors. We emphasise that where several abiotic stress factors are present they may act synergistically, but that this net effect is still likely to be symbiosis-specific. We acknowledge that genetic transformation in situ is providing new strain variability with which we must contend. We also put forward the suggestion that opportunities exist for the managed introduction of selected genotypes of agricultural legumes that effectively interact with rhizobial communities to achieve optimal N-fixation. In doing so, we give more precise definition to the widely used terms 'exclusive', 'selective' and 'promiscuous' nodulation. © 2004 Published by Elsevier Ltd.},
   Keywords = {Abiotic stress
Acidity
Competition
Legumes
N fixation
Nodulation
Rhizobia},
   Year = {2004} }




@inproceedings{
Howieson05,
   Author = {Howieson, J. G. and Brockwell, J.},
   Title = {Nomenclature of legume root nodule bacteria in 2005 and implications for collection of strains from the field},
   BookTitle = {14th Australian nitrogen fixation conference},
   Editor = {Brockwell, J.},
   Address= {Katoomba, Australia},
   Publisher = {The Australian Society for Nitrogen Fixation},
   Pages = {17-23},
      Year = {2005} }




@article{
Howieson00,
   Author = {Howieson, J. G. and O'Hara, G. W. and Carr, S. J.},
   Title = {Changing roles for legumes in Mediterranean agriculture: Developments from an Australian perspective},
   Journal = {Field Crops Research},
   Volume = {65},
   Number = {2-3},
   Pages = {107-122},
   Abstract = {Pulse and pasture legumes have maintained productivity in Mediterranean agricultural systems since antiquity, providing biologically fixed nitrogen and helping to control pests, diseases and weeds. Throughout the last 500 years many species from the Mediterranean basin have been transferred either accidentally or deliberately to the new-world, and integrated into a multitude of farming systems. During the past 30 years biological, economic and environmental forces have caused failure/breakdown of some of these productive systems. This paper examines the factors influencing legume usage in Mediterranean agriculture and uses the changing focus on legumes in southern Australia to illustrate new roles for legumes in evolving farming systems. An essential factor in developing new roles for legumes is the matching of root-nodule bacteria to both legume hosts and soil conditions. New roles for annual and perennial pastures in Mediterranean-type agriculture are discussed in relation to an analysis of the role of root-nodule bacteria in maximising productivity in these systems. (C) 2000 Elsevier Science B.V.},
   Keywords = {Farming systems
Ley-farming
Pasture
Pulse
Rhizobium},
   Year = {2000} }




@article{
Hu00,
   Author = {Hu, J.-M. and Lavin, M. and Wojciechowski, M.F. and Sanderson, M.J.},
   Title = {Phylogenetic systematics of the tribe Millettieae (Leguminosae) based on chloroplast trnK/matK sequences and its implications for evolutionary patterns in Papilionoideae},
   Journal = {American Journal of Botany},
   Volume = {87},
   Number = {3},
   Pages = {418-430},
   Abstract = {Phylogenetic relationships in the tribe Millettieae and allies in the subfamily Papilionoideae (Leguminosae) were reconstructed from chloroplast trnK/matK sequences. Sixty-two accessions representing 57 traditionally recognized genera of Papilionoideae were sampled, including 27 samples from Millettieae. Phylogenies were constructed using maximum parsimony and are well resolved and supported by high bootstrap values. A well-supported 'core Millettieae' clade is recognized, comprising the four large genera Millettia, Lonchocarpus, Derris, and Tephrosia. Several other small genera of Millettieae are not in the core Millettieae clade. Platycyamus is grouped with Phaseoleae (in part). Ostryocarpus, Austrosteenisia, and Dalbergiella are neither in the core Millettieae or Phaseoleae clade. These taxa, along with core Millettieae and Phaseoleae, form a monophyletic sister group to Indigofereae. Cyclolobium and Poecilanthe are close to Brongniartieae. Callerya and Wisteria belong to a large clade that includes all the legumes that lack the inverted repeat in their chloroplast genome, which confirms previous rbcL and phytochrome gene family phylogenies. The evolutionary history of four characters was examined in Millettieae and allies: the presence of canavanine, inflorescence types, the dehiscence of pods, and the presence of winged pods. trnK/matK sequence analysis suggests that the presence of a pseudoraceme or pseudopanicle and the accumulation of nonprotein amino acids are phylogenetically informative for Millettieae and allies with only a few exceptions.},
   Keywords = {Fabaceae
matK
Millettieae
Papilionoideae
Phylogeny
trnK},
   Year = {2000} }




@article{
Hu02,
   Author = {Hu, J.-M. and Lavin, M. and Wojciechowski, M.F. and Sanderson, M.J. and Davis, J.I.},
   Title = {Phylogenetic analysis of nuclear ribosomal ITS/5.8S sequences in the tribe Millettieae (Fabaceae): Poecilanthe-Cyclolobium, the core Millettieae, and the Callerya group},
   Journal = {Systematic Botany},
   Volume = {27},
   Number = {4},
   Pages = {722-733},
   Abstract = {The taxonomic composition of three principal and distantly related groups of the former tribe Millettieae, which were first identified from nuclear phytochrome and chloroplast trnK/matK sequences, was more extensively investigated with a phylogenetic analysis of nuclear ribosomal DNA ITS/5.8S sequences. The first of these groups includes the neotropical genera Poecilanthe and Cyclolobium, which are resolved as basal lineages in a clade that otherwise includes the neotropical genera Brongniartia and Harpalyce and the Australian Templetonia and Hovea. The second group includes the large millettioid genera, Millettia, Lonchocarpus, Derris, and Tephrosia, which are referred to as the "core Millettieae" group. Phylogenetic analysis of nuclear ribosomal DNA ITS/5.8S sequences reveals that Millettia is polyphyletic, and that subclades of the core Millettieae group, such as the New World Lonchocarpus or the pantropical Tephrosia and segregate genera (e.g., Chadsia and Mundulea), each form well supported monophyletic subgroups. The third lineage includes the genera Afgekia, Callerya, and Wisteria. These genera are resolved as a basal subclade in the inverted-repeat-lacking clade, which is a large legume group that includes the many well known temperate and herbaceous legumes, such as Astragalus, Medicago and Pisum, but not any other Millettieae.},
      Year = {2002} }




@article{
Hubber04,
   Author = {Hubber, A. and Sullivan, J. T. and Ronson, C. W. and Vergunst, A. C. and Hooykaas, P. J. J.},
   Title = {Symbiotic phenotypes and translocated effector proteins of the Mesorhizobium loti strain R7A VirB/D4 type IV secretion system},
   Journal = {Molecular Microbiology},
   Volume = {54},
   Number = {2},
   Pages = {561-574},
   Abstract = {The symbiosis island of Mesorhizobium loti strain R7A contains genes with strong similarity to the structural vir genes (virB1-11; virD4) of Agrobacterium tumefaciens that encode the type IV secretion system (T4SS) required for T-DNA transfer to plants. In contrast, M. loti strain MAFF303099 lacks these genes but contains genes not present in strain R7A that encode a type III secretion system (T3SS). Here we show by hybridization analysis that most M. loti strains contain the VirB/D4 T4SS and not the T3SS. Strikingly, strain R7A vir gene mutants formed large nodules containing bacteroids on Leucaena leucocephala in contrast to the wild-type strain that formed only uninfected tumour-like structures. A rhcJ T3SS mutant of strain MAFF303099 also nodulated L leucocephala, unlike the wild type. On Lotus corniculatus, the vir mutants were delayed in nodulation and were less competitive compared with the wild type. Two strain R7A genes, msi059 and msi061, were identified through their mutant phenotypes as possibly encoding translocated effector proteins. Both Msi059 and Msi061 were translocated through the A. tumefaciens VirB/D4 system into Saccharomyces cerevisiae and Arabidopsis thaliana, as shown using the Cre recombinase Reporter Assay for Translocation (CRAfT). Taken together, these results suggest that the VirB/D4 T4SS of M. loti R7A plays an analogous symbiotic role to that of T3SS found in other rhizobia. The heterologous translocation of rhizobial proteins by the Agrobacterium VirB/D4 T4SS is the first demonstration that rhizobial effector proteins are translocated into plant cells and confirms functional conservation between the M. loti and A. tumefaciens T4SS.},
      Year = {2004} }




@article{
Huber04,
   Author = {Huber, T. and Faulkner, G. and Hugenholtz, P.},
   Title = {Bellerophon: A program to detect chimeric sequences in multiple sequence alignments},
   Journal = {Bioinformatics},
   Volume = {20},
   Number = {14},
   Pages = {2317-2319},
   Abstract = {Summary: Bellerophon is a program for detecting chimeric sequences in multiple sequence datasets by an adaption of partial treeing analysis. Bellerophon was specifically developed to detect 16S rRNA gene chimeras in PCR-clone libraries of environmental samples but can be applied to other nucleotide sequence alignments. © Oxford University Press 2004; all rights reserved.},
      Year = {2004} }




@article{
Hueck98,
   Author = {Hueck, C. J.},
   Title = {Type III protein secretion systems in bacterial pathogens of animals and plants},
   Journal = {Microbiology and Molecular Biology Reviews},
   Volume = {62},
   Number = {2},
   Pages = {379-433},
   Abstract = {Various gram-negative animal and plant pathogens use a novel, sec- independent protein secretion system as a basic virulence mechanism. It is becoming increasingly clear that these so-called type III secretion systems inject (translocate) proteins into the cytosol of eukaryotic cells, where the translocated proteins facilitate bacterial pathogenesis by specifically interfering with host cell signal transduction and other cellular processes. Accordingly, some type III secretion systems are activated by bacterial contact with host cell surfaces. Individual type II1 secretion systems direct the secretion and translocation of a variety of unrelated proteins, which account for species-specific pathogenesis phenotypes. In contrast to the secreted virulence factors, most of the 15 to 20 membrane-associated proteins which constitute the type HI secretion apparatus are conserved among different pathogens. Most of the inner membrane components of the type III secretion apparatus show additional homologies to flagellar biosynthetic proteins, while a conserved outer membrane factor is similar to secretins from type 11 and other secretion pathways. Structurally conserved chaperones which specifically bind to individual secreted proteins play an important role in type III protein secretion, apparently by preventing premature interactions of the secreted factors with other proteins. The genes encoding type III secretion systems are clustered, and various pieces of evidence suggest that these systems have been acquired by horizontal genetic transfer during evolution. Expression of type II1 secretion systems is coordinately regulated in response to host environmental stimuli by networks of transcription factors. This review comprises a comparison of the structure, function, regulation, and impact on host cells of the type III secretion systems in the animal pathogens Yersinia spp., Pseudomonas aeruginosa, Shigella flexneri, Salmonella typhimurium, entero pathogenic Escherichia coli, and Chlamydia spp. and the plant pathogens Pseudomonas sytingae, Erwinia spp., Ralstonia solanacearum, Xanthomonas campestris, and Rhizobium spp.},
      Year = {1998} }




@article{
Huelsenbeck97,
   Author = {Huelsenbeck, J. P.},
   Title = {Is the Felsenstein zone a fly trap?},
   Journal = {Systematic Biology},
   Volume = {46},
   Number = {1},
   Pages = {69-74},
   Abstract = {Although long-branch attraction, the incorrect grouping of long lineages in a phylogeny because of systematic error, has been identified as a potential source of error in phylogenetic analysis for almost two decades, no empirical examples of the phenomenon exist. Here, I outline several criteria for identifying long-branch attraction and apply these criteria to 18S ribosomal DNA (rDNA) sequence data for 13 insects. Parsimony and minimum evolution with p distances group the two longest branches together (those leading to Strepsiptera and Diptera). Simulation studies show that the long branches are long enough to attract. When a tree is assumed in which Strepsiptera and Diptera are separated and many data sets are simulated for that tree (using the parameter estimates for that tree for the original data), parsimony analysis of the simulated data consistently groups Strepsiptera and Diptera. Analyses of the 18S rDNA sequences using methods that are less sensitive to the problem of long-branch attraction estimate trees in which the long branches are separate.},
   Keywords = {Felsenstein zone
Insect phylogeny
Long-branch attraction
Neighbor joining
Parsimony},
   Year = {1997} }




@article{
Huelsenbeck01,
   Author = {Huelsenbeck, J. P. and Ronquist, F.},
   Title = {MRBAYES: Bayesian inference of phylogenetic trees},
   Journal = {Bioinformatics},
   Volume = {17},
   Number = {8},
   Pages = {754-755},
   Abstract = {Summary: The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo.},
      Year = {2001} }




@article{
Hugenholtz03,
   Author = {Hugenholtz, P. and Huber, T.},
   Title = {Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases},
   Journal = {International Journal of Systematic and Evolutionary Microbiology},
   Volume = {53},
   Number = {1},
   Pages = {289-293},
   Abstract = {A significant number of chimeric 16S rDNA sequences of diverse origin were identified in the public databases by partial treeing analysis. This suggests that chimeric sequences, representing phylogenetically novel non-existent organisms, are routinely being overlooked in molecular phylogenetic surveys despite a general awareness of PCR-generated artefacts amongst researchers.},
   Keywords = {bacterial DNA
DNA 16S
DNA sequence
Databases, Nucleic Acid},
   Year = {2003} }




@article{
Hughes02,
   Author = {Hughes, D.},
   Title = {Sophora - The Kowhais of New Zealand},
   Journal = {International Plant Propagators' Society. Combined Proceedings of Annual Meetings},
   Volume = {52},
   Pages = {201-205},
   Abstract = {Cultivation of kowhais in New Zealand is discussed. A genus of over 50 species originated from a geographical area making a Pacific triangle formed by New Zealand, South America and Hawaii. The criteria for a kowhai tree in suburbia are very different to a revegetation project. The natural kowhai have subtle differences in different major watersheds.},
   Keywords = {Cultivation
Geographical regions
Plants (botany)
Revegetation
Rivers
Seed
Watersheds
Flowering
Biodiversity},
   Year = {2002} }




@article{
Hung05,
   Author = {Hung, M.-H. and Bhagwath, A.A. and Shen, F.-T. and Devasya, R.P. and Young, C.-C.},
   Title = {Indigenous rhizobia associated with native shrubby legumes in Taiwan},
   Journal = {Pedobiologia},
   Volume = {49},
   Number = {6},
   Pages = {577-584},
   Abstract = {Root-nodulating bacteria were isolated and characterized from seven native shrubby legumes growing in Taiwan. Phenotypic characteristics measured included growth rates in various media, colony morphology, and tolerances to extremes of temperature, salt and pH. The isolates were very diverse phenotypically. Among the 83 isolates that were screened, the majority were fast-growing rhizobia. Twenty eight strains tolerated high concentration of salt (4.5% NaCl) and grew well between temperatures of 37 and 45°C. The majority of the strains also tolerated extreme pH in their medium from 3.5 to 12. All strains formed nitrogen fixing nodules, and the highest activity was detected in the legume Hedysarum crinita L. PCR restriction fragment length polymorphism (PCR-RFLP) and sequencing of the small subunit ribosomal RNAs revealed that the majority of the isolates belonged to the genera Rhizobium, Bradyrhizobium and Agrobacterium. Only a single strain represented the genus Sinorhizobium. In addition, a strain related to Burkholderia from the ?-class of the Proteobacteria (CC-CC-5) was found within nodules of the legume Catenaria caudatum. The study contributes to the understanding of symbiotic nitrogen fixation in selected wild legumes that are native to Taiwan and provides insights into the distribution of nodulating and nitrogen-fixing bacteria from other distinct lineages. © 2005 Elsevier GmbH. All rights reserved.},
   Keywords = {16S rRNA
Nitrogen fixation
PCR-RFLP
Rhizobia
Shrubby legumes},
   Year = {2005} }




@article{
Hungria91b,
   Author = {Hungria, M. and Joseph, C. M. and Phillips, D. A.},
   Title = {Anthocyanidins and flavonols, major nod gene inducers from seeds of a black-seeded common bean (Phaseolus vulgaris L.)},
   Journal = {Plant Physiology},
   Volume = {97},
   Number = {2},
   Pages = {751-758},
   Abstract = {Eleven compounds released from germinating seeds of a black-seeded bean (Phaseolus vulgaris L., cv PI165426CS) induce transcription of nod genes in Rhizobium leguminosarum biovar phaseoli. Aglycones from 10 of those compounds were identified by spectroscopic methods (ultraviolet/visible, proton nuclear magnetic resonance, and mass spectroscopy), and their biological activities were demonstrated by induction of ?-galactosidase activity in R. leguminosarum strains containing nodA-lacZ or nodC-lacZ fusions controlled by R. leguminosarum biovar phaseoli nodD genes. By making comparisons with authentic standards, the chemical structures for aglycones from the 10 molecules were confirmed as being anthocyanidins (delphinidin, petunidin, and malvidin) and flavonols (myricetin, quercetin, and kaempferol). All anthocyanidins and flavonols had 3-O-glycosylation and free hydroxyl groups at the 4?, 5, and 7 positions. Hydrolysis experiments showed that the mean concentration required for half-maximum nod gene induction (I50) by the 10 glycosides was about half that of the corresponding aglycones. The mean I50 value for the three anthocyanidins (360 nanomolar) was less (P < 0.05) than that of the three flavonol aglycones (980 nanomolar). Each seed released approximately 2500 nanomoles of anthocyanidin and 450 nanomoles of flavonol nod gene inducers in conjugated forms during the first 6 hours of imbibition. Based on amounts and activities of the compounds released, anthocyanins contributed approximately 10-fold more total nod-inducing activity than flavonol glycosides. These anthocyanidins from bean seeds represent the first nod-inducing compounds identified from that group of flavonoids.},
      Year = {1991} }




@article{
Hungria91a,
   Author = {Hungria, M. and Joseph, C. M. and Phillips, D. A.},
   Title = {Rhizobium nod gene inducers exuded naturally from roots of common bean (Phaseolus vulgaris L.)},
   Journal = {Plant Physiology},
   Volume = {97},
   Number = {2},
   Pages = {759-764},
   Abstract = {Four compounds exuded from young roots of a black-seeded bean (Phaseolus vulgaris L., cv PI165426CS) induce transcription of nod genes in Rhizobium leguminosarum biovar phaseoli. The three most active nod gene inducers were identified by spectroscopic methods (ultraviolet/visible absorbance, proton nuclear magnetic resonance, and mass spectrometry) as being eriodictyol (5,7,3?,4?-tetrahydroxyflavanone), naringenin (5,7,4?-trihydroxyflavanone), and a 7-O-glycoside of genistein (5,7,4?-trihydroxyisoflavone). Comparisons with authentic standards verified the chemical structures of the aglycones and their capacity to induce ?-galactosidase activity in R. leguminosarum strains containing nodA-lacZ or nodC-lacZ fusions controlled by R. leguminosarum biovar phaseoli nodD genes. Roots of 9-day-old seedlings released 42, 281, and 337 nanomoles per plant per day of genistein, eriodictyol, and naringenin, respectively. Genistein and naringenin induced higher maximum ?-galactosidase activities and required lower concentrations for half-maximum induction than eriodictyol. Comparing the nod gene-inducing activity of seed rinses with root exudate from PI165426CS bean showed that root flavonoids were released at about 6% the rate of those from seeds on a molar basis, but on average the individual compounds from roots were approximately three times more active than nod gene inducers from seeds.},
      Year = {1991} }




@article{
Hurr99,
   Author = {Hurr, Kathryn A and Lockhart, Peter J and Heenan, Peter B and Penny, David},
   Title = {Evidence for the recent dispersal of \emph{Sophora} (Leguminosae) around the southern oceans: Molecular data},
   Journal = {Journal of Biogeography},
   Volume = {26},
   Number = {3},
   Pages = {565-577},
   Abstract = {Summary  Aim The aim is to use DNA sequence data to test between vicariance and long range dispersal (by floating seed-pods) explanations for the origin and range of the Edwardsia species of Sophora (Sophoreae: Papilionoideae: Leguminosae).  Location This group is widely distributed around the South Pacific and into the South Atlantic on both continental fragments and oceanic islands.  Methods DNA sequences from an intergene region (atpB-rbcL) of the chloroplast were determined for twelve taxa (including outgroups) and used to test these hypotheses. Sophora fossils were used to calibrate the evolutionary tree.  Results The Edwardsia group of Sophora appears monophyletic and is well differentiated from other Sophora. However, the genetic difference between species within the South Pacific and to the South Atlantic is very low.  Main conclusionsThe results eliminate vicariance explanations for this section of Sophora and strongly support an origin from other (non-Edwardsia) Sophora in the north-west Pacific. Dispersal appears initially to be to Tuvalu, Lord Howe Island, New Zealand, and subsequently across the South Pacific, probably within the last 2-5 million years. Dispersal of buoyant Sophora seeds to oceanic islands is the most likely explanation of its distributions. Fossil pollen dates in New Zealand are consistent with the conclusion.},
      Year = {1999} }




@article{
Huson06,
   Author = {Huson, D. H. and Bryant, D.},
   Title = {Application of phylogenetic networks in evolutionary studies},
   Journal = {Molecular Biology and Evolution},
   Volume = {23},
   Number = {2},
   Pages = {254-267},
   Abstract = {The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known that more complex evolutionary scenarios are poorly described by such models. Further, even when evolution proceeds in a tree-like manner, analysis of the data may not be best served by using methods that enforce a tree structure but rather by a richer visualization of the data to evaluate its properties, at least as an essential first step. Thus, phylogenetic networks should be employed when reticulate events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved, and, even in the absence of such events, phylogenetic networks have a useful role to play. This article reviews the terminology used for phylogenetic networks and covers both split networks and reticulate networks, how they are defined, and how they can be interpreted. Additionally, the article outlines the beginnings of a comprehensive statistical framework for applying split network methods. We show how split networks can represent confidence sets of trees and introduce a conservative statistical test for whether the conflicting signal in a network is treelike. Finally, this article describes a new program, SplitsTree4, an interactive and comprehensive tool for inferring different types of phylogenetic networks from sequences, distances, and trees. © The Author 2005. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved.},
   Keywords = {Confidence intervals
Networks
Phylogeny
Software},
   Year = {2006} }




@article{
Huson04,
   Author = {Huson, D. H. and Dezulian, T. and Kl\"opper, T. and Steel, M. A.},
   Title = {Phylogenetic super-networks from partial trees},
   Journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics},
   Volume = {1},
   Number = {4},
   Pages = {151-158},
   Abstract = {In practice, one is often faced with incomplete phylogenetic data, such as a collection of partial trees or partial splits. This paper poses the problem of Inferring a phylogenetic super-network from such data and provides an efficient algorithm for doing so, called the Z-closure method. Additionally, the questions of assigning lengths to the edges of the network and how to restrict the "dimensionality" of the network are addressed. Applications to a set of five published partial gene trees relating different fungal species and to six published partial gene trees relating different grasses illustrate the usefulness of the method and an experimental study confirms Its potential. The method Is implemented as a plug-in for the program SplitsTree4. © 2004 IEEE.},
   Keywords = {Closure operations
Molecular evolution
Networks
Partial trees
Phylogeny},
   Year = {2004} }




@article{
Huss-Danell97,
   Author = {Huss-Danell, K.},
   Title = {Actinorhizal symbioses and their N2 fixation},
   Journal = {New Phytologist},
   Volume = {136},
   Number = {3},
   Pages = {375-405},
   Abstract = {More than 200 angiosperms, distributed in 25 genera, develop root nodule symbioses (actinorhizas) with soil bacteria of the actinomycetous genus Frankia. Although most soils studied contain infective Frankia, cultured strains are available only after isolation from root nodules. Frankia infects roots via root hairs in some hosts or via intercellular penetration in others. The nodule originates in the pericycle. The number of nodules in Alnus is determined by the plant in an autoregulated process that, in turn, is modulated by nutrients such as nitrogen and phosphate. Except in the genera Allocausarina and Casuarina, Frankia in nodules develops so-called vesicles where nitrogenase is localized. Sporulation of Frankia occurs in some symbioses. As a group, actinorhizal plants show a large range of anatomical and biochemical adaptations in order to balance the oxygen tension near nitrogenase. In symbioses with well aerated nodule tissue like Alnus, the vesicles have a multilayered envelope composed mainly of lipids, bacterio-hopanetetrol and their derivatives. This envelope is assumed to retard the diffusion of oxygen into the nitrogenase-containing vesicle. In symbioses like Casuarina, the infected plant cells themselves, rather than Frankia, appear to retard oxygen diffusion, and high concentrations of haemoglobin indicate an infected region with a low oxygen tension. At least in Alnus spp., ammonia resulting from N2 fixation is assimilated by glutamine synthetase in the plant. The carbon compound(s) used by Frankia in nodules is not yet known. Nitrogenase activity decreases in response to a number of environmental factors but recovers upon return to normal conditions. This dynamism in nitrogenase activity is often explained by loss and recovery of active nitrogenase and has been traced to loss and recovery of the nitrogenase proteins themselves. Recovery is partly due to growth of Frankia and to development of new vesicles in the Alnus nodules. In the field, varying conditions continuously affect the plants and the measured rate of N2 fixation is a result not only of the conditions prevailing at the moment but also of the conditions experienced over preceding days. N2 fixed by actinorhizal plants is substantial and actinorhizal plants have great potential in soil reclamation and in various types of forestry. Several species are also useful in horticulture.},
   Keywords = {Environmental effects
Frankia
N2 fixation
Nodules
Oxygen},
   Year = {1997} }




@article{
Ibewiro01,
   Author = {Ibewiro, B. and Onuh, M. and Sanginga, N. and Bernard, V. and Merckx, R.},
   Title = {Symbiotic performance of herbaceous legumes in tropical cover cropping systems},
   Journal = {ScientificWorldJournal},
   Volume = {1 Suppl 2},
   Pages = {17-21},
   Abstract = {Increasing use of herbaceous legumes such as mucuna ( Mucuna pruriens var. utilis [Wright] Bruck) and lablab ( Lablab purpureus [L.] Sweet) in the derived savannas of West Africa can be attributed to their potential to fix atmospheric nitrogen (N2). The effects of management practices on N2 fixation in mucuna and lablab were examined using 15N isotope dilution technique. Dry matter yield of both legumes at 12 weeks was two to five times more in in situ mulch (IM) than live mulch (LM) systems. Land Equivalent Ratios, however, showed 8 to 30% more efficient utilization of resources required for biomass production under LM than IM systems. Live mulching reduced nodule numbers in the legumes by one third compared to values in the IM systems. Similarly, nodule mass was reduced by 34 to 58% under LM compared to the IM systems. The proportion of fixed N2 in the legumes was 18% higher in LM than IM systems. Except for inoculated mucuna, the amounts of N fixed by both legumes were greater in IM than LM systems. Rhizobia inoculation of the legumes did not significantly increase N2 fixation compared to uninoculated plots. Application of N fertilizer reduced N2 fixed in the legumes by 36 to 51% compared to inoculated or uninoculated systems. The implications of cover cropping, N fertilization, and rhizobia inoculation on N contributions of legumes into tropical low-input systems were discussed.},
   Keywords = {Comparative Study
Crops, Agricultural/*growth \& development
Fabaceae/*growth \& development/microbiology
Fertilizers
Nigeria
Nitrogen Compounds/analysis
Nitrogen Fixation
Nitrogen Isotopes
Rhizobium/*growth \& development
*Symbiosis
Tropical Climate
Zea mays/growth \& development},
   Year = {2001} }




@article{
Imaizumi-Anraku05,
   Author = {Imaizumi-Anraku, H. and Umehara, Y. and Kouchi, H. and Murakami, Y. and Kawasaki, S. and Takeda, N. and Yoshikawa, M. and Murooka, Y. and Hayashi, M. and Charpentier, M. and Perry, J. and Mulder, L. and Vickers, K. and Pike, J. and Parniske, M. and Miwa, H. and Downie, J.A. and Wang, T. and Kawaguchi, M. and Sato, S. and Asamizu, E. and Tabata, S. and Wu, G.-J.},
   Title = {Plastid proteins crucial for symbiotic fungal and bacterial entry into plant roots},
   Journal = {Nature},
   Volume = {433},
   Number = {7025},
   Pages = {527-531},
   Abstract = {The roots of most higher plants form arbuscular mycorrhiza, an ancient, phosphate-acquiring symbiosis with fungi, whereas only four related plant orders are able to engage in the evolutionary younger nitrogen-fixing root-nodule symbiosis with bacteria. Plant symbioses with bacteria and fungi require a set of common signal transduction components that redirect root cell development. Here we present two highly homologous genes from Lotus japonicus, CASTOR and POLLUX, that are indispensable for microbial admission into plant cells and act upstream of intracellular calcium spiking, one of the earliest plant responses to symbiotic stimulation. Surprisingly, both twin proteins are localized in the plastids of root cells, indicating a previously unrecognized role of this ancient endosymbiont in controlling intracellular symbioses that evolved more recently.},
      Year = {2005} }




@article{
Intrieri01,
   Author = {Intrieri, M. C. and Buiatti, M.},
   Title = {The horizontal transfer of Agrobacterium rhizogenes genes and the evolution of the genus Nicotiana},
   Journal = {Molecular Phylogenetics and Evolution},
   Volume = {20},
   Number = {1},
   Pages = {100-10},
   Abstract = {With the aim of understanding better the distribution and evolution of Agrobacterium rhizogenes genes transferred in the genus Nicotiana, 42 species were screened for presence of rolB, rolC, ORF13, and ORF14. The transferred sequences were then compared within the genus and with current bacterial sequences. The results obtained showed the presence of at least one bacterial gene in 15 species belonging to different subgenera. Sequence analyses supported the hypothesis of coevolution of bacterial and plant sequences, thus suggesting a possible role for the transferred genes in the early events of Nicotiana species differentiation. The high level of conservation of Agrobacterium sequences and the dependence of their expression from the plant physiological context along with previous data suggesting their involvement in the determination of the plant hormonal balance were all consistent with this hypothesis. The results are finally discussed also as to their relevance for the hypothesis of mono and multi ancient infection by Agrobacterium.},
   Keywords = {Bacterial Proteins/genetics
Base Sequence
DNA, Plant/chemistry/genetics
*Evolution, Molecular
Gene Transfer, Horizontal
Molecular Sequence Data
Phylogeny
Plants, Genetically Modified/genetics
*Plants, Toxic
Rhizobium/*genetics
Sequence Alignment
Sequence Analysis, DNA
Sequence Homology, Nucleic Acid
Tobacco/classification/*genetics
Transgenes/*genetics
beta-Glucosidase/genetics},
   Year = {2001} }




@book{
Irwin05,
   Author = {Irwin, Geoff  and Walrond, Carl},
   Title = {When was New Zealand first settled?},
   Publisher = {Ministry for Culture and Heritage},
   Address = {Wellington},
   Series = {Te Ara -- The Encyclopedia of New Zealand},
      Year = {2005} }




@article{
Ishizawa53,
   Author = {Ishizawa, S.},
   Title = {Studies on the root-nodule bacteria of leguminous plants},
   Journal = {Journal of Science of Soil Manure (Japan)},
   Volume = {23},
   Pages = {125-130; 189-195; 241-244},
      Year = {1953} }




@article{
IUPAC-IUB,
   Author = {IUB-IUPAC},
   Title = {Nomenclature committee of IUB (NC-IUB) and IUB-IUPAC joint commission on biochemical nomenclature (JCBN), Newsletter 1984},
   Journal = {Archives of Biochemistry and Biophysics},
   Volume = {229},
   Number = {1},
   Pages = {399-401},
   Abstract = {  • ANNOUNCEMENT, Volume 229, Issue 1, 15 February 1984, Pages 399-401
 Order Document
1. IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN),
,.Newsletter 1984, Arch.
Biochem. Biophys., 1984, 229, 237-245; Biochem. Internat., 1984, 8,
following p 202; Biochem. J., 1984, 217, I-IV; Biosci. Rep., 1984,
4, 177-180; Chem. Internat., 1984(3), 24-25; Eur. J. Biochem., 1984,
138, 5-7; Hoppe-Seyler's Z. Physiol. Chem., 1984, 365, I-IV; Trends
Biochem. Sci., 1984, 9, various issues.},
      Year = {1984} }




@article{
Iyer04,
   Author = {Iyer, L. M. and Koonin, E. V. and Aravind, L.},
   Title = {Evolution of bacterial RNA polymerase: implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer},
   Journal = {Gene},
   Volume = {335},
   Pages = {73-88},
   Abstract = {Comparative analysis of the domain architectures of the beta, beta', and sigma(70) subunits of bacterial DNA-dependent RNA polymerases (DdRp), combined with sequence-based phylogenetic analysis, revealed a fundamental split among bacteria. DNA-dependent RNA polymerase subunits of Group I, which includes Proteobacteria, Aquifex, Chlamydia, Spirochaetes, Cytophaga-Chlorobium, and Planctomycetes, are characterized by three distinct inserts, namely a Sandwich Barrel Hybrid Motif domain in the beta subunit, a beta-beta' module (BBM) 1 domain in the beta' subunit, and a distinct helical module in the sigma subunit. The DdRp subunits of remaining bacteria, which comprise Group II, lack these inserts, although some additional inserted domains are present in individual lineages. The separation of bacteria into Group I and Group II is generally compatible with the topologies of phylogenetic trees of the conserved regions of DdRp subunits and concatenated ribosomal proteins and might represent the primary bifurcation in bacterial evolution. A striking deviation from this evolutionary pattern is Aquifex whose DdRp subunits cluster within Group I, whereas phylogenetic analysis of ribosomal proteins identifies Aquifex as grouping with Thermotoga another bacterial hyperthemophile belonging to Group II. The inferred evolutionary scenario for the DdRp subunits includes domain accretion and rearrangement, with some likely horizontal transfer events. Although evolution of bacterial DdRp appeared to be generally dominated by vertical inheritance, horizontal transfer of complete genes for all or some of the subunits, resulting in displacement of the ancestral genes, might have played a role in several lineages, such as Aquifex, Thermotoga, and Fusobacterium.},
      Year = {2004} }




@article{
Jaftha02,
   Author = {Jaftha, J. B. and Strijdom, B. W. and Steyn, P. L.},
   Title = {Characterization of pigmented methylotrophic bacteria which nodulate Lotononis bainesii},
   Journal = {Systematic and Applied Microbiology},
   Volume = {25},
   Number = {3},
   Pages = {440-449},
   Abstract = {Root nodule isolates from a shrubby legume, Lotononis bainesii, were characterized by 16S rRNA gene sequencing and morphologically by substrate utilization patterns. The symbiotic genome of these isolates was analysed by partial sequencing of the nifH gene. Based on the results of numerical taxonomy, the isolates formed a closely related cluster, showing no correspondence to any of the known rhizobial clusters. Analysis of nearly full-length 16S rDNA sequences demonstrated that these isolates were related to Methylobacterium nodulans (SY et al., 2001). In the absence of nifH sequence data for the genus Methylobacterium, the nifH phylogeny showed these isolates to be related to Azospirillum brasilense. The facultative methylotrophic nature of these isolates was also demonstrated by their ability to grow in the presence of methanol as a sole carbon source.},
      Year = {2002} }




@article{
Jain76,
   Author = {Jain, M. K. and Rewari, R. B.},
   Title = {Studies on seed coat toxicity to rhizobia of urid (Phaseolus mungo), mung (Phaseolus aureus), and soybean (Glycine max)},
   Journal = {Zentralbl Bakteriol Parasitenkd Infektionskr Hyg},
   Volume = {131},
   Number = {2},
   Pages = {163-9},
   Keywords = {Anti-Bacterial Agents/*pharmacology
Rhizobium/*drug effects
*Seeds
Soybeans
Species Specificity
Vegetables},
   Year = {1976} }




@article{
Jain03,
   Author = {Jain, R. and Rivera, M. C. and Moore, J. E. and Lake, J. A.},
   Title = {Horizontal gene transfer accelerates genome innovation and evolution},
   Journal = {Mol Biol Evol},
   Volume = {20},
   Number = {10},
   Pages = {1598-602},
   Abstract = {Horizontal gene transfer (HGT) spreads genetic diversity by moving genes across species boundaries. By rapidly introducing newly evolved genes into existing genomes, HGT circumvents the slow step of ab initio gene creation and accelerates genome innovation. However, HGT can only affect organisms that readily exchange genes (exchange communities). In order to define exchange communities and understand the internal and external environmental factors that regulate HGT, we analyzed approximately 20,000 genes contained in eight free-living prokaryotic genomes. These analyses indicate that HGT occurs among organisms that share similar factors. The most significant are genome size, genome G/C composition, carbon utilization, and oxygen tolerance.},
      Year = {2003} }




@article{
Jarabo03,
   Author = {Jarabo-Lorenzo, A. and P\'erez-Galdona, R. and Donate-Correa, J. and Rivas, R. and Vel\'azquez, E. and Hernandez, M. and Temprano, F. and Mart\'inez-Molina, E. and Ruiz-Argueso, T. and Le\'on-Barrios, M.},
   Title = {Genetic diversity of bradyrhizobial populations from diverse geographic origins that nodulate \emph{Lupinus} spp. and \emph{Ornithopus} spp},
   Journal = {Systematic and Applied Microbiology},
   Volume = {26},
   Number = {4},
   Pages = {611-623},
   Abstract = {The genetic diversity of 45 bradyrhizobial isolates that nodulate several Lupinus and Ornithopus species in different geographic locations was investigated by 16S rDNA PCR-RFLP and sequence analysis, 16S-23S rDNA intergenic spacer (IGS) PCR-RFLP analysis, and ERIC-PCR genomic fingerprinting. Reference strains of Bradyrhizobium japonicum, B. liaoningense and B. elkanii and some Canarian isolates from endemic woody legumes in the tribe Genisteae were also included. The 16S rDNA-RFLP analysis resolved 9 genotypes of lupin isolates, a group of fourteen isolates presented restriction-genotypes identical or very similar to B. japonicum, while another two main groups of isolates (69%) presented genotypes that clearly separated them from the reference species of soybean. 16S rDNA sequencing of representative strains largely agreed with restriction analysis, except for a group of six isolates, and showed that all the lupin isolates are relatives of B. japonicum, but different lineages were observed. The 16S-23S IGS-RFLP analysis showed a high resolution level, resolving 19 distinct genotypes among 30 strains analysed, and so demonstrating the heterogeneity of the 16S-RFLP groups. ERIC-PCR fingerprint analysis showed an enormous genetic diversity producing a different pattern for each but two of the isolates. Phylogeny of nodC gene was independent from the 16S rRNA phylogeny, and showed a tight relationship in the symbiotic region of the lupin isolates with isolates from Canarian genistoid woody legumes, and in concordance, cross-nodulation was found. We conclude that Lupinus is a promiscuous host legume that is nodulated by rhizobia with very different chromosomal genotypes, which could even belong to several species of Bradyrhizobium. No correlation among genomic background, original host plant and geographic location was found, so, different chromosomal genotypes could be detected at a single site and in a same plant species, on the contrary, an identical genotype was detected in very different geographical locations and plants.},
      Year = {2003} }




@article{
Jarabo00,
   Author = {Jarabo-Lorenzo, A. and Vel\'azquez, E. and P\'erez-Galdona, R. and Vega-Hernandez, M. C. and Mart\'inez-Molina, E. and Mateos, P. F. and Vinuesa, P. and Mart\'inez-Romero, E. and Le\'on-Barrios, M.},
   Title = {Restriction fragment length polymorphism analysis of 16S rDNA and low molecular weight RNA profiling of rhizobial isolates from shrubby legumes endemic to the Canary islands},
   Journal = {Systematic and Applied Microbiology},
   Volume = {23},
   Number = {3},
   Pages = {418-425},
   Abstract = {Thirty-six strains of slow-growing rhizobia isolated from nodules of four woody legumes endemic to the Canary islands were characterised by 16S rDNA PCR-RFLP analyses (ARDRA) and LMW RNA profiling, and compared with reference strains representing Bradyrhizobium japonicum, B. elkanii, B. liaoningense, and two unclassified Bradyrhizobium sp. (Lupinus) strains. Both techniques showed similar results, indicating the existence of three genotypes among the Canarian isolates. Analysis of the combined RFLP patterns obtained with four endonucleases, showed the existence of predominant genotype comprising 75% of the Canarian isolates (BTA-1 group) and the Bradyrhizobium sp. (Lupinus) strains. A second genotype was shared by nine Canarian isolates (BGA-1 group) and the B. japonicum and B. liaoningense reference strains. The BES-5 strain formed an independent group, as also did the B. elkanii reference strains. LMW RNA profile analysis consistently resolved the same three genotypes detected by 16S ARDRA among the Canarian isolates, and suggested that all these isolates are genotypically more related to B. japonicum than to B. elkanii or B. liaoningense. Cluster analysis of the combined 16S ARDRA and LMW RNA profiles resolved the BTA-1 group with the Bradyrhizobium sp. (Lupinus) strains, and the BES-5 isolate, as a well separated sub-branch of the B. japonicum cluster. Thus, the two types of analyses indicated that the isolates related to BTA-1 conform a group of bradyrhizobial strains that can be clearly distinguishable from representants of the tree currently described Bradyrhizobium species. No correlation between genotypes, host legumes, and geographic location was found.},
   Keywords = {16S rDNA RFLP analysis
Bradyrhizobium
Canary Islands
Genetic diversity
LMW RNA profiles
Tagasaste (Chamaecytisus proliferus)},
   Year = {2000} }




@article{
Jarvis83a,
   Author = {Jarvis, B. D. W.},
   Title = {Genetic diversity of Rhizobium strains which nodulate Leucaena leucocephala},
   Journal = {Current Microbiology},
   Pages = {153-158},
   Keywords = {dna dna hybridization
rhizobium},
   Year = {1983} }




@article{
Jarvis80,
   Author = {Jarvis, B. D. W. and Dick, A. G. and Greenwood, R. M.},
   Title = {Deoxyribonucleic acid homology among strains of \emph{Rhizobium trifolii} and related species},
   Journal = {International Journal of Systematic Bacteriology},
   Volume = {30},
   Number = {1},
   Pages = {42-52},
   Keywords = {dna dna hybridization
rhizobium trifolii},
   Year = {1980} }




@article{
Jarvis92,
   Author = {Jarvis, B. D. W. and Downer, H. L. and Young, J. P. W.},
   Title = {Phylogeny of Fast-Growing Soybean-Nodulating Rhizobia Supports Synonymy of Sinorhizobium and Rhizobium and Assignment to Rhizobium-Fredii},
   Journal = {International Journal of Systematic Bacteriology},
   Volume = {42},
   Number = {1},
   Pages = {93-96},
   Abstract = {We determined the sequences for a 260-base segment amplified by the polymerase chain reaction (corresponding to positions 44 to 337 in the Escherichia coli 16S rRNA sequence) from seven strains of fast-growing soybean-nodulating rhizobia (including the type strains of Rhizobium fredii chemovar fredii, Rhizobium fredii chemovar siensis, Sinorhizobium fredii, and Sinorhizobium xinjiangensis) and broad-host-range Rhizobium sp. strain NGR 234. These sequences were compared with the corresponding previously published sequences of Rhizobium leguminosarum, Rhizobium meliloti, Agrobacterium tumefaciens, Azorhizobium caulinodans, and Bradyrhizobium japonicum. All of the sequences of the fast-growing soybean rhizobia, including strain NGR 234, were identical to the sequence of R. meliloti and similar to the sequence of R. leguminosarum. These results are discussed in relation to previous findings; we concluded that the fast-growing soybean-nodulating rhizobia belong in the genus Rhizobium and should be called Rhizobium fredii.},
      Year = {1992} }




@article{
Jarvis86,
   Author = {Jarvis, B. D. W. and Gillis, M. and De Ley, J.},
   Title = {Intra- and intergeneric similarities between the ribosomal ribonucleic acid cistrons of Rhizobium and Bradyrhizobium species and some related bacteria},
   Journal = {International Journal of Systematic Bacteriology},
   Pages = {129-138},
   Keywords = {ribosome rna
agrobacterium tumefaciens
bradyrhizobium
rhizobium
rhodopseudomonas palustris
taxonomy},
   Year = {1986} }




@article{
Jarvis77,
   Author = {Jarvis, B. D. W. and MacLean, T. S. and Robertson, I. G. C. and Fanning, G. R.},
   Title = {Phenetic similarity and DNA base sequence homology of root nodule bacteria from New Zealand native legumes and \emph{Rhizobium} strains from agricultural plants},
   Journal = {New Zealand Journal of Agricultural Research},
   Volume = {20},
   Pages = {235-248},
      Year = {1977} }




@article{
Jarvis82,
   Author = {Jarvis, B. D. W. and Pankhurst, C. E. and Patel, J. J.},
   Title = {\emph{Rhizobium loti}, a new species of legume root nodule bacteria},
   Journal = {International Journal of Systematic Bacteriology},
   Volume = {32},
   Number = {3},
   Pages = {378-380},
   Abstract = {Comparative studies of fast-growing Lotus rhizobia were reviwed, and as a result a new species, Rhizobium loti, is proposed. Then type strain of this species, which was isolated from a root nodule on Lotus corniculatus (bird's-foot trefoil), is NZP 2213 (= ATCC 33669). Plant specificity, phage relationships, the soluable-protetin pattern, and deoxyribonucleic acid base sequence homology distingushed R. loti from currently recognised Rhizobium species.},
      Year = {1982} }




@article{
Jarvis83b,
   Author = {Jarvis, B. D. W. and Scott, K. F. and Hughes, J. E.},
   Title = {Conservation of genetic information between different Rhizobium species},
   Journal = {Canadian Journal of Microbiology},
   Pages = {200-209},
   Keywords = {nitrogenase
mutagenesis
rhizobium
transposon},
   Year = {1983} }




@article{
Jarvis96,
   Author = {Jarvis, B. D. W. and Sivakumaran, S. and Tighe, S. W. and Gillis, M.},
   Title = {Identification of \emph{Agrobacterium} and \emph{Rhizobium} species based on cellular fatty acid composition},
   Journal = {Plant and Soil},
   Volume = {184},
   Number = {1},
   Pages = {143-158},
   Abstract = {The increasing number of phylogenetically defined species in the genera Agrobacterium, Rhizobium and Sinorhizobium suggests a need for a rapid identification method which will distinguish between these species. We have examined 65 strains of Agrobacterium representing: A. tumefaciens, (34); A. rhizogenes, (16) A. vitis, (10) Al rubi (2) and some unclassified strains, and 150 strains of Rhizobium and Sinorhizobium representing: R. etli (21); R. galegae (20); R. huakuii (17); R, leguminosarum (20); R. loti (16); R. topici (18); S. fredii( 19); and S. meliloti (20). Fatty acid methyl esters (FAME) were obtained from each strain, as previously described, and analysed by gas-chromatography using the MIDI Hewlett-Packard Microbial Identification System (MIS). Fatty acid profiles were recorded, characteristic fatty acids noted and the overall similarities between fatty acid profiles for each species calculated. Relationships between species were also derived from the fatty acid data by principal component analysis. This showed overlapping clusters for strains of R, leguminosarum and R, etli, R. topici and A. rhizogenes and S. fredii and S. meliloti within one supercluster. Strains of A. tumefaciens, A I nbi, A. vitis and R. galegae formed a second supercluster while R. loti and R. huakuii strains formed a third cluster well separated from all the other strains. The fatty acid profiles were used to correctly identify at least 94% of the strains representing each species in the collection except R. etli. R. etli strains (23.8%) were misidentified as R. leguminosarum. This was attributed to the high similarity (44.7%) between R. etli and R. leguminosarum. It is concluded that whole cell fatty acid analysis should form part of the polyphasic description of new species of root nodule bacteria, with the proviso that growth conditions and analytical methods be carefully standardized. It is suggested that FAME-MIS system and the database we have compiled provide a basis for future development.},
      Year = {1996} }




@article{
Jarvis97,
   Author = {Jarvis, B. D. W. and Van Berkum, P. and Chen, W. X. and Nour, S. M. and Fernandez, M. P. and Cleyet-Marel, J. C. and Gillis, M.},
   Title = {Transfer of \emph{Rhizobium loti}, \emph{Rhizobium huakuii}, \emph{Rhizobium ciceri}, \emph{Rhizobium mediterraneum}, and \emph{Rhizobium tianshanense} to \emph{Mesorhizobium} gen. nov.},
   Journal = {International Journal of Systematic Bacteriology},
   Volume = {47},
   Number = {3},
   Pages = {895-898},
   Abstract = {Reasons are advanced for removal of Rhizobium ciceri, Rhizobium huakuii, Rhizobium loti, Rhizobium mediterraneum, and Rhizobium tianshanense from the genus Rhizobium and for establishment of Mesorhizobium gen. nov. for these species. A description of the genus Mesorhizobium and amended descriptions of Mesorhizobium ciceri, Mesorhizobium huakuii, Mesorhizobium loti, Mesorhizobium mediterraneum, and Mezorhizobium tianshanense are provided.},
   Keywords = {bacterium identification
taxonomy},
   Year = {1997} }




@article{
Jaspers04,
   Author = {Jaspers, Elke and Overmann, Jorg},
   Title = {Ecological Significance of Microdiversity: Identical 16S rRNA Gene Sequences Can Be Found in Bacteria with Highly Divergent Genomes and Ecophysiologies},
   Journal = {Applied and Environmental Microbiology},
   Volume = {70},
   Number = {8},
   Pages = {4831-4839},
   Abstract = {A combination of cultivation-based methods with a molecular biological approach was used to investigate whether planktonic bacteria with identical 16S rRNA gene sequences can represent distinct eco- and genotypes. A set of 11 strains of Brevundimonas alba were isolated from a bacterial freshwater community by conventional plating or by using a liquid most-probable-number (MPN) dilution series. These strains had identical 16S rRNA gene sequences and represented the dominant phylotype in the plateable fraction, as well as in the highest positive dilutions of the MPN series. However, internally transcribed spacer and enterobacterial repetitive intergenic consensus PCR fingerprinting analyses, as well as DNA-DNA hybridization analyses, revealed great genetic diversity among the 11 strains. Each strain utilized a specific combination of 59 carbon substrates, and the niche overlap indices were low, suggesting that each strain occupied a different ecological niche. In dialysis cultures incubated in situ, each strain had a different growth rate and cell yield. We thus demonstrated that the B. alba strains represent distinct populations with genetically determined adaptations and probably occupy different ecological niches. Our results have implications for assessment of the diversity and biogeography of bacteria and increase the perception of natural diversity beyond the level of 16S rRNA gene sequences.},
      Year = {2004} }




@article{
Jing90,
   Author = {Jing, Y. and Zhang, B. T. and Shan, X. Q.},
   Title = {Pseudonodules formation on barley roots induced by Rhizobium astragali},
   Journal = {FEMS Microbiology Letters},
   Volume = {69},
   Number = {1-2},
   Pages = {123-128},
   Abstract = {Symbiotic association Rhizobium astragali with barley roots was induced by a permanent magnetic field. Initially root hairs were deformed. Later, pseudonodules were formed, showing infected cells with infection threads, and bacteroids each enclosed within a peribacteroid membrane. The overall picture is similar to that of legume root nodules. No acetylene reduction activity could be detected in pseudonodules.},
   Keywords = {barley
Rhizobium astragali
symbiotic association},
   Year = {1990} }




@article{
Johnson89,
   Author = {Johnson, D. and Roth, L. E. and Stacey, G.},
   Title = {Immunogold localization of the NodC and NodA proteins of Rhizobium meliloti},
   Journal = {Journal of Bacteriology},
   Volume = {171},
   Number = {9},
   Pages = {4583-8},
   Abstract = {Monospecific, polyclonal antibodies to the nodC and nodA gene products of Rhizobium meliloti were used in combination with immunogold labeling and transmission electron microscopy to localize the NodC and NodA proteins in cultures of R. meliloti. Both NodC and NodA were detected in the cytoplasm and cell envelope in thin sections of free-living rhizobia treated with luteolin, a known inducer of nod gene expression; however, only NodC was detected on cell surfaces when immunolabeling was performed with intact induced cells. In view of biochemical data characterizing NodC as an outer membrane protein with a large extracellular domain, the pattern of immunolabeling on thin sections suggests that NodC is produced on free cytoplasmic ribosomes prior to assembly in the membrane. The pattern of NodA labeling on thin sections is consistent with biochemical data detecting NodA in both soluble and membrane fractions of NodA-overexpressing strains of R. meliloti.},
   Keywords = {*Acyltransferases
Antibodies
Antibodies, Monoclonal
Bacterial Outer Membrane Proteins/analysis/*genetics
Bacterial Proteins/analysis/*genetics
*Genes, Bacterial
Genes, Structural
Immunohistochemistry
Microscopy, Electron
*N-Acetylglucosaminyltransferases
Rhizobium/*genetics/ultrastructure
Support, U.S. Gov't, Non-P.H.S.
Support, U.S. Gov't, P.H.S.},
   Year = {1989} }




@article{
Johnson52,
   Author = {Johnson, M. D. and Allen, O. N.},
   Title = {Cultural reactions of rhizobia with special reference to strains isolated from Sesbania species},
   Journal = {Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology},
   Volume = {18},
   Number = {1},
   Pages = {1-12},
      Year = {1952} }




@article{
Johnson97,
   Author = {Johnson, N. C. and Graham, J. H. and Smith, F. A.},
   Title = {Functioning of mycorrhizal associations along the mutualism-parasitism continuum},
   Journal = {New Phytologist},
   Volume = {135},
   Number = {4},
   Pages = {575-586},
   Abstract = {A great diversity of plants and fungi engage in mycorrhizal associations. In natural habitats, and in an ecologically meaningful time span, these associations have evolved to improve the fitness of both plant and fungal symbionts. In systems managed by humans, mycorrhizal associations often improve plant productivity, but this is not always the case. Mycorrhizal fungi might be considered to be parasitic on plants when net cost of the symbiosis exceeds net benefits. Parasitism can be developmentally induced, environmentally induced, or possibly genotypically induced. Morphological, phenological, and physiological characteristics of the symbionts influence the functioning of mycorrhizas at an individual scale. Biotic and abiotic factors at the rhizosphere, community, and ecosystem scales further mediate mycorrhizal functioning. Despite the complexity of mycorrhizal associations, it might be possible to construct predictive models of mycorrhizal functioning. These models will need to incorporate variables and parameters that account for differences in plant responses to, and control of, mycorrhizal fungi, and differences in fungal effects on, and responses to, the plant. Developing and testing quantitative models of mycorrhizal functioning in the real world requires creative experimental manipulations and measurements. This work will be facilitated by recent advances in molecular and biochemical techniques. A greater understanding of how mycorrhizas function in complex natural systems is a prerequisite to managing them in agriculture, forestry, and restoration.},
   Keywords = {Cost-benefit analysis
Fitness
Mutualism
Mycorrhizal functioning
Parasitism},
   Year = {1997} }




@article{
Johnston78,
   Author = {Johnston, A. W. B. and Beynon, J. L. and Buchanan-Wollaston, A. V.},
   Title = {High frequency transfer of nodulating ability between strains and species of \emph{Rhizobium}},
   Journal = {Nature},
   Volume = {276},
   Number = {5688},
   Pages = {634-636},
   Abstract = {THE most striking and important feature of members of the genus Rhizobium is their ability to nodulate and fix nitrogen in the roots of legumes. There is specificity in this interaction. Legumes belonging to one cross-inoculation group are nodulated only by certain classes of Rhizobium and indeed Rhizobium species are defined in terms of the host legumes that they can nodulate—for example, R. leguminosarum nodulates peas, R. trifolii nodulates clover and R. phaseoli nodulates beans of the genus Phaseolus. The genetic bases of the nodulation process and of host specificity are poorly understood. Many Rhizobium strains harbour plasmids1-4 and genetic evidence has suggested that such plasmids might carry some of the information required for the development of the symbiosis5,6. We report here that the ability to nodulate peas can be transferred at high frequency from a strain of R. leguminosarum to a non-nodulating strain of R. leguminosarum and to three other species of Rhizobium that nodulate legumes other than peas. We infer from this that some of the genetic information required for nodulation is plasmid-linked.},
      Year = {1978} }




@article{
Jordan82,
   Author = {Jordan, D. C.},
   Title = {Transfer of \emph{Rhizobium japonicum} Buchanan 1980 to \emph{Bradyrhizobium} gen. nov., a genus of slow-growing, root nodule bacteria from leguminous plants},
   Journal = {International Journal of Systematic Bacteriology},
   Volume = {32},
   Number = {1},
   Pages = {136-139},
   Keywords = {rhizobium japonicum
taxonomy},
   Year = {1982} }




@incollection{
Bergeys84,
   Author = {Jordan, D. C.},
   Title = {Family III. Rhizobiaceae},
   BookTitle = {Bergey's Manual of Systematic Bacteriology},
   Editor = {Krieg, R. K. and Holt, J. G.},
   Publisher = {Williams and Wilkins},
   Address = {Baltimore},
   Volume = {1},
   Pages = {234-256},
      Year = {1984} }




@incollection{
Jordan74,
   Author = {Jordan, D. C. and Allen, O. N.},
   Title = {Rhizobiaceae},
   BookTitle = {Bergey's Manual of Determinative Bacteriology},
   Editor = {Buchanan, R. E. and Gibbons, N. E.},
   Publisher = {Williams \& Wilkins},
   Address = {Baltimore},
   Edition = {8th},
   Pages = {261-264},
      Year = {1974} }




@article{
Jordan01,
   Author = {Jordan, M. and Larrain, M. and Tapia, A. and Roveraro, C.},
   Title = {In vitro regeneration of Sophora toromiro from seedling explants},
   Journal = {Plant Cell Tissue and Organ Culture},
   Volume = {66},
   Number = {2},
   Pages = {89-95},
   Abstract = {Embryonic axes with cotyledons, shoot-tips of embryonic axes, isolated cotyledons, as well as axillary buds and leaves from 20-year-old trees of Sophora toromiro, were evaluated for their capacity to trigger organogenesis and to regenerate plantlets under in vitro conditions. Embryonic shoot-tips were the only explants capable of regenerating plants. They developed rapidly in vitro in the presence of NAA and BA while in subculture roots were induced at the proximal end in the presence of 0.49 muM IBA within 40-60 days. Development was completed with a subculture phase under non-sterile conditions using a mixture of equal parts of sterilized vermiculite/sand/soil in growth chambers, before final acclimation in the greenhouse. In the presence of NAA, BA and GA(3), whole embryonic axes formed multiple shoots that branched when grown in 2.27 or 11.35 muM TDZ in subculture. Similarly, callus was initiated at the embryo axis base, developing into several new shoots in the presence of TDZ. Because of the relatively high shoot induction rate along the embryonic axis, this axis presents a valuable source of new juvenile explants. Growth and rhizogenesis was satisfactory only when organs from seed pods of the year or from the previous season were used. Experiments with isolated cotyledons produced callus only, while axillary buds and leaves did not show any responses in the presence of several growth regulators assayed. Inoculation of seedlings with various strains of rhizobia under in vitro conditions resulted in root outgrowths, but not in nodules that are typical of rhizobia infection.},
      Year = {2001} }




@article{
Jourand04,
   Author = {Jourand, P. and Giraud, E. and B\'ena, G. and Sy, A. and Dreyfus, B. and de Lajudie, P. and Willems, A. and Gillis, M.},
   Title = {\emph{Methylobacterium nodulans} sp. nov., for a group of aerobic, facultatively methylotrophic, legume root-nodule-forming and nitrogen-fixing bacteria},
   Journal = {International Journal of Systematic and Evolutionary Microbiology},
   Volume = {54},
   Number = {6},
   Pages = {2269-2273},
   Abstract = {Data on 72 non-pigmented bacterial strains that specifically induce nitrogen-fixing root nodules on the legume species Crotalaria glaucoides, Crotalaria perrottetii and Crotalaria podocarpa are reviewed. By SDS-PAGE analysis of total protein patterns and by 16S rRNA PCR-RFLP, these strains form a homogeneous group that is separate from other legume root-nodule-forming bacteria. The 16S rRNA gene-based phylogeny indicates that these bacteria belong to the genus Methylobacterium. They can grow on C<sub>1</sub>, compounds such as methanol, formate and formaldehyde but not methylamine as sole carbon source, and carry an mxaF gene, encoding methanol dehydrogenase, which supports their methylotrophic metabolism. Presence of a nodA nodulation gene, and ability to nodulate plants of Crotalaria species and to fix nitrogen are features that separate the strains currently included in this group from other members of the genus Methylobacterium. The present study includes additional genotypic and phenotypic characterization of this novel Methylobacterium species, i.e. nifH gene sequence, morphology, physiology, enzymic and carbon source assimilation tests and antibiotic resistance. The name Methylobacterium nodulans sp. nov. (type strain, ORS 2060<sup>T</sup>=CNCM I 2342<sup>T</sup>=LMG 21967<sup>T</sup>) is proposed for this group of root-nodule-forming bacteria. © 2004 IUMS.},
      Year = {2004} }




@incollection{
Jukes69,
   Author = {Jukes, T. and Cantor, C.},
   Title = {Evolution of protein molecules},
   BookTitle = {Mammalian Protein Metabolism},
   Editor = {Munro, H.},
   Publisher = {Academic Press},
   Address = {New York},
   Pages = {21-132},
      Year = {1969} }




@article{
Kass95,
   Author = {K\"ass, E. and Wink, M.},
   Title = {Molecular phylogeny of the papilionoideae (family Leguminosae): \emph{RbcL} gene sequences versus chemical taxonomy},
   Journal = {Botanica Acta},
   Volume = {108},
   Number = {2},
   Pages = {149-162},
      Year = {1995} }




@article{
Kass96,
   Author = {K\"ass, E. and Wink, M.},
   Title = {Molecular evolution of the leguminosae: Phylogeny of the three subfamilies based on \emph{rbcL}-sequences},
   Journal = {Biochemical Systematics and Ecology},
   Volume = {24},
   Number = {5},
   Pages = {365-378},
   Abstract = {The rbcL gene of 49 species (37 genera, 24 tribes of the Leguminosae and two species of the Polygalaceae) was amplified by polymerase chain reaction (PCR) and sequenced directly. rbcL sequences were evaluated with character state (Maximum Parsimony) and distance methods (Neighbour-Joining). The traditional classification of Leguminosae, especially in case of the basal groups, was assumed to be based on apparently ancestral or derived features. Analyses of molecular data show that such seemingly 'old' taxa, i.e. Cercideae, Gleditsia, Gymnocladus and Ceratonia, form distinct evolutionary lines, but not necessarily basal groups of the Leguminosae. Using Polygalaceae as an outgroup, the analysis of rbcL sequences showed that the tribes Detarieae/Amherstieae and Cercideae appear to have diverged earlier than the remaining tribes of Caesalpinioideae and might deserve a subfamily rank. The next groups to separate were the sister groups of Caesalpinieae/Cassieae and Papilionoideae. The closely interconnected Caesalpinieae/Cassieae complex forms the base of the Mimosoideae. Papilionoideae and Mimosoideae are monophyletic. Caesalpinioideae is paraphyletic to the other subfamilies, and the classical division of Leguminosae into three subfamilies is not supported. Within Papilionoideae, molecular data indicate that the tribe Sophoreae (and even the genus Sophora) is a heterogeneous collection of species that needs a comprehensive revision.},
   Keywords = {Caesalpinioideae
Leguminosae
Mimosoideae
nucleotide sequences
Papilionoideae
phylogeny
rbcL},
   Year = {1996} }




@article{
Kass97,
   Author = {K\"ass, E. and Wink, M.},
   Title = {Phylogenetic relationships in the Papilionoideae (family Leguminosae) based on nucleotide sequences of cpDNA (\emph{rbcL}) and ncDNA (ITS 1 and 2).},
   Journal = {Molecular Phylogenetics and Evolution},
   Volume = {8},
   Number = {1},
   Pages = {65-88},
   Abstract = {Sequences of cpDNA (rbcL) were determined for 94 species and of ncDNA [ITS 1 + 2 regions (internal transcribed spacer) of rDNA] for 75 species representing mainly the papilionoid tribes Sophoreae, Thermopsideae Podalyrieae, Liparieae, Crotalarieae, and Genisteae. Sequence data were used to reconstruct the underlying molecular phylogeny. Several clusters and furcations were identical in the rbcL and ITS trees of the Papilionoideae, indicating that a reticulate evolution due to past hybridization of members from different tribes and genera is unlikely: The Sophoreae (especially Styphnolobium japonicum (syn. Sophora japonica) and Sophora secundiflora) are positioned at the base of the papilionoid tree, whereas some other Sophora species (Sophora davidii, flavescens, jaubertii, microphylla) are closely related to Thermopsideae/Podalyrieae. The Thermopsideae/Podylyrieae cluster (including Liparieae) shares ancestry with the Crotalarieae and Genisteae. Argyrolobium (African taxa) and Melolobium cluster between Crotalarieae and Genisteae. In the Genisteae three clusters are apparent: the monophyletic genus Lupinus, the Cytisus-, and the Genista-group. According to this analysis, the Cytisus-complex includes Cytisus, Lembotropis, Chamaecytisus, Spartocytisus, and Calicotome. The Genista-group consists of Genista, Teline, and Chamaespartium sagittale. Other genera (e.g., Adenocarpus, Argyrocytisus, Cytisophyllum, Erinacea, Laburnum, Petteria, Retama, Spartium, and Ulex) could not be attributed unequivocally to the Cytisus or Genista complex.},
   Keywords = {medicinal plant
phylogeny
Phylogeny
Plants, Medicinal},
   Year = {1997} }




@article{
Kado81,
   Author = {Kado, C. I. and Liu, S.-T.},
   Title = {Rapid procedure for detection and isolation of large and small plasmids},
   Journal = {Journal of Bacteriology},
   Volume = {145},
   Number = {3},
   Pages = {1365-1373},
   Abstract = {Procedures are described for the detection and isolation of plasmids of various sizes (2.6 to 350 megadaltons) that are harbored in species of Agrobacterium, Rhizobium, Escherichia, Salmonella, Erwinia, Pseudomonas and Xanthomonas. The method utilized the molecular characteristics of covalently closed circular deoxyribonucleic acid (DNA) that is released from cells under conditions that denature chromosomal DNA by using alkaline sodium dodecyl sulfate (pH 12.6) at elevated temperatures. Proteins and cell debris were removed by extraction with phenol-chloroform. Under these conditions chromosomal DNA concentrations were reduced or eliminated. The clarified extract was used directly for electrophoretic analysis. These procedures also permitted the selective isolation of plasmid DNA that can be used directly in nick translation, restriction endonuclease analysis, transformation, and DNA cloning experiments.},
      Year = {1981} }




@article{
Kadrmas98,
   Author = {Kadrmas, J. L. and Raetz, C. R. H. and Studholme, R. E. and Sullivan, J. T. and Ronson, C. W. and Allaway, D. and Poole, P. S.},
   Title = {Cloning and overexpression of glycosyltransferases that generate the lipopolysaccharide core of Rhizobium leguminosarum},
   Journal = {Journal of Biological Chemistry},
   Volume = {273},
   Number = {41},
   Pages = {26432-26440},
   Abstract = {The lipopolysaccharide (LPS) core of the Gram-negative bacterium Rhizobium leguminosarum is more amenable to enzymatic study than that of Escherichia coli because much of it is synthesized from readily available sugar nucleotides. The inner portion of the R. leguminosarum core contains mannose, galactose, and three 3-deoxy-D-manno-octulosonate (Kdo) residues, arranged in the order: lipid A-(Kdo)2-Man-Gal-Kdo-[O antigen]. A mannosyltransferase that uses GDP-mannose and the conserved precursor Kdo2- [4'-32P]lipid IV(A) (Kadrmas, J. L., Brozek, K. A., and Raetz, C. R. H. (1996) J. Biol. Chem. 271, 32119-32125) is proposed to represent a key early enzyme in R. leguminosarum core assembly. Conditions for demonstrating efficient galactosyl- and distal Kdo-transferase activities are now described using a coupled assay system that starts with GDP-mannose and Kdo2-[4'- 32p]lipid IV(A). As predicted, mannose incorporation precedes galactose addition, which in turn precedes distal Kdo transfer. LPS core mutants with Tn5 insertions in the genes encoding the putative galactosyltransferase (lpcA) and the distal Kdo-transferase (lpcB) are shown to be defective in the corresponding in vitro glycosylation of Kdo2-[4'-32p]lipid IV(A). We have also discovered the new gene (IpcC) that encodes the mannosyltransferase. The gene is separated by several kilobase pairs from the lpcAB cluster. All three glycosyltransferases are carried on cosmid pIJ1848, which contains at least 20 kilobase pairs of R. leguminosarum DNA. Transfer of pIJ1848 into R. meliloti 1021 results in heterologous expression of all three enzymes, which are not normally present in strain 1021. Expression of the lpc genes individually behind the T7 promoter results in the production of each R. leguminosarum glycosyltransferase in E. coli membranes in a catalytically active form, demonstrating that lpcA, lpcB, and lpcC are structural genes.},
      Year = {1998} }




@article{
Kajita01,
   Author = {Kajita, T. and Ohashi, H. and Tateishi, Y. and Bailey, C.D. and Doyle, J.J.},
   Title = {rbcL and legume phylogeny, with particular reference to Phaseoleae, Millettieae, and allies},
   Journal = {Systematic Botany},
   Volume = {26},
   Number = {3},
   Pages = {515-536},
   Abstract = {A parsimony analysis was conducted on 319 rbcL sequences, comprising 242 from 194 genera of Leguminosae and 77 from other families. Results support earlier conclusions from rbcL and other molecular data that a monophyletic Leguminosae is part of a Fabales that includes Polygalaceae, Surianaceae, and the anomalous rosid genus Quillaja. Within legumes, results of previous analyses were also supported, such as the paraphyletic nature of Caesalpinioideae and monophyly of Mimosoideae and Papilionoideae. Most new data (74 sequences) were from Papilionoideae, particularly Phaseoleae, Millettieae, and allies. Although the overall topology for Papilionoideae was largely unresolved, several large clades were well-supported. The analysis contained a large sample of Phaseoleae and Millettieae, and not surprisingly showed both tribes to be polyphyletic, though with all taxa except Wisteria and allied Millettieae belonging to a single well supported clade. Within this clade was a strongly supported group that included Phaseoleae subtribes Erythrininae, Glycininae, Phaseolinae, Kennediinae, and Cajaninae, with only the last two being monophyletic. Desmodieae and Psoraleeae were also part of this clade. The monophyletic Phaseoleae subtribes Ophrestiinae and Diocleinae grouped with most Millettieae in a clade that included a group similar to the core Millettieae identified in other studies. All but one of the remaining Millettieae sampled formed an additional clade within the overall millettioid/phaseoloid group.},
      Year = {2001} }




@article{
Kalia02,
   Author = {Kalia, A. and Gupta, R. P.},
   Title = {Nodule induction in non-legumes by rhizobia},
   Journal = {Indian Journal of Microbiology},
   Volume = {42},
   Number = {3},
   Pages = {183-193},
   Abstract = {Although nitrogenous fertilizers benefit plants, they also cause pollution as reduced nitrogen may lead to acidification through nitrification, if significant leaching of nitrates occurs. Hence, systems capable of fixing nitrogen will exploit the environment less and may even contribute positively. Such systems appear to be symbiosis or loose associations of the host plants with various diazotrophs. About 170 million t nitrogen is contributed annually through biological nitrogen fixation by many bacteria and some actinomycetes in association with legumes and non-legumes. Extending legume-Rhizobium symbiosis to non-legumes will significantly increase the amount of available nitrogen and thereby biomass of several cereal and other non-legume crops. Both the genetic and non-genetic approaches could be used to express hac genes in monocots like rice, maize, wheat and sorghum. The latter techniques involve use of specific rhizobia that show loose association with roots of non-legume or enzymatic removal of cell wall of root-cells that facilitates rhizobial infection into the root cortex or treatment of seedling-roots with phytohormones as 2,4-D, NAA, IBA or cytokinins along with inoculation by Azorhizobium caulinodans or treatment with the signal compounds (flavonoids), that are involved in nodule development and colonization by rhizobia. Rhizobia may invade the roots of non-legumes by specialized crack entry at the ruptured corners of the roots that occur due to emerging lateral roots. The nitrogen fixation is attributed to presence of nod, nif and fix genes that code for nitrogenase complex and other accessory proteins needed for proper functioning of the nitrogenase complex. A feeble nitrogen fixation was observed in paranodules of non-legumes since they lack the important O2 scavenger, leghaemoglobin. Therefore, other possible sites of colonization as xylem vessels should be studied and possible techniques of transfer and expression of this gene in non-legumes should be pursued. Though induced nodulation in non-legumes holds possibility of extending rhizobial symbiosis and biological nitrogen fixation to cereals but this arena remains to be sheathed by numerous similar cascades of reactions, present in legumes, to be deciphered in non-legumes.},
   Keywords = {Auxins
Azorhizobium
Nodulation
Non-legume
Paranodule
Signal compounds},
   Year = {2002} }




@article{
Kalita04,
   Author = {Kalita, M. and Ma{\l}ek, W. and Kaznowski, A.},
   Title = {Analysis of genetic relationship of Sarothamnus scoparius microsymbionts and Bradyrhizobium sp. by hybridization in microdilution wells},
   Journal = {Journal of Bioscience and Bioengineering},
   Volume = {97},
   Number = {3},
   Abstract = {DNA-DNA hybridization in microdilution wells was successfully used to determine the overall genomic similarity among Sarothamnus scoparius [Cytisus scoparius] microsymbionts isolated from Poland and Japan and representatives of Bradyrhizobium species including Bradyrhizobium sp. (Lupinus) USDA3045. The other Bradyrhizobium species include: B. japonicum, B. liaoningense and B. elkanii. Geographically different S. scoparius rhizobia diverged into two genomospecies at the DNA-DNA similarity level of approx equal to 49%. Polish isolates exhibited high DNA similarity levels to the DNA of B. japonicum strains (approx equal to 78%) and formed a common genomospecies. Japanese S. scoparius rhizobia were allocated into a new genomic species due to the low similarity levels of their DNA to the DNA of representative strains of the Bradyrhizobium genus (from 19 to 52%).},
      Year = {2004} }




@article{
Kamst99,
   Author = {Kamst, E. and Bakkers, J. and Quaedvlieg, N. E. and Pilling, J. and Kijne, J. W. and Lugtenberg, B. J. and Spaink, H. P.},
   Title = {Chitin oligosaccharide synthesis by rhizobia and zebrafish embryos starts by glycosyl transfer to O4 of the reducing-terminal residue},
   Journal = {Biochemistry},
   Volume = {38},
   Number = {13},
   Pages = {4045-52},
   Abstract = {Lipochitin oligosaccharides are organogenesis-inducing signal molecules produced by rhizobia to establish the formation of nitrogen-fixing root nodules in leguminous plants. Chitin oligosaccharide biosynthesis by the Mesorhizobium loti nodulation protein NodC was studied in vitro using membrane fractions of an Escherichia coli strain expressing the cloned M. loti nodC gene. The results indicate that prenylpyrophosphate-linked intermediates are not involved in the chitin oligosaccharide synthesis pathway. We observed that, in addition to N-acetylglucosamine (GlcNAc) from UDP-GlcNAc, NodC also directly incorporates free GlcNAc into chitin oligosaccharides. Further analysis showed that free GlcNAc is used as a primer that is elongated at the nonreducing terminus. The synthetic glycoside p-nitrophenyl-beta-N-acetylglucosaminide (pNPGlcNAc) has a free hydroxyl group at C4 but not at C1 and could also be used as an acceptor by NodC, confirming that chain elongation by NodC takes place at the nonreducing-terminal residue. The use of artificial glycosyl acceptors such as pNPGlcNAc has not previously been described for a processive glycosyltransferase. Using this method, we show that also the DG42-directed chitin oligosaccharide synthase activity, present in extracts of zebrafish embryos, is able to initiate chitin oligosaccharide synthesis on pNPGlcNAc. Consequently, chain elongation in chitin oligosaccharide synthesis by M. loti NodC and zebrafish DG42 occurs by the transfer of GlcNAc residues from UDP-GlcNAc to O4 of the nonreducing-terminal residue, in contrast to earlier models on the mechanism of processive beta-glycosyltransferase reactions.},
   Keywords = {Acetylgalactosamine/analogs \& derivatives/chemistry/metabolism
*Acetylglucosamine/*analogs \& derivatives
Animals
Bacterial Proteins/chemistry/metabolism
Carbohydrate Conformation
Chitin/antagonists \& inhibitors/biosynthesis/*chemistry
Embryo, Nonmammalian/metabolism
Escherichia coli/chemistry/genetics
Glucosamine/analogs \& derivatives/chemistry/metabolism
N-Acetylglucosaminyltransferases/chemistry/metabolism
Oligosaccharides/antagonists \& inhibitors/*biosynthesis/chemistry
Rhizobiaceae/*chemistry/genetics/metabolism
Substrate Specificity
Support, Non-U.S. Gov't
Uridine Diphosphate N-Acetylglucosamine/analogs \& derivatives/pharmacology
Zebrafish/embryology/*metabolism},
   Year = {1999} }




@article{
Kaneko00,
   Author = {Kaneko, T. and Nakamura, Y. and Sato, S. and Asamizu, E. and Kato, T. and Sasamoto, S. and Watanabe, A. and Idesawa, K. and Ishikawa, A. and Kawashima, K. and Kimura, T. and Kishida, Y. and Kiyokawa, C. and Kohara, M. and Matsumoto, M. and Matsuno, A. and Mochizuki, Y. and Nakayama, S. and Nakazaki, N. and Shimpo, S. and Sugimoto, M. and Takeuchi, C. and Yamada, M. and Tabata, S.},
   Title = {Complete genome structure of the nitrogen-fixing symbiotic bacterium \emph{Mesorhizobium loti}},
   Journal = {DNA Research},
   Volume = {7},
   Number = {6},
   Pages = {331-338},
   Abstract = {The complete nucleotide sequence of the genome of a symbiotic bacterium Mesorhizobium loti strain MAFF303099 was determined. The genome of M. loti consisted of a single chromosome (7,036,071 bp) and two plasmids, designated as pMLa (351,911 bp) and pMLb (208, 315 bp). The chromosome comprises 6752 potential protein-coding genes, two sets of rRNA genes and 50 tRNA genes representing 47 tRNA species. Fifty-four percent of the potential protein genes showed sequence similarity to genes of known function, 21% to hypothetical genes, and the remaining 25% had no apparent similarity to reported genes. A 611-kb DNA segment, a highly probable candidate of a symbiotic island, was identified, and 30 genes for nitrogen fixation and 24 genes for nodulation were assigned in this region. Codon usage analysis suggested that the symbiotic island as well as the plasmids originated and were transmitted from other genetic systems. The genomes of two plasmids, pMLa and pMLb, contained 320 and 209 potential protein-coding genes, respectively, for a variety of biological functions. These include genes for the ABC-transporter system, phosphate assimilation, two-component system, DNA replication and conjugation, but only one gene for nodulation was identified.},
   Keywords = {ATP-Binding Cassette Transporters
genetics
Chromosomes
Codon
Conjugation
Genetic
DNA Replication
Genome
Bacterial
Molecular Sequence Data
Multigene Family
Nitrogen
metabolism
Phosphates
Plasmids
Proteobacteria
RNA
Ribosomal
Transfer
Sequence Analysis
DNA
Support
Non-U.S.Gov't},
   Year = {2000} }




@article{
Kaneko02,
   Author = {Kaneko, T. and Nakamura, Y. and Sato, S. and Minamisawa, K. and Uchiumi, T. and Sasamoto, S. and Watanabe, A. and Idesawa, K. and Iriguchi, M. and Kawashima, K. and Kohara, M. and Matsumoto, M. and Shimpo, S. and Tsuruoka, H. and Wada, T. and Yamada, M. and Tabata, S.},
   Title = {Complete genomic sequence of nitrogen-fixing symbiotic bacterium \emph{Bradyrhizobium japonicum} USDA110},
   Journal = {DNA Research},
   Volume = {9},
   Number = {6},
   Pages = {189-197},
   Abstract = {The complete nucleotide sequence of the genome of a symbiotic bacterium Bradyrhizobium japonicum USDA110 was determined. The genome of B. japonicum was a single circular chromosome 9,105,828 bp in length with an average GC content of 64.1%. No plasmid was detected. The chromosome comprises 8317 potential protein-coding genes, one set of rRNA genes and 50 tRNA genes.. Fifty-two percent of the potential protein genes showed sequence similarity to genes of known function and 30% to hypothetical genes. The remaining 18% had no apparent similarity to reported genes. Thirty-four percent of the B. japonicum genes showed significant sequence similarity to those of both Mesorhizobium loti and Sinorhizobium meliloti, while 23% were unique to this species. A presumptive symbiosis island 681 kb in length, which includes a 410-kb symbiotic region previously reported by Gottfert et al., was identified. Six hundred fifty-five putative protein-coding genes were assigned in this region, and the functions of 301 genes, including those related to symbiotic nitrogen fixation and DNA transmission, were deduced. A total of 167 genes for transposases/104 copies of insertion sequences were identified in the genome. It was remarkable that 100 out of 167 transposase genes are located in the presumptive symbiotic island. DNA segments of 4 to 97 kb inserted into tRNA genes were found at 14 locations in the genome, which generates partial duplication of the target tRNA genes. These observations suggest plasticity of the B. japonicum genome, which is probably due to complex genome rearrangements such as horizontal transfer and insertion of various DNA elements, and to homologous recombination.},
      Year = {2002} }




@article{
Kannenberg94,
   Author = {Kannenberg, E. L. and Brewin, N. J.},
   Title = {Host-plant invasion by Rhizobium: the role of cell-surface components},
   Journal = {Trends in Microbiology},
   Volume = {2},
   Number = {8},
   Pages = {277-83},
   Abstract = {Rhizobia are soil bacteria that can become endosymbionts, reducing atmospheric nitrogen within nodules formed on the roots of legume plants. During tissue and cell invasion, bacterial cell-surface components adapt the bacterium to survive as an endophyte without eliciting host-defence responses. The structures of many of these components have been established recently, allowing their possible roles in invasion to be defined more clearly.},
   Keywords = {Bacterial Adhesion
Fabaceae/*microbiology
Host-Parasite Relations
Plant Roots/physiology
*Plants, Medicinal
Polysaccharides, Bacterial/*physiology
Rhizobium/growth \& development/*physiology
Support, Non-U.S. Gov't
Symbiosis/physiology},
   Year = {1994} }




@article{
Kannenberg01,
   Author = {Kannenberg, E. L. and Carlson, R. W.},
   Title = {Lipid A and O-chain modifications cause Rhizobium lipopolysaccharides to become hydrophobic during bacteroid development},
   Journal = {Molecular Microbiology},
   Volume = {39},
   Number = {2},
   Pages = {379-91},
   Abstract = {Modifications to the lipopolysaccharide (LPS) structure caused by three different growth conditions were investigated in the pea-nodulating strain Rhizobium leguminosarum 3841. The LPSs extracted by hot phenol-water from cultured cells fractionated into hydrophilic water and/or hydrophobic phenol phases. Most of the LPSs from cells grown under standard conditions extracted into the water phase, but a greater proportion of LPSs were extracted into the phenol phase from cells grown under acidic or reduced-oxygen conditions, or when isolated from root nodules as bacteroids. Compared with the water-extracted LPSs, the phenol-extracted LPSs contained greater degrees of glycosyl methylation and O-acetylation, increased levels of xylose, glucose and mannose and increased amounts of long-chain fatty acids attached to the lipid A moiety. The water- and phenol-phase LPSs also differed in their reactivity with monoclonal antibodies and in their polyacrylamide gel electrophoretic banding patterns. Phenol-extracted LPSs from rhizobia grown under reduced-oxygen conditions closely resembled the bulk of LPSs isolated from pea nodule bacteria (i.e. mainly bacteroids) in their chemical properties, reactivities with monoclonal antibodies and extraction behaviour. This finding suggests that, during symbiotic bacteroid development, reduced oxygen tension induces structural modifications in LPSs that cause a switch from predominantly hydrophilic to predominantly hydrophobic molecular forms. Increased hydrophobicity of LPSs was also positively correlated with an increase in the surface hydrophobicity of whole cells, as shown by the high degree of adhesion to hydrocarbons of bacterial cells isolated from nodules or from cultures grown under low-oxygen conditions. The implications of these LPS modifications are discussed for rhizobial survival and function in different soil and in planta habitats.},
   Keywords = {Bacterial Adhesion
Chromatography
methods
Culture Media
Electrophoresis
Polyacrylamide Gel
Hydrocarbons
Lipid A
chemistry
metabolism
Lipopolysaccharides
isolation \& purification
O Antigens
Oxygen
pharmacology
Peas
microbiology
physiology
Rhizobium leguminosarum
genetics
growth \&
development
Support
Non-U.S.Gov't
U.S.Gov't
Non-P.H.S.
P.H.S.
Surface Properties},
   Year = {2001} }




@article{
Kato00,
   Author = {Kato, T. and Kaneko, T. and Sato, S. and Nakamura, Y. and Tabata, S.},
   Title = {Complete structure of the chloroplast genome of a legume, Lotus japonicus},
   Journal = {DNA Research},
   Volume = {7},
   Number = {6},
   Pages = {323-330},
   Abstract = {The nucleotide sequence of the entire chloroplast genome (150,519 bp) of a legume, Lotus japonicus, has been determined. The circular double-stranded DNA contains a pair of inverted repeats of 25,156 bp which are separated by a small and a large single copy region of 18,271 bp and 81,936 bp, respectively. A total of 84 predicted protein-coding genes including 7 genes duplicated in the inverted repeat regions, 4 ribosomal RNA genes and 37 tRNA genes (30 gene species) representing 20 amino acids species were assigned on the genome based on similarity to genes previously identified in other chloroplasts. All the predicted genes were conserved among dicot plants except that rpl22, a gene encoding chloroplast ribosomal protein CL22, was missing in L. japonicus. Inversion of a 51-kb segment spanning rbcL to rps16 (positions 5161-56,176) in the large single copy region was observed in the chloroplast genome of L. japonicus. The sequence data and gene information are available on our World Wide Web database at http://www.kazusa.or.jp/en/plant/database.html.},
   Keywords = {Chloroplast
Genome sequencing
Legume
Lotus japonicus},
   Year = {2000} }




@article{
Katznelson57,
   Author = {Katznelson, H. and Zagallo, A. C.},
   Title = {Metabolism of rhizobia in relation to effectiveness},
   Journal = {Canadian Journal of Microbiology},
   Volume = {3},
   Number = {6},
   Pages = {879-84},
      Year = {1957} }




@article{
Keister75,
   Author = {Keister, D. L.},
   Title = {Acetylene reduction by pure cultures of Rhizobia},
   Journal = {Journal of Bacteriology},
   Volume = {123},
   Number = {3},
   Pages = {1265-8},
   Abstract = {Acetylene reduction has been demonstrated in pure cultures of rhizobia. The requirements and conditions necessary for the activity in Rhizobium sp. 32H1 are described. The most important factors are a low cell density and a very low oxygen concentration.},
   Keywords = {Acetylene/*metabolism
Ammonia/pharmacology
Azides/pharmacology
Carbon Monoxide/pharmacology
Cyanides/pharmacology
Enzyme Induction/drug effects
Nitrates/pharmacology
Nitrogenase/biosynthesis/*metabolism
Oxygen/pharmacology
Rhizobium/growth \& development/*metabolism
Species Specificity},
   Year = {1975} }




@article{
Keister76,
   Author = {Keister, D. L. and Evans, W. R.},
   Title = {Oxygen requirement for acetylene reduction by pure cultures of rhizobia},
   Journal = {Journal of Bacteriology},
   Volume = {127},
   Number = {1},
   Pages = {149-53},
   Abstract = {The oxygen and nutritional requirements for acetylene reduction by Rhizobium japonicum and Rhizobium sp. in liquid culture are described. The optimal oxygen concentration was about 0.1% in the gas phase, which is lower than that of any other known aerobic nitrogen-fixing microorganism. these organisms are also unique in that nitrogenase synthesis is not repressed in the presence of ammonium chloride under certain cultural conditions, in contrast to other wild-type bacteria.},
   Keywords = {Acetylene/*metabolism
Ammonium Chloride/pharmacology
Enzyme Repression
Nitrogenase/biosynthesis
Oxidation-Reduction
*Oxygen Consumption
Rhizobium/enzymology/growth \& development/*metabolism},
   Year = {1976} }




@article{
Khbaya98,
   Author = {Khbaya, Bouchaib and Neyra, Marc and Normand, Philippe and Zerhari, Karim and Filali-Maltouf, Abdelkarim},
   Title = {Genetic Diversity and Phylogeny of Rhizobia That Nodulate Acacia spp. in Morocco Assessed by Analysis of rRNA Genes},
   Journal = {Applied and Environmental Microbiology},
   Volume = {64},
   Number = {12},
   Pages = {4912-4917},
   Abstract = {Forty rhizobia nodulating four Acacia species (A. gummifera, A. raddiana, A. cyanophylla, and A. horrida) were isolated from different sites in Morocco. These rhizobia were compared by analyzing both the 16S rRNA gene (rDNA) and the 16S-23S rRNA spacer by PCR with restriction fragment length polymorphism (RFLP) analysis. Analysis of the length of 16S-23S spacer showed a considerable diversity within these microsymbionts, but RFLP analysis of the amplified spacer revealed no additional heterogeneity. Three clusters were identified when 16S rDNA analysis was carried out. Two of these clusters include some isolates which nodulate, nonspecifically, the four Acacia species. These clusters, A and B, fit within the Sinorhizobium lineage and are closely related to S. meliloti and S. fredii, respectively. The third cluster appeared to belong to the Agrobacterium-Rhizobium galegae phylum and is more closely related to the Agrobacterium tumefaciens species. These relations were confirmed by sequencing a representative strain from each cluster.},
      Year = {1998} }




@article{
Kiefert96,
   Author = {Kiefert, L. and Mctainsh, G. H.},
   Title = {Oxygen isotope abundance in the quartz fraction of aeolian dust: Implications for soil and ocean sediment formation in the Australasian region},
   Journal = {Australian Journal of Soil Research},
   Volume = {34},
   Number = {4},
   Pages = {467-473},
   Abstract = {Oxygen isotope ratios of quartz in soils and ocean sediments in the Australasian region have been used to infer aeolian dust contributions; however, few oxygen isotope data are available for Australian dusts. Dust isotope ratios are in the range 13.17-5.1‰, which correlate well with dust- derived soils (13.6-14.5‰) and dust-affected soils (11.6-11.7‰) in Australia, and New Zealand (12.6-13.9‰), and Pacific Ocean sediments of dust origin (12.6 15.8‰). These results provide support for the hypothesis that dust deposition has played an important role in soil and ocean deposit formation in the Australasian region.},
      Year = {1996} }




@article{
Kiers02,
   Author = {Kiers, E. T. and West, S. A. and Denison, R. F.},
   Title = {Mediating mutualisms: Farm management practices and evolutionary changes in symbiont co-operation},
   Journal = {Journal of Applied Ecology},
   Volume = {39},
   Number = {5},
   Pages = {745-754},
   Abstract = {1. Root symbionts (rhizobia and arbuscular mycorrhizae) are often assumed to increase agricultural productivity consistently. However, rhizobial and mycorrhizal strains vary in effectiveness, resulting in symbiotic associations that range from parasitic to mutualistic. 2. The extent to which different farming practices mediate evolutionary changes along this continuum of symbiont effectiveness is rarely discussed. However, evolutionary theory suggests that (i) fertilizer use will favour parasitism unless host-plants impose sanctions against less-effective mutualists; (ii) tillage will have contrasting effects because it decreases within-plant symbiont relatedness but also decreases the risk that mutualism will benefit future competitors; (iii) crop rotation can act as a selective agent against dominating symbiont genotypes; and (iv) rhizobial inoculation adds beneficial strains to the soil but may increase the frequency of mixed nodules that allow parasitic strains to escape host sanctions. 3. However, the existing empirical data are inadequate to test our predictions thoroughly. Changes in species composition have been documented as a result of management practices, but evolutionary changes in symbiont effectiveness are difficult to detect. Therefore, a major aim of this study was to stimulate research that will assesses directly changes in symbiotic effectiveness as a function of management practices.},
   Keywords = {Arbuscular mycorrhizae
Crop rotations
Inoculation
Parasitism
Rhizobia
Symbiosis
Tillage},
   Year = {2002} }




@article{
Kijne97,
   Author = {Kijne, J. W. and Bauchrowitz, M. A. and Diaz, C. L.},
   Title = {Root Lectins and Rhizobia},
   Journal = {Plant Physiol},
   Volume = {115},
   Number = {3},
   Pages = {869-873},
      Year = {1997} }




@article{
Kim01,
   Author = {Kim, J. and Salisbury, B. A.},
   Title = {A tree obscured by vines: horizontal gene transfer and the median tree method of estimating species phylogeny},
   Journal = {Pac Symp Biocomput},
   Pages = {571-82},
   Abstract = {A phylogeny is a tree graph representation of genealogical relationships between biological objects. It is of general interest to estimate the phylogeny of whole organisms (species trees) using bio-molecular sequences. When multiple sequences are available for each organism such as with whole genome data, individual phylogenies estimated by each molecule (gene trees) may not be concordant. The lack of concordance may be due to actual biological mechanisms such as horizontal transfer of the molecules. Here, we present a new phylogeny estimation method designed to estimate the species tree despite such horizontal transfer. It uses the idea that horizontal transfer distorts distance relationships between pairs of species but a median estimate of the distances is robust to such distortions. We demonstrate the utility of our method using a simulation study.},
   Keywords = {*Algorithms
Computer Simulation
*Gene Transfer, Horizontal
Models, Genetic
*Phylogeny
Species Specificity
Support, U.S. Gov't, Non-P.H.S.},
   Year = {2001} }




@book{
King-PC,
   Author = {King, David},
   Publisher = {Department of Conservation, Gisborne, New Zealand},
      Year = {personal communication} }




@article{
Kirchner96,
   Author = {Kirchner, O.},
   Title = {Die Wurzelkn\"ollchen der Sojabohne},
   Journal = {Beir\"age zur Biologie der Pflanzen},
   Volume = {7},
   Pages = {213-224},
      Year = {1896} }




@article{
Kiss97,
   Author = {Kiss, E. and Kondorosi, A?.},
   Title = {Complete sequence of a Rhizobium plasmid carrying genes necessary for symbiotic association with the plant host},
   Journal = {BioEssays},
   Volume = {19},
   Number = {10},
   Pages = {843-846},
   Abstract = {The soil bacteria rhizobia have the capacity to establish nitrogen-fixing symbiosis with their leguminous host plants. In most Rhizobium species the genes for nodule development and nitrogen fixation have been localized on large indigenous plasmids that are transmissible, allowing lateral transfer of symbiotic functions. A recent paper reports on the complete sequencing of the symbiotic plasmid pNGR234a from Rhizobium species NGR234(1), revealing not only putative new symbiotic genes but also possible mechanisms for evolution and lateral dispersal of symbiotic nitrogen-fixing abilities among rhizobia.},
      Year = {1997} }




@article{
Klein75,
   Author = {Klein, G. E. and Jemison, P. and Haak, R. A. and Matthysse, A. G.},
   Title = {Physical evidence of a plasmid in \emph{Rhizobium japonicum}.},
   Journal = {Experientia},
   Volume = {31},
   Number = {5},
   Pages = {532-533},
      Year = {1975} }




@article{
Kloepper89,
   Author = {Kloepper, Joseph W. and Lifshitz, Ran and Zablotowicz, Robert M.},
   Title = {Free-living bacterial inocula for enhancing crop productivity},
   Journal = {Trends in Biotechnology},
   Volume = {7},
   Number = {2},
   Pages = {39-44},
   Abstract = {Early work on free-living bacteria in soil indicated that certain strains, when applied to seeds or roots, may benefit crops by stimulating plant growth or by reducing the damage from soil-borne plant pathogens. Free-living bacteria may also influence the symbiosis between microorganisms and plants and thereby stimulate plant growth indirectly. This represents another potential commercial application for bacterial inocula within the next decade. However, fundamental work is still required to make bacterial inocula consistently effective.},
      Year = {1989} }




@article{
Knapp05,
   Author = {Knapp, Michael  and St\"ockler, Karen  and Havell, David  and Delsuc, Fr\'ed\'eric  and Sebastiani, Federico  and Lockhart, Peter J.},
   Title = {Relaxed Molecular Clock Provides Evidence for Long-Distance Dispersal of Nothofagus (Southern Beech)},
   Journal = {PLoS Biology},
   Volume = {3},
   Number = {1},
   Pages = {e14},
   Abstract = {Nothofagus (southern beech), with an 80-million-year-old fossil record, has become iconic as a plant genus whose ancient Gondwanan relationships reach back into the Cretaceous era. Closely associated with Wegener{#39}s theory of {#8220}Kontinentaldrift{#8221}, Nothofagus has been regarded as the {#8220}key genus in plant biogeography{#8221}. This paradigm has the New Zealand species as passengers on a Moa{#39}s Ark that rafted away from other landmasses following the breakup of Gondwana. An alternative explanation for the current transoceanic distribution of species seems almost inconceivable given that Nothofagus seeds are generally thought to be poorly suited for dispersal across large distances or oceans. Here we test the Moa{#39}s Ark hypothesis using relaxed molecular clock methods in the analysis of a 7.2-kb fragment of the chloroplast genome. Our analyses provide the first unequivocal molecular clock evidence that, whilst some Nothofagus transoceanic distributions are consistent with vicariance, trans-Tasman Sea distributions can only be explained by long-distance dispersal. Thus, our analyses support the interpretation of an absence of Lophozonia and Fuscospora pollen types in the New Zealand Cretaceous fossil record as evidence for Tertiary dispersals of Nothofagus to New Zealand. Our findings contradict those from recent cladistic analyses of biogeographic data that have concluded transoceanic Nothofagus distributions can only be explained by vicariance events and subsequent extinction. They indicate that the biogeographic history of Nothofagus is more complex than envisaged under opposing polarised views expressed in the ongoing controversy over the relevance of dispersal and vicariance for explaining plant biodiversity. They provide motivation and justification for developing more complex hypotheses that seek to explain the origins of Southern Hemisphere biota.},
      Year = {2005} }




@article{
Knight95,
   Author = {Knight, A. W. and McTainsh, G. H. and Simpson, R. W.},
   Title = {Sediment loads in an Australian dust storm: Implications for present and past dust processes},
   Journal = {Catena},
   Volume = {24},
   Number = {3},
   Pages = {195-213},
      Year = {1995} }




@article{
Knox04,
   Author = {Knox, Oliver G. G. and Killham, Ken and Artz, Rebekka R. E. and Mullins, Chris and Wilson, Michael},
   Title = {Effect of Nematodes on Rhizosphere Colonization by Seed-Applied Bacteria},
   Journal = {Applied and Environmental Microbiology},
   Volume = {70},
   Number = {8},
   Pages = {4666-4671},
   Abstract = {There is much interest in the use of seed-applied bacteria for biocontrol and biofertilization, and several commercial products are available. However, many attempts to use this strategy fail because the seed-applied bacteria do not colonize the rhizosphere. Mechanisms of rhizosphere colonization may involve active bacterial movement or passive transport by percolating water or plant roots. Transport by other soil biota is likely to occur, but this area has not been well studied. We hypothesized that interactions with soil nematodes may enhance colonization. To test this hypothesis, a series of microcosm experiments was carried out using two contrasting soils maintained under well-defined physical conditions where transport by mass water flow could not occur. Seed-applied Pseudomonas fluorescens SBW25 was capable of rhizosphere colonization at matric potentials of -10 and -40 kPa in soil without nematodes, but colonization levels were substantially increased by the presence of nematodes. Our results suggest that nematodes can have an important role in rhizosphere colonization by bacteria in soil.},
      Year = {2004} }




@article{
Kobayashi04,
   Author = {Kobayashi, H. and Naciri-Graven, Y. and Broughton, W. J. and Perret, X.},
   Title = {Flavonoids induce temporal shifts in gene-expression of nod-box controlled loci in \emph{Rhizobium} sp. NGR234},
   Journal = {Molecular Microbiology},
   Volume = {51},
   Number = {2},
   Pages = {335-347},
   Abstract = {Rhizobia, soil bacteria of the Rhizobiales, enter the roots of homologous legumes, where they induce the formation of nitrogen-fixing nodules. Signals emanating from both symbiotic partners control nodule development. Efficient nodulation requires precise, temporal regulation of symbiotic genes. Roots continuously release flavonoids that interact with transcriptional activators of the LysR family. NodD proteins, which are members of this family, act both as sensors of the environment and modulate the expression of genes preceded by conserved promoter sequences called nod-boxes. The symbiotic plasmid of the broad host-range Rhizobium sp. NGR234 caries 19 nod-boxes (NB1 to NB19), all of which were cloned upstream of a lacZ-reporter gene. A flavonoid, daidzein was able to induce 18 of the 19 nod-boxes in a NodD1-dependent manner. Interestingly, induction of four nod-boxes (NB6, NB15, NB16 and NB17) is highly dependent on NodD2 and was delayed in comparison with the others. In turn, NodD2 is involved in the repression of the NB8 nodABCIJnolOnoeI operon. Activation of transcription of nodD2 is also dependent on flavonoids despite the absence of a nod-box like sequence in the upstream promoter region. Mutational analysis showed that syrM 2 (another member of the LysR family), which is controlled by NB19, is also necessary for expression of nodD 2. Thus, NodD1, NodD2 and SyrM2 co-modulate a flavonoid-inducible regulatory cascade that coordinates the expression of symbiotic genes with nodule development.},
   Keywords = {Base Sequence
Cloning, Molecular
DNA Primers
Escherichia coli/genetics
Flavonoids/*pharmacology
*Gene Expression Regulation, Bacterial/drug effects
Kinetics
Lipopolysaccharides/*biosynthesis
Molecular Sequence Data
Polymerase Chain Reaction
Recombinant Proteins/metabolism
Rhizobium/drug effects/*genetics
Support, Non-U.S. Gov't},
   Year = {2004} }




@article{
Koonin01,
   Author = {Koonin, E. V. and Makarova, K. S. and Aravind, L.},
   Title = {Horizontal gene transfer in prokaryotes: quantification and classification},
   Journal = {Annual Review of Microbiology},
   Volume = {55},
   Pages = {709-42},
   Abstract = {Comparative analysis of bacterial, archaeal, and eukaryotic genomes indicates that a significant fraction of the genes in the prokaryotic genomes have been subject to horizontal transfer. In some cases, the amount and source of horizontal gene transfer can be linked to an organism's lifestyle. For example, bacterial hyperthermophiles seem to have exchanged genes with archaea to a greater extent than other bacteria, whereas transfer of certain classes of eukaryotic genes is most common in parasitic and symbiotic bacteria. Horizontal transfer events can be classified into distinct categories of acquisition of new genes, acquisition of paralogs of existing genes, and xenologous gene displacement whereby a gene is displaced by a horizontally transferred ortholog from another lineage (xenolog). Each of these types of horizontal gene transfer is common among prokaryotes, but their relative contributions differ in different lineages. The fixation and long-term persistence of horizontally transferred genes suggests that they confer a selective advantage on the recipient organism. In most cases, the nature of this advantage remains unclear, but detailed examination of several cases of acquisition of eukaryotic genes by bacteria seems to reveal the evolutionary forces involved. Examples include isoleucyl-tRNA synthetases whose acquisition from eukaryotes by several bacteria is linked to antibiotic resistance, ATP/ADP translocases acquired by intracellular parasitic bacteria, Chlamydia and Rickettsia, apparently from plants, and proteases that may be implicated in chlamydial pathogenesis.},
   Keywords = {Eukaryotic Cells/physiology
Gene Transfer, Horizontal/*physiology
Phylogeny
Prokaryotic Cells/*classification/*physiology
Species Specificity
Support, U.S. Gov't, Non-P.H.S.},
   Year = {2001} }




@article{
Kovacs95,
   Author = {Kovacs, L. G. and Balatti, P. A. and Krishnan, H. B. and Pueppke, S. G.},
   Title = {Transcriptional organization and expression of nolXQBTUV, a locus that regulates cultivar-specific nodulation of soybean by Rhizobium fredii USDA257},
   Journal = {Molecular Microbiology},
   Volume = {17},
   Number = {5},
   Pages = {923-933},
   Abstract = {Rhizobium fredii is a nitrogen-fixing bacterial symbiont of soybean and a number of other legume species. We have studied the transcriptional organization of a Sym plasmid locus that restricts the host range of R. fredii USDA257 at both the host species and cultivar level. The genes of this host-specificity locus, nolXWBTUV, are transcribed from three promoters. Two of these, which are upstream of nolW and nolBTUV, are oriented face to face and initiate transcription at sites that are 14 bp apart. The third lies upstream from nolX. The nolW promoter is constitutive, whereas the nolB and nolX promoters are inducible by flavonoid signals. We have attempted to express genes from this locus in Escherichia coli systems, both invivo and in vitro. We detected the insert- and orientation-specific expression of two genes, nolX and nolW, but we were unable to obtain expression of nolBTUV. Antiserum raised against NolT nevertheless detected an abundantly expressed polypeptide of the predicted size in protein extracts of USDA257. This observation, as well as RNA dot blot data from a series of mutants, indicates that nolBTUV is expressed as a single transcriptional unit in R. fredii. Immunological detection of NolT, and of a second protein, NolX, was strictly dependent on flavonoid induction. The NolX protein was larger than the size predicted from the previously published nucleotide sequence, and this led to resequencing and revision of the open reading frame.},
      Year = {1995} }




@article{
Krause84,
   Author = {Krause, M. A. and Beck, A. C. and Dent, J. B.},
   Title = {The economics of controlling gorse in hill country: Goats versus chemicals.},
   Journal = {Research Report - University of Canterbury, New Zealand Agricultural Economics Research Unit, Lincoln College},
   Volume = {149},
   Abstract = {All goat Capra hircus and sheep Ovis aries control options proved to be more profitable than the chemical method of controlling Ulex europaeus in New Zealand hill country, with the feral does X angora bucks option proving particularly profitable.-from WAERSA},
      Year = {1984} }




@article{
Kurland03,
   Author = {Kurland, C. G. and Canback, B. and Berg, O. G.},
   Title = {Horizontal gene transfer: a critical view},
   Journal = {Proceedings of the National Academy of Sciences of the United States of America},
   Volume = {100},
   Number = {17},
   Pages = {9658-62},
   Abstract = {It has been suggested that horizontal gene transfer (HGT) is the "essence of phylogeny." In contrast, much data suggest that this is an exaggeration resulting in part from a reliance on inadequate methods to identify HGT events. In addition, the assumption that HGT is a ubiquitous influence throughout evolution is questionable. Instead, rampant global HGT is likely to have been relevant only to primitive genomes. In modern organisms we suggest that both the range and frequencies of HGT are constrained most often by selective barriers. As a consequence those HGT events that do occur most often have little influence on genome phylogeny. Although HGT does occur with important evolutionary consequences, classical Darwinian lineages seem to be the dominant mode of evolution for modern organisms.},
   Keywords = {Animals
Archaea/genetics
Bacteria/genetics
*Evolution
*Gene Transfer, Horizontal
Genome
Human
*Models, Genetic
Phylogeny
RNA, Ribosomal/genetics
Support, Non-U.S. Gov't},
   Year = {2003} }




@article{
Kuykendall77,
   Author = {Kuykendall, L. D. and Elkan, G. H.},
   Title = {Some features of mannitol metabolism in Rhizobium japonicum},
   Journal = {Journal of General Microbiology},
   Volume = {98},
   Number = {1},
   Pages = {291-295},
   Keywords = {mannitol
bacterium
metabolism
rhizobium
Soil Microbiology},
   Year = {1977} }




@article{
Kuykendall93,
   Author = {Kuykendall, L. D. and Gaur, Y. D. and Dutta, S. K.},
   Title = {Genetic diversity among \emph{Rhizobium} strains from \emph{Cicer arietinum} L.},
   Journal = {Letters in Applied Microbiology},
   Volume = {17},
   Number = {6},
   Pages = {259-263},
   Abstract = {Following bacteriological cloning and determination of their symbiotic performance, 15 representative, diverse strains of chickpea rhizobia were genetically analysed for restriction fragment length polymorphisms. Analyses of genomic DNAs showed several different groups. Almost half (7) of the strains examined were very similar and clearly represented a single species. There was a related group of four strains which could be a subspecies. There was also one distinct group of four strains which were apparently unrelated to the reference strain 3377. This latter group may constitute a separate species. Phenotypic differences should be investigated further.},
   Keywords = {dna determination
rhizobium
symbiosis},
   Year = {1993} }




@article{
Kuykendall97,
   Author = {Kuykendall, L. D. and Hunter, W. J.},
   Title = {The sequence of a symbiotically essential Bradyrhizobium japonicum operon consisting of trpD, trpC and moaC-like gene},
   Journal = {Biochimica et Biophysica Acta},
   Volume = {1350},
   Number = {3},
   Pages = {277-281},
   Abstract = {The 2767 bp BamHI-HindIII fragment specifying the trpDC genes of B. japonicum I-110 was sequenced. The trpD and trpC genes each have three highly conserved 'Crawford' consensus sequences and are part of an operon with three open reading frames (ORFs). The third ORF has a predicted product with 58% amino-acid sequence identity with the gene product of E. coli moaC, a gene encoding an enzyme involved in biosynthesis of the molybdenum cofactor required for the activity of nitrate reductase and other Mo cofactor-requiring enzymes.},
   Keywords = {Bradyrhizobium japonicum
legumes
molybdenum cofactor
nitrate reductase
nitrogen fixation
nodulation
gene product
nitrate reductase
amino acid sequence
nucleotide sequence
open reading frame
operon
sequence homology},
   Year = {1997} }




@article{
Kuykendall92,
   Author = {Kuykendall, L. D. and Saxena, B. and Devine, T. E. and Udell, S. E.},
   Title = {Genetic diversity in Bradyrhizobium japonicum Jordan 1982 and a proposal for Bradyrhizobium elkanii sp. nov.},
   Journal = {Canadian Journal of Microbiology},
   Volume = {38},
   Number = {6},
   Pages = {501-505},
   Abstract = {Fourteen randomly selected clones from cosmid libraries of Bradyrhizobium were used as hybridization probes in Southern blot analysis. Seven of the probes used were from strain USDA 83, a group II strain, and the other seven were from strain I-110, a group Ia strain. The 30 strains examined included 9 strains of Rj4-incompatible soybean bradyrhizobia. Considerable polynucleotide sequence dissimilarity between DNA homology groups was evidenced by striking differences in the number of hybridizing bands, except where the probe carried repetitive DNA. Predictable, simple restriction fragment length polymorphism differences were observed only within DNA homology groups. The previous description that 8 of 9 Rj4-incompatible strains belonged to DNA homology group II was verified. The new data, together with many previously documented differences, make it clear that the DNA homology group II organisms should be classified as a new species, for which the name Bradyrhizobium elkanii is proposed, and strain USDA 76 is designated the type strain. The ATCC number for the type strain is 49852.},
   Keywords = {bacteria
DNA:DNA hybridization
host compatibility
nitrogen fixation
nodulation
soybean
symbiosis
dna dna hybridization
genetic variability
nitrogen fixation
rhizobium
symbiosis},
   Year = {1992} }




@incollection{
Kuykendall05,
   Author = {Kuykendall, L. D. and Young, J. M. and Mart\'inez-Romero, E. and Kerr, A. and Sawada, H.},
   Title = {Genus I. \emph{Rhizobium} Frank 1889, 338$^{\mathrm{AL}}$},
   BookTitle = {Part C, The Alpha-, Beta-, Delta-, and Epsilonproteobacteria, Bergey's Manual of Systematic Bacteriology},
   Editor = {Brenner, D. J. and Krieg, R. K. and Staley, J. T. and Garrity, G. M.},
   Publisher = {Springer},
   Address = {New York},
   Volume = {2},
   Edition = {2nd},
      Year = {2005} }




@article{
Kwon05,
   Author = {Kwon, S.-W. and Park, J.-Y. and Cho, Y.-H. and Lee, G.-B. and Kim, J.-S. and Kang, J.-W. and Lim, C.-K. and Parker, M. A.},
   Title = {Phylogenetic analysis of the genera Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium on the basis of 16S rRNA gene and internally transcribed spacer region sequences},
   Journal = {International Journal of Systematic and Evolutionary Microbiology},
   Volume = {55},
   Number = {1},
   Pages = {263-270},
   Abstract = {A total of 128 strains was isolated from more than 23 legume hosts in Korea. Phylogenetic relationships between these Korean isolates and reference strains of the genera Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium were analysed using their 16S rRNA gene and internally transcribed spacer (ITS) region sequences. Among the Bradyrhizobium strains, dendrograms based on both the 16S rRNA gene and ITS region sequences produced two main groups. The ITS tree yielded at least two new clusters that were discernable from the seven previously delineated genospecies. Large discrepancies were revealed between phylogenetic dendrograms based on 16S rRNA gene and ITS region sequences for members of the genus Rhizobium, reflecting their taxonomic heterogeneity. The amalgamation of Rhizobium and former members of Agrobacterium was confirmed using the 16S rRNA tree. Phylogenetic analysis of ITS region sequences showed that the Rhizobium giardinii clade (group II) and the Rhizobium radiobacter/Rhizobium rubi clade (group III) could be tentatively recognized as groups that are separable from the core group (group I), which includes Rhizobium leguminosarum. Dendrograms based on the 16S rRNA gene and ITS region sequences of Mesorhizobium strains were highly conflicting due to the poor taxonomic resolution of the 16S rRNA gene sequences and the low confidence in the ITS dendrogram. Several Korean isolates within the genus Mesorhizobium are thought to represent novel taxa when considering their relatively low ITS region sequence similarities (<80%) to the reference strains. © 2005 IUMS.},
      Year = {2005} }




@article{
Lachman91,
   Author = {Lachman, J.},
   Title = {\"Uber Knollen an den Wurzeln der Leguminosen},
   Journal = {Biedermann's Zentralbl. Agric.},
   Volume = {20},
   Pages = {837-845},
      Year = {1891} }




@article{
Laeremans99,
   Author = {Laeremans, T. and Snoeck, C. and Marien, J. and Verreth, C. and Mart\'inez-Romero, E. and Prome, J. C. and Vanderleyden, J.},
   Title = {Phaseolus vulgaris recognizes Azorhizobium caulinodans nod factors with a variety of chemical substituents},
   Journal = {Molecular Plant-Microbe Interactions},
   Volume = {12},
   Number = {9},
   Pages = {820-824},
   Abstract = {Phaseolus vulgaris is a promiscuous host plant that can be nodulated by many different rhizobia representing a wide spectrum of Nod factors. In this study, we introduced the Rhizobium tropici CFN299 Nod factor sulfation genes nodHPQ into Azorhizobium caulinodans. The A. caulinodans transconjugants produce Nod factors that are mostly if not all sulfated and often with an arabinosyl residue as the reducing end glycosylation, Using A. caulinodans mutant strains, affected in reducing end decorations, and their respective transconjugants in a bean nodulation assay, we demonstrated that bean nodule induction efficiency, in decreasing order, is modulated by the Nod factor reducing end decorations fucose, arabinose or sulfate, and hydrogen.},
      Year = {1999} }




@article{
Laeremans98,
   Author = {Laeremans, T. and Vanderleyden, J.},
   Title = {Infection and nodulation signalling in \emph{Rhizobium}--\emph{Phaseolus vulgaris} symbiosis},
   Journal = {World Journal of Microbiology and Biotechnology},
   Volume = {14},
   Number = {6},
   Pages = {787-808},
   Abstract = {During the Rhizobium-legume symbiosis, a mutual exchange of signalling molecules occurs. Distinct oligo- and polysaccharides are involved in nodule formation and rhizobial invasion. The common bean is a promiscuous host plant that can be nodulated by a wide range of rhizobia. Reviewing the literature on nodulation suggests that the Nod factor oligosaccharide backbone of bean-nodulating rhizobia does not require a specific attached group, except for the acyl chain at the non-reducing end. However, in Rhizobium strains that elicit nitrogen-fixing nodules on Phaseolus vulgaris and that produce methylated Nod factors, NodS mediated decorations are indispensable for invasion and/or subsequent nitrogen-fixation. Finally, we present a model that links the pathways for methylation and sulphation in nodule signalling and invasion processes.},
      Year = {1998} }




@article{
Lafay98,
   Author = {Lafay, Benedicte and Burdon, Jeremy J.},
   Title = {Molecular diversity of rhizobia occurring on native shrubby legumes in southeastern Australia},
   Journal = {Applied and Environmental Microbiology},
   Volume = {64},
   Number = {10},
   Pages = {3989-3997},
   Abstract = {The structure of rhizobial communities nodulating native shrubby legumes in open eucalypt forest of southeastern Australia was investigated by a molecular approach. Twenty-one genomic species were characterized by small-subunit ribosomal DNA PCR-restriction fragment length polymorphism and phylogenetic analyses, among 745 rhizobial strains isolated from nodules sampled on 32 different legume host species at 12 sites. Among these rhizobial genomic species, 16 belonged to the Bradyrhizobium subgroup, 2 to the Rhizobium leguminosarum subgroup, and 3 to the Mesorhizobium subgroup. Only one genomic species corresponded to a known species (Rhizobium tropici). The distribution of the various genomic species was highly unbalanced among the 745 isolates, legume hosts, and sites. Bradyrhizobium species were by far the most abundant, and Rhizobium tropici dominated among the Rhizobium and Mesorhizobium isolates in the generally acid soils where nodules were collected. Although a statistically significant association occurred between the eight most common genomic species and the 32 hosts, there was sufficient overlap in distributions that no clear specificity between rhizobial genomic species and legume taxa was observed. However, for three legume species, some preference for particular genomic species was suggested. Similarly, no geographical partitioning was found.},
      Year = {1998} }




@article{
Lafay01,
   Author = {Lafay, Benedicte and Burdon, Jeremy J.},
   Title = {Small-subunit rRNA genotyping of rhizobia nodulating Australian \emph{Acacia} spp.},
   Journal = {Applied and Environmental Microbiology},
   Volume = {67},
   Number = {1},
   Pages = {396-402},
   Abstract = {The structure of rhizobial communities nodulating Acacia in southeastern Australia from south Queensland to Tasmania was investigated by a molecular approach. A total of 118 isolates from nodule samples from 13 different Acacia species collected at 44 sites were characterized by small-subunit (SSU) ribosomal DNA (rDNA) PCR-restriction fragment length polymorphism analysis. Nine rhizobial genomospecies were identified, and these taxa corresponded to previously described genomospecies (B. Lafay and J. J. Burdon, Appl. Environ. Microbiol. 64:3989-3997, 1998). Eight of these genomospecies belonged to the Bradyrhizobium lineage and accounted for 96.6% of the isolates. The remaining genomospecies corresponded to Rhizobium tropici. For analysis of geographic patterns, results were grouped into five latitudinal regions regardless of host origin. In each region, as observed previously for rhizobial isolates taken from non-Acacia legumes (Lafay and Burdon, Appl. Environ. Microbiol. 64:3989-3997, 1998), rhizobial communities were dominated by one or two genomospecies, the identities of which varied from place to place. Despite this similarity in patterns, the most abundant genomospecies for Acacia isolates differed from the genomospecies found in the non-Acacia-derived rhizobial collection, suggesting that there is a difference in nodulation patterns of the Mimosoideae and the Papilionoideae. Only two genomospecies were both widespread and relatively abundant across the range of sites sampled. Genomospecies A was found in all regions except the most northern sites located in Queensland, whereas genomospecies B was not detected in Tasmania. This suggests that genomospecies A might be restricted to the more temperate regions of Australia, whereas in contrast, genomospecies B occurs in different climatic and edaphic conditions across the whole continent. The latter hypothesis is supported by the presence of genomospecies B in southwestern Australia, based on partial SSU rDNA sequence data (N. D. S. Marsudi, A. R. Glenn, and M. J. Dilworth, Soil Biol. Biochem. 31:1229-1238, 1998).},
      Year = {2001} }




@article{
Lagares01,
   Author = {Lagares, Antonio and Hozbor, Daniela F. and Niehaus, Karsten and Otero, Augusto J. L. Pich and Lorenzen, Jens and Arnold, Walter and Puhler, Alfred},
   Title = {Genetic Characterization of a Sinorhizobium meliloti Chromosomal Region Involved in Lipopolysaccharide Biosynthesis},
   Journal = {Journal of Bacteriology},
   Volume = {183},
   Number = {4},
   Pages = {1248-1258},
   Abstract = {The genetic characterization of a 5.5-kb chromosomal region of Sinorhizobium meliloti 2011 that contains lpsB, a gene required for the normal development of symbiosis with Medicago spp., is presented. The nucleotide sequence of this DNA fragment revealed the presence of six genes: greA and lpsB, transcribed in the forward direction; and lpsE, lpsD, lpsC, and lrp, transcribed in the reverse direction. Except for lpsB, none of the lps genes were relevant for nodulation and nitrogen fixation. Analysis of the transcriptional organization of lpsB showed that greA and lpsB are part of separate transcriptional units, which is in agreement with the finding of a DNA stretch homologous to a "nonnitrogen" promoter consensus sequence between greA and lpsB. The opposite orientation of lpsB with respect to its first downstream coding sequence, lpsE, indicated that the altered LPS and the defective symbiosis of lpsB mutants are both consequences of a primary nonpolar defect in a single gene. Global sequence comparisons revealed that the greA-lpsB and lrp genes of S. meliloti have a genetic organization similar to that of their homologous loci in R. leguminosarum bv. viciae. In particular, high sequence similarity was found between the translation product of lpsB and a core-related biosynthetic mannosyltransferase of R. leguminosarum bv. viciae encoded by the lpcC gene. The functional relationship between these two genes was demonstrated in genetic complementation experiments in which the S. meliloti lpsB gene restored the wild-type LPS phenotype when introduced into lpcC mutants of R. leguminosarum. These results support the view that S. meliloti lpsB also encodes a mannosyltransferase that participates in the biosynthesis of the LPS core. Evidence is provided for the presence of other lpsB-homologous sequences in several members of the family Rhizobiaceae.},
      Year = {2001} }




@article{
Laguerre94,
   Author = {Laguerre, G. and Allard, M.-R. and Revoy, F. and Amarger, N.},
   Title = {Rapid identification of rhizobia by restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA genes},
   Journal = {Applied and Environmental Microbiology},
   Volume = {60},
   Number = {1},
   Pages = {56-63},
   Abstract = {Forty-eight strains representing the eight recognized Rhizobium species, two new Phaseolus bean Rhizobium genomic species, Bradyrhizobium spp., Agrobacterium spp., and unclassified rhizobia from various host plants were examined by restriction fragment length polymorphism (RFLP) analysis of 16S rRNA genes amplified by polymerase chain reaction (PCR). Twenty-one composite genotypes were obtained from the combined data of the RFLP analysis with nine endonucleases. Species assignments were in full agreement with the established taxonomic classification. Estimation from these data of genetic relationships between and within genera and species correlated well with previously published data based on DNA-rRNA hybridizations and sequence analysis of 16S rRNA genes. This PCR-RFLP method provides a rapid tool for the identification of root nodule isolates and the detection of new taxa.},
      Year = {1994} }




@article{
Laguerre03,
   Author = {Laguerre, G. and Louvrier, P. and Allard, M. R. and Amarger, N.},
   Title = {Compatibility of rhizobial genotypes within natural populations of Rhizobium leguminosarum biovar viciae for nodulation of host legumes},
   Journal = {Applied and Environmental Microbiology},
   Volume = {69},
   Number = {4},
   Pages = {2276-2283},
   Abstract = {Populations of Rhizobium leguminosarum biovar viciae were sampled from two bulk soils, rhizosphere, and nodules of host legumes, fava bean (Vicia faba) and pea (Pisum sativum) grown in the same soils. Additional populations nodulating peas, fava beans, and vetches (Vicia sativa) grown in other soils and fava bean-nodulating strains from various geographic sites were also analyzed. The rhizobia were characterized by repetitive extragenomic palindromic-PCR fingerprinting and/or PCR-restriction fragment length polymorphism (RFLP) of 16S-23S ribosomal DNA intergenic spacers as markers of the genomic background and PCR-RFLP of a nodulation gene region, nodD, as a marker of the symbiotic component of the genome. Pairwise comparisons showed differences among the genetic structures of the bulk soil, rhizosphere, and nodule populations and in the degree of host specificity within the Vicieae cross-inoculation group. With fava bean, the symbiotic genotype appeared to be the preponderant determinant of the success in nodule occupancy of rhizobial genotypes independently of the associated genomic background, the plant genotype, and the soil sampled. The interaction between one particular rhizobial symbiotic genotype and fava bean seems to be highly specific for nodulation and linked to the efficiency of nitrogen fixation. By contrast with bulk soil and fava bean-nodulating populations, the analysis of pea-nodulating populations showed preferential associations between genomic backgrounds and symbiotic genotypes. Both components of the rhizobial genome may influence competitiveness for nodulation of pea, and rhizosphere colonization may be a decisive step in competition for nodule occupancy.},
      Year = {2003} }




@article{
Laguerre92,
   Author = {Laguerre, G. and Mazurier, S. I. and Amarger, N.},
   Title = {Plasmid profiles and restriction fragment length polymorphism of Rhizobium leguminosarum bv. viciae in field populations},
   Journal = {FEMS Microbiology Ecology},
   Volume = {101},
   Number = {1},
   Pages = {17-26},
   Abstract = {56 isolates of Rhizobium leguminosarum biovar viciae from one field were characterized by analysis of plasmid profile, total DNA restriction pattern and restriction fragment length polymorphism (RFLP) of 2 chromosomal regions and of symbiotic (Sym) plasmid. Different levels of similarity exist in patterns generated by the different techniques. At the level of partial similarity these techniques give comparable results for more than 80% of the isolates, with the exception of RFLP profiling with the Sym probe. Analysis at this level allows the grouping of the isolates that have most of their non-Sym genome similarly organized. At the level of total similarity, the techniques are no more equivalent and provide complementary information on possible evolution of the different elements of the genome identified by each specific technique. The non-Sym plasmids defining classes were strongly associated with specific chromosomal backgrounds. In contrast, variations in Sym plasmids were not related with variations in the remaining genome. Host range towards chromosomes was variable among the Sym plasmids, which may reflect plasmid transfer between strains.},
   Keywords = {DNA fingerprint
Genetic diversity
Plasmid profiles
Restriction fragment length polymorphism
Rhizobium leguminosarum
Symbiotic plasmid},
   Year = {1992} }




@article{
Laguerre01,
   Author = {Laguerre, G. and Nour, S. M. and Macheret, V. and Sanjuan, J. and Drouin, P. and Amarger, N.},
   Title = {Classification of rhizobia based on \emph{nodC} and \emph{nifH} gene analysis reveals a close phylogenetic relationship among \emph{Phaseolus vulgaris} symbionts},
   Journal = {Microbiology},
   Volume = {147},
   Number = {4},
   Pages = {981-93},
   Abstract = {The nodC and nifH genes were characterized in a collection of 83 rhizobial strains which represented 23 recognized species distributed in the genera Rhizobium, Sinorhizobium, Mesorhizobium and Bradyrhizobium, as well as unclassified rhizobia from various host legumes. Conserved primers were designed from available nucleotide sequences and were able to amplify nodC and nifH fragments of about 930 bp and 780 bp, respectively, from most of the strains investigated. RFLP analysis of the PCR products resulted in a classification of these rhizobia which was in general well-correlated with their known host range and independent of their taxonomic status. The nodC and nifH fragments were sequenced for representative strains belonging to different genera and species, most of which originated from Phaselous vulgaris nodules. Phylogenetic trees were constructed and revealed close relationships among symbiotic genes of the Phaseolus symbionts, irrespective of their 16S-rDNA-based classification. The nodC and nifH phylogenies were generally similar, but cases of incongruence were detected, suggesting that genetic rearrangements have occurred in the course of evolution. The results support the view that lateral genetic transfer across rhizobial species and, in some instances, across Rhizobium and Sinorhizobium genera plays a role in diversification and in structuring the natural populations of rhizobia.},
   Keywords = {Bradyrhizobium
classification
genetics
DNA
Bacterial
analysis
Ribosomal
Fabaceae
microbiology
Molecular Sequence Data
N-Acetylglucosaminyltransferases
Oxidoreductases
Phylogeny
Plants
Medicinal
Polymerase Chain Reaction
Polymorphism
Restriction Fragment Length
RNA
16S
Rhizobiaceae
Sequence Homology
Nucleic Acid
Sinorhizobium
Support
Non-U.S.Gov't
Symbiosis},
   Year = {2001} }




@article{
Laguerre97,
   Author = {Laguerre, G. and vanBerkum, P. and Amarger, N. and Prevost, D.},
   Title = {Genetic diversity of rhizobial symbionts isolated from legume species within the genera Astragalus, Oxytropis, and Onobrychis},
   Journal = {Applied and Environmental Microbiology},
   Volume = {63},
   Number = {12},
   Pages = {4748-4758},
   Abstract = {The genetic diversity of 44 rhizobial isolates from Astragalus, Oxytropis, and Onobrychis spp. originating from different geographic locations was evaluated by mapped restriction site polymorphism (MRSP) analysis of 16S rRNA genes and by PCR DNA fingerprinting with repetitive sequences (REP-PCR). A comparison of tree topologies of reference strains constructed with data obtained by MRSP and by 16S rRNA gene sequence analyses showed that the topologies were in good agreement, indicating that the MSRP approach results in reasonable estimates of rhizobial phylogeny. The isolates were distributed into 14 distinct 16S rRNA gene types clustering into three major groups which corresponded with three of the genera within the legume symbionts. Most of the isolates were within the genus Mesorhizobium. Five were identified with different genomic species nodulating Lotus spp. and Cicer arietinum. Three Astragalus isolates were classified as Bradyrhizobium, one being similar to Bradyrhizobium elkanii and another being similar to Bradyrhizobium japonicum. Six of the isolates were related to species within the genus Rhizobium. Two were similar to Rhizobium leguminosarum, and the remainder were identified as Rhizobium gallicum. DNA fingerprinting by REP-PCR revealed a high level of diversity within single 16S ribosomal DNA types. The 44 isolates mere distributed into 34 REP groups. Rhizobial classification at the genus and probably also the species levels was independent of geographic origin and host plant affinity.},
      Year = {1997} }




@article{
Laird94,
   Author = {Laird, M. G.},
   Title = {Geological aspects of the opening of the Tasman Sea},
   Journal = {Evolution of the Tasman Sea Basin},
   Pages = {1-17},
      Year = {1994} }




@article{
Laird04,
   Author = {Laird, M. G. and Bradshaw, J. D.},
   Title = {The break-up of a long-term relationship: The Cretaceous separation of New Zealand from Gondwana},
   Journal = {Gondwana Research},
   Volume = {7},
   Number = {1},
   Pages = {273-286},
   Abstract = {After a prolonged period of convergent margin tectonics in the Late Paleozoic and Mesozoic, resulting in terrane accretion, uplift and erosion of the New Zealand segment of Gondwana, the region saw a rapid change to extensional tectonics in mid-Cretaceous times. The change in regime is commonly marked by a major angular unconformity that separates the older, often strongly-deformed subduction-related 'basement' rocks from the younger, less-deformed 'cover' strata. The youngest 'basement' strata locally contain Albian fossils, and the youngest associated zircons have been radiometrically dated at ca. 100 Ma. In general the oldest strata overlying the unconformity contain fossils of similar Albian age, and the oldest radiometric dates also give similar dates of ca. 100 Ma, indicating a very rapid transition between the two tectonic regimes. The onset of extension resulted in the widespread development of grabens and half grabens, associated in the northwest of the South Island with a metamorphic core complex. In the west and south, on the thicker and more buoyant crust of most of the South Island, the new basins were infilled with mainly non-marine deposits. Non-marine graben infill consists of locally-derived breccia deposited as talus or debris flows on alluvial fans, passing directly as fan deltas or via fluvial deposits into lacustrine deposits. Active faulting continued in some areas until the initiation of sea floor spreading in Santonian times. Post-subduction strata on the thinner continental crust of the northeastern South Island and eastern North Island (East Coast Basin) were mainly marine. Initial sedimentary deposits in the west of the basin, reflecting extensional tectonism, consist of coarse-grained debris-flow deposits or olistostromes, generally fining upwards as tectonic activity waned: those in the east, including allochthonous sediments derived from the northeast, are dominated by turbidites. Early Cenomanian (ca. 96-98 Ma) injection of intraplate alkaline igneous rocks in central New Zealand caused updoming, resulting in shallowing and local uplift of the basin floor above sea level. A long (ca. 10 Ma) period of slow subsidence and transgressive marine sedimentation interrupted by episodic relative sea level changes followed. This pattern changed in the Late Coniacian (ca. 87-86 Ma), with a sudden influx of coarse, transgressive sands in eastern New Zealand. This was immediately preceded in parts of the region by uplift and erosion, probably driven by convective upwelling of the mantle just prior to sea-floor spreading, resulting in a 'break-up' unconformity. In the Late Santonian (ca. 85-84 Ma), development of a new, diachronous, widespread low-relief erosion surface, overlain by fine-grained deposits accompanying a rapid rise in relative sea level, coincided with the beginning of sea-floor spreading, rapid passive margin subsidence, and final separation of New Zealand from Gondwana.},
   Keywords = {Cretaceous
Gondwana
New Zealand
Rifting
Seafloor
Spreading
continental breakup
Cretaceous
Gondwana
plate tectonics
rifting
seafloor spreading
Australasia
New Zealand},
   Year = {2004} }




@book{
Lapage90,
   Author = {Lapage, S. P. and Sneath, P.H. A. and Lessel, E. F. and Skerman, V. B. D. and Seeliger, H. P. R. and Clark, W. A.},
   Title = {International Code of Nomenclature of Bacteria},
   Publisher = {American Society of Microbiology},
   Address = {Washington},
      Year = {1990} }




@article{
Laranjo02,
   Author = {Laranjo, M. and Branco, C. and Soares, R. and Alho, L. and Carvalho, M.D.E. and Oliveira, S.},
   Title = {Comparison of chickpea rhizobia isolates from diverse Portuguese natural populations based on symbiotic effectiveness and DNA fingerprint},
   Journal = {Journal of Applied Microbiology},
   Volume = {92},
   Number = {6},
   Pages = {1043-1050},
   Abstract = {Aims: To test the hypothesis that differences in chickpea yields obtained in four distinct Portuguese regions (Beja, Elvas-Casas Velhas, Elvas-Estaça?o Nacional de Melhoramento de Plantas (ENMP) and E?vora) could be due to variation between the natural rhizobia populations. Methods and Results: Estimation of the size of the different rhizobial populations showed that Elvas-ENMP population was the largest one. Elvas-ENMP population also revealed a higher proportion of isolates carrying more than one plasmid. Assessment of genetic diversity of the native rhizobia populations by a DNA fingerprinting PCR method, here designated as DAPD (Direct Amplified Polymorphic DNA), showed a higher degree of variation in Elvas-ENMP and Beja populations. The symbiotic effectiveness (SE) of 39 isolates was determined and ranged 13-34%. Statistical analysis showed that SE was negatively correlated with plasmid number of the isolate. Conclusions: The largest indigenous rhizobia population was found in Elvas-ENMP. DAPD pattern and plasmid profile analysis both suggested a higher genetic diversity among the populations of Elvas-ENMP and Beja. No relationship was found between SE of the isolates and their origin site. Significance and Impact of Study: The large native population, rather than the symbiotic performance of individual rhizobia, could contribute to the higher chickpea yields obtained in Elvas-ENMP.},
      Year = {2002} }




@article{
Laranjo04,
   Author = {Laranjo, M. and Machado, J. and Young, J. P. W. and Oliveira, S.},
   Title = {High diversity of chickpea Mesorhizobium species isolated in a Portuguese agricultural region},
   Journal = {FEMS Microbiology Ecology},
   Volume = {48},
   Number = {1},
   Pages = {101-107},
   Abstract = {Chickpea rhizobia isolated from Portuguese soils were assigned to the genus Mesorhizobium by 16S-rDNA sequencing. High species diversity was found within populations of an agricultural region in the south of Portugal.;Besides the expected Mesorhizobium ciceri and M. mediterraneum, some isolates were close to M. loti or M. tianshanense and some formed a clade that may represent a new species. A new PCR-based approach, named direct amplified polymorphic DNA (DAPD) analysis, supported the 16S-based phylogeny. This suggests that this method could be used as a molecular tool to assess genetic relationships. Evaluation of genetic diversity by 16S-rDNA sequence, DAPD and protein profiles showed different levels of heterogeneity in natural populations. 2004 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved.},
      Year = {2004} }




@article{
Laranjo01,
   Author = {Laranjo, M. and Rodrigues, R. and Alho, L. and Oliveira, S.},
   Title = {Rhizobia of chickpea from southern Portugal: Symbiotic efficiency and genetic diversity},
   Journal = {Journal of Applied Microbiology},
   Volume = {90},
   Number = {4},
   Pages = {662-667},
   Abstract = {Aims: In order to evaluate differences between chickpea rhizobial populations from three geographical areas in southern Portugal (Beja, Elvas and E?vora), isolates from the three regions were obtained and analysed. Methods and Results: The genetic characterization of the isolates was done by plasmid profiles and restriction analysis of the nif H gene. Symbiotic efficiency of the isolates was also determined. Relationships between geographical origin, symbiotic efficiency and molecular characteristics were established. Beja soil revealed a larger rhizobia population as well as the presence of some of the isolates with higher symbiotic efficiency values. Isolates with a single plasmid showed a significantly higher symbiotic efficiency. Conclusions: Genetic and phenotypic differences were detected between the natural rhizobial populations from the three locations. Significance and Impact of the Study: The different yield potential with cultivars of chickpea usually obtained in the three regions of southern Portugal could be due to their different natural rhizobial populations.},
      Year = {2001} }




@article{
Larimer04,
   Author = {Larimer, F. W. and Hauser, L. and Land, M. L. and Pelletier, D. A. and Chain, P. and Lamerdin, J. and Malfatti, S. and Do, L. and Beatty, J. T. and Lang, A. S. and Tabita, F. R. and Gibson, J. L. and Hanson, T. E. and Bobst, C. and Torres Y Torres, J. L. and Peres, C. and Harrison, F. H. and Gibson, J. and Harwood, C. S.},
   Title = {Complete genome sequence of the metabolically versatile photosynthetic bacterium \emph{Rhodopseudomonas palustris}},
   Journal = {Nature Biotechnology},
   Volume = {22},
   Number = {1},
   Pages = {55-61},
   Abstract = {Rhodopseudomonas palustris is among the most metabolically versatile bacteria known. It uses light, inorganic compounds, or organic compounds, for energy. It acquires carbon from many types of green plant-derived compounds or by carbon dioxide fixation, and it fixes nitrogen. Here we describe the genome sequence of R. palustris, which consists of a 5,459,213-base-pair (bp) circular chromosome with 4,836 predicted genes and a plasmid of 8,427 bp. The sequence reveals genes that confer a remarkably large number of options within a given type of metabolism, including three nitrogenases, five benzene ring cleavage pathways and four light harvesting 2 systems. R. palustris encodes 63 signal transduction histidine kinases and 79 response regulator receiver domains. Almost 15% of the genome is devoted to transport. This genome sequence is a starting point to use R. palustris as a model to explore how organisms integrate metabolic modules in response to environmental perturbations.},
      Year = {2004} }




@article{
Lavin90,
   Author = {Lavin, M. and Doyle, J. J. and Palmer, J. D.},
   Title = {Evolutionary significance of the loss of the chloroplast-DNA inverted repeat in the Leguminosae subfamily Papilionoideae},
   Journal = {Evolution},
   Volume = {44},
   Pages = {390-402},
      Year = {1990} }




@article{
Lavin04,
   Author = {Lavin, M. and Schrire, B. P. and Lewis, G. and Pennington, R. T. and Delgado-Salinas, A. and Thulin, M. and Hughes, C. E. and Matos, A. B. and Wojciechowski, M. F.},
   Title = {Metacommunity process rather than continental tectonic history better explains geographically structured phylogenies in legumes},
   Journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences},
   Volume = {359},
   Number = {1450},
   Pages = {1509-1522},
   Abstract = {Penalized likelihood estimated ages of both densely sampled intracontinental and sparsely sampled transcontinental crown clades in the legume family show a mostly Quaternary to Neogene age distribution. The mode ages of the intracontinental crown clades range from 4-6 Myr ago, whereas those of the transcontinental crown clades range from 8-16 Myr ago. Both of these young age estimates are detected despite methodological approaches that bias results toward older ages. Hypotheses that resort to vicariance or continental history to explain continental disjunct distributions are dismissed because they require mostly Palaeogene and older tectonic events. An alternative explanation centring on dispersal that may well explain the geographical as well as the ecological phylogenetic structure of legume phylogenies is Hubbell's unified neutral theory of biodiversity and biogeography. This is the only dispersalist theory that encompasses evolutionary time and makes predictions about phylogenetic structure.},
   Keywords = {Bayesian likelihood analysis
Intracontinental crown clades
Molecular age determination
Penalized likelihood rate smoothing
Transcontinental sister clades
Unified neutral theory of biodiversity and biogeography},
   Year = {2004} }




@article{
Lavin03,
   Author = {Lavin, M. and Wojciechowski, M. F. and Gasson, P. and Hughes, C. and Wheeler, E.},
   Title = {Phylogeny of robinioid legumes (Fabaceae) revisited: Coursetia and Gliricidia recircumscribed, and a biogeographical appraisal of the Caribbean endemics},
   Journal = {Systematic Botany},
   Volume = {28},
   Number = {2},
   Pages = {387-409},
   Abstract = {Morphological data and sequences from the nuclear ribosomal ITS region, and the chloroplast trnL intron and matK locus were sampled from robinioid legumes to infer phylogenetic relationships. The monophyletic robinioid clade includes 11 genetically and often morphologically distinct subclades ranked as genera with the following well supported higher level relationships: ((Hebestigma, Lennea), ((Gliricidia, Poitea), (Olneya, Robinia, Poissonia, Coursetia, Peteria, Genistidium, and Sphinctospermum))). In order to render all 11 robinioid genera monophyletic, the genus Hybosema is synonymized with Gliricidia, and the genus Poissonia is resurrected to accommodate four morphologically disparate species previously classified in Coursetia. Three new combinations are required to accommodate these two generic recircumscriptions: Gliricidia robustum, Poissonia heterantha, and Poissonia weberbaueri. Ages of clades and evolutionary substitution rates are derived from a rate-smoothed Bayesian likelihood approach on sequences from the ITS region and the matK locus. Time constraints are derived from the Tertiary fossil wood species Robinia zirkelii, which shares apomorphic wood characters with the Robinia stem clade. The Cuban endemic Hebestigma is estimated to have diverged at least 38 Ma from its Mesoamerican sister genus Lennea, whereas the Greater Antillean Poitea is estimated to have diverged at least 16 Ma from its continental sister Gliricidia. This study reveals that sequences from the ITS region are amenable to exhaustive taxon sampling because of the high levels of variation at and below the species level. The evolutionary substitution rate for the ITS region is estimated at 3.1-3.5 × 10-9 substitutions/site/year, approximately an order of magnitude faster than that estimated for the matK locus.},
      Year = {2003} }




@article{
Lavin01,
   Author = {Lavin, M. and Wojciechowski, M. F. and Richman, A. and Rotella, J. and Sanderson, M. J. and Matos, A. B.},
   Title = {Identifying tertiary radiations of fabaceae in the greater antilles: Alternatives to cladistic vicariance analysis},
   Journal = {International Journal of Plant Sciences},
   Volume = {162},
   Number = {6 SUPPL.},
   Abstract = {The fossil record shows that the legume family was abundant and taxonomically diverse in Early Tertiary tropical deciduous forests of North America. Today, woody members of this family are almost nonexistent in temperate deciduous forests. This former North American legume diversity now lies in the Tropics, including the Greater Antilles. To show the Antillean refugia, we detail a phylogenetic and biogeographic analysis of two legume groups, the Ormocarpum and Robinia clades, which have either a Tertiary fossil record in North America or a sister clade with such a fossil record. A combined analysis of molecular and nonmolecular data is used for the cladistic vicariance approaches, while an exhaustively sampled data set of nrDNA ITS/5.8S sequences is used for the molecular biogeographic analysis. Results from component, three-area-statements, and Brooks parsimony analysis are equivocal in suggesting an influence of Tertiary history on the distribution of the woody genera Pictetia (Ormocarpum clade) and Poitea (Robinia clade), two of the most speciose endemic legume radiations in the Greater Antilles. Alternatively, nucleotide diversity, evolutionary rates, and coalescent analyses of molecular phylogenies all suggest a Tertiary diversification of Pictetia and Poitea. The results are corroborated by a regression analysis that implicates both age of island biota and island area in accurately predicting numbers of endemic legume taxa. These findings, combined with the legume fossil record, suggest that both Pictetia and Poitea stem from Tertiary North American boreotropical groups. J. A. Wolfe's hypothesis that the Greater Antilles harbor boreotropical relicts is supported.},
   Keywords = {Cladistic vicariance analysis
Coalescent theory
Fabaceae
Island biogeography
Molecular biogeography
Penalized likelihood},
   Year = {2001} }




@article{
Lawrence02,
   Author = {Lawrence, J. G. and Ochman, H.},
   Title = {Reconciling the many faces of lateral gene transfer},
   Journal = {Trends in Microbiology},
   Volume = {10},
   Number = {1},
   Pages = {1-4},
      Year = {2002} }




@article{
Lawver03,
   Author = {Lawver, L. A. and Gahagan, L. M.},
   Title = {Evolution of cenozoic seaways in the circum-antarctic region},
   Journal = {Palaeogeography, Palaeoclimatology, Palaeoecology},
   Volume = {198},
   Number = {1-2},
   Pages = {11-37},
   Abstract = {A complete circum-Antarctic seaway did not open until both the South Tasman Rise cleared the Oates Land coast of East Antarctica and Drake Passage opened between the southern tip of South America and the northern end of the Antarctic Peninsula. Major plate motions based on dated seafloor spreading anomalies and distinct fracture zone lineations constrain the age of the opening of a seaway between the South Tasman Rise and Antarctica as very close to the Eocene-Oligocene boundary, with an unrestricted opening deeper than 2000 m dating from ?32 Ma. Timing of the opening of Drake Passage is more circumstantial because the exact motions of certain micro-continental fragments are not known. The motion of Africa with respect to South America as well as the motion of East . Antarctica with respect to Africa are well constrained for the Cenozoic. These major plate motions are used with the reasonable assumption of no Cenozoic motion of the Antarctic Peninsula with respect to East Antarctica to constrain the location of the Antarctic Peninsula with respect to the southern tip of South America for the critical period of late Eocene to late Oligocene. Uncertainty of motion of the South Georgia and South Orkney microcontinents and other possible continental fragments make an exact time for opening of Drake Passage difficult to ascertain. Even so, the early Oligocene position of the Antarctic Peninsula with respect to South America requires a through-going, deep-water seaway to have been open at Drake Passage prior to 28 Ma, even given the unconstrained motion of various high-standing crustal fragments in the Scotia Sea. With reasonable assumptions concerning motion of the crustal fragments in the western and central Scotia Sea, it is likely that Drake Passage or passage through Powell Basin was open to deep water circulation by ?31±2 Ma. © 2003 Elsevier B.V. All rights reserved.},
   Keywords = {Antarctic seaways
Drake Passage
Eocene-Oligocene boundary
South Tasman Rise},
   Year = {2003} }




@article{
Leary04,
   Author = {Leary, James J. K.  and Singleton, Paul W.  and Borthakur, Dulal.},
   Title = {Canopy nodulation of the endemic tree legume \emph{Acacia koa} in the mesic forests of Hawaii},
   Journal = {Ecology},
   Volume = {85},
   Number = {11},
   Pages = {3151-3157},
   Abstract = {Canopy nodulation of Acacia koa (koa) is the result of a unique symbiosis between the host adventitious root system and the bradyrhizobia residing in “pockets” within the canopy of koa. These canopy pockets contain trapped organic soils that are mainly derived from decomposing heartwood and phyllode litter of the host tree. These canopy soils have significantly higher levels of exchangeable cations, total nitrogen content, and significantly lower aluminum levels than the terrestrial soils. Canopy Bradyrhizobium isolates from separate koa trees of different locations do not share matching box-polymerase chain reaction (PCR) fingerprints, showing that there is no single type that is specific to canopy nodulation. Within the canopy pocket of a single tree, however, we observed a homogenous Bradyrhizobium population that was distinct from the proximal terrestrial population. Canopy nodulation has only been observed on mature koa trees and may function in maintaining symbiosis under stresses occurring within the rhizosphere of the terrestrial environment.},
      Year = {2004} }




@article{
Leary06,
   Author = {Leary, J. K. and Hue, N. V. and Singleton, P. W. and Borthakur, D.},
   Title = {The major features of an infestation by the invasive weed legume gorse (\emph{Ulex europaeus}) on volcanic soils in Hawaii},
   Journal = {Biology and Fertility of Soils},
   Volume = {42},
   Number = {3},
   Pages = {215-223},
   Abstract = {Gorse (Ulex europaeus) infestation occupies over 4,000 ha of agriculture and conservation lands on the southeastern slope of Mauna Kea on the Island of Hawaii. The aim of this investigation is to identify ecological features associated with this weed invasion by comparing the gorse-infested areas to the surrounding uninfested areas of this landscape. The soils within the gorse infestation are more acidic, resulting in higher levels of KCl-extractable Al and lower levels of Mehlich III-extractable Ca, Mg, Mn, and Zn. Yet, gorse accumulates higher concentrations of Ca, Zn and, Cu than the kikuyu grass (Pennesitum clandestinum), which is ubiquitous throughout the site. The Ca:Al and Mg:Al molar charge ratios of the soils are lowest within the epicenter of the gorse infestation, while the molar ratios are highest in the gorse apical stem tissues. All gorse plants are nodulated and have higher nitrogen contents than the surrounding kikuyu grass. Furthermore, the ?15N of the gorse stem tissues approaches 0‰, suggesting that nitrogen is being symbiotically fixed from the atmosphere. Characterization of the Bradyrhizobium isolated from gorse nodules shows similarities and distinctions to Bradyrhizobium isolated from the endemic legume koa (Acacia koa) within the same location. Population densities of the indigenous Bradyrhizobium are higher within the gorse rhizosphere than the kikuyu grass. Soil acidification, nutrient depletion, and symbiotic nitrogen fixation distinguish gorse-infested areas from the surrounding uninfested areas. These observations suggest that gorse has a competitive advantage over kikuyu grass under conditions of soil nutrient deficiency.},
   Keywords = {In press, published online: doi: 10.1007/s00374-005-0018-9},
   Year = {2006} }




@article{
Lechtova31,
   Author = {Lechtova-Trnka, M.},
   Title = {\'Etude sur les bact\'eries des l\'egumineuses et observations sur quelques champignons parasites des nodosit\'es.},
   Journal = {Botaniste},
   Volume = {23},
   Pages = {301-530},
      Year = {1931} }




@article{
Lee48,
   Author = {Lee, A. T.},
   Title = {The genus Swainsona},
   Journal = {Contributions from the New South Wales National Herbarium},
   Volume = {1},
   Pages = {131-271},
      Year = {1948} }




@article{
Lee01,
   Author = {Lee, D. E. and Lee, W. G. and Mortimer, N.},
   Title = {Where and why have all the flowers gone? Depletion and turnover in the New Zealand Cenozoic angiosperm flora in relation to palaeogeography and climate},
   Journal = {Australian Journal of Botany},
   Volume = {49},
   Number = {3},
   Pages = {341-356},
   Abstract = {The modern New Zealand angiosperm flora has many notable characteristics, such as a predominance of evergreen, perennial life forms, few nitrogen-fixing species, despecialised floral features and asymmetric genus-species relations. The origin of these features has been attributed to antiquity of the flora, isolation and/or environmental history. Using evidence from palynology and macrofossils, we investigate the characteristics of the mid-late Cenozoic angiosperm flora and the impact of environmental changes in land area and configuration, physiography and climate on the depletion and composition of the New Zealand flora. Climatic cooling, increasing isolation and tectonism have each acted as important environmental filters, contributing to regional extinctions and decreasing floral diversity, and inducing major turnover in the floristic composition of New Zealand. During the Miocene and Pliocene at least 15 families and a minimum of 36 genera were lost from the New Zealand flora. These included a range of life forms and physiognomically important taxa such as Acacia, Bombax, Casuarina, Eucalyptus, Ilex, many Proteaceae and several palms. The extinction and decline in richness of subtropical families was caused by the onset of cooling conditions in the Late Miocene-Pliocene, and exacerbated by the absence of significant land areas to act as refugia at lower latitudes. Many of these genera/families persist today on islands to the north (e.g. New Caledonia), reflecting mid-Cenozoic land conduits, and in Australia. The close floristic links with New Caledonia were probably maintained by intermittent island stepping-stones which facilitated interchange of subtropical taxa until the Late Miocene. The Pleistocene extinction of some genera, tolerant of warm-temperate environments (e.g. Acacia, Eucalyptus) may be a reflection of the fact that persistent mesic conditions favoured widespread dominance of dense rainforest during interglacials. The loss of these groups, containing diverse life forms and floral structures, suggests that many of the present characteristics of the New Zealand flora reflect strong selective pressures, mainly driven by climate change, in the Late Miocene, Pliocene and Pleistocene, rather than events of greater geological antiquity.},
   Keywords = {climate
extinction
paleogeography
population density
Acacia
Bombax
Casuarina
Eucalyptus
Ilex},
   Year = {2001} }




@article{
Lee04,
   Author = {Lee, W. K. and Tokuoka, T. and Heo, K.},
   Title = {Molecular evidence for the inclusion of the Korean endemic genus "Echinosophora" in Sophora (Fabaceae), and embryological features of the genus},
   Journal = {Journal of Plant Research},
   Volume = {117},
   Number = {3},
   Pages = {209-219},
   Abstract = {Although Echinosophora Nakai has been known as a monotypic and endemic genus of Papillionoideae of Fabaceae in Korea, it has been controversial whether it is distinct from or merged with Sophora. To resolve this matter, we conducted molecular phylogenetic analyses using nucleotide sequence data from the plastid rbcL gene and trnL (UAA) intron. Parsimony analysis, using a total of 53 taxa of the Papillionoideae (including E. koreensis [Nakai] Nakai and several species of Sophora and related genera) and using 20 taxa of Caesalpinioideae and Mimosoideae as outgroups, showed that, although the examined species of Sophora are split into two clades, E. koreensis formed a common clade with S. tomentosa (the type species of the genus) and S. flavescens. E. koreensis therefore should be treated as S. koreensis Nakai, and the generic name Echinosophora be eliminated. We also investigated the embryology of S. koreensis (= E. koreensis) and S. flavescens and found that no differences existed between them. Our molecular study, like other studies, strongly suggested that Sophora is polyphyletic. In this study we presented a summary of embryological features of the core Sophora for future critical comparison with related and unrelated taxa.},
      Year = {2004} }




@article{
Legocki80,
   Author = {Legocki, R. P. and Verma, D. P.},
   Title = {Identification of "nodule-specific" host proteins (nodoulins) involved in the development of rhizobium-legume symbiosis},
   Journal = {Cell},
   Volume = {20},
   Number = {1},
   Pages = {153-63},
   Abstract = {Infection of legume roots with Rhizobium species results in the development of a root nodule structure in which the bacteria form an intracellular symbiosis with the plant. We report here that the infection of soybean (Glycine max L.) roots with Rhizobium japonicum results in the synthesis by the plant of at least 18-20 polypeptides other than leghemoglobin during the development of root nodules. Identification of these "nodule-specific" host polypeptides (referred to as nodulins) was accomplished by two-dimensional gel analysis of the immunoprecipitates formed by a "nodule-specific" antiserum with in vitro translation products of root-nodule polysomes that are free of bacteroidal contaminations. Nodulins account for 7-11% of the total 35S-methionine-labeled protein synthesized in the host cell cytoplasm, and the majority of them are of 12,000-20,000 molecular weight. These proteins are absent from the uninfected roots, bacteroids and free-living Rhizobium, and appear to be coded for the plant genes that may be obligatory for the development of symbiosis in the legume root nodules. Analysis of nodulins in ineffective (unable to fix nitrogen) nodules developed due to Rhizobium strains SM5 and 61A24 showed that their synthesis is reduced and their expression differentially influenced by mutations in rhizobia. Two polypeptides of bacterial origin were also found to be cross-reactive with the "nodule-specific" antiserum, suggesting that they are secreted by Rhizobium into the host cell cytoplasm during symbiotic nitrogen fixation.},
   Keywords = {Fabaceae/genetics/*microbiology
Immunoelectrophoresis, Two-Dimensional
*Membrane Proteins
Molecular Weight
Plant Proteins/biosynthesis/*genetics/immunology
*Plants, Medicinal
RNA, Messenger/genetics
Rhizobium/genetics/*physiology
Symbiosis},
   Year = {1980} }




@article{
Leigh92,
   Author = {Leigh, J. A. and Coplin, D. L.},
   Title = {Exopolysaccharides in plant-bacterial interactions},
   Journal = {Annual Review of Microbiology},
   Volume = {46},
   Pages = {307-346},
   Abstract = {Rhizobial plant symbionts and bacterial plant pathogens produce exopolysaccharides that often play essential roles in the plant interaction. Many of these exopolysaccharides are acidic heteropolysaccharides that have repeating subunit structures with carbohydrate and noncarbohydrate substituents, while others are homopolysaccharides such as alginate, levan, cellulose, and glucan. While the homopolysaccharides are synthesized by mechanisms that vary with the particular polysaccharide, the heteropolysaccharides as a rule are synthesized by subunit assembly from nucleotide diphosphate-sugar precursors on a membrane-bound lipid carrier followed by polymerization and secretion. Many mutants in exopolysaccharide synthesis have been isolated, and in several cases this has led to the identification of genes that function in particular steps of biosynthesis, as well as in regulation of exopolysaccharide biosynthesis. The genetic regulation of exopolysaccharide synthesis in many plant pathogens is complex, perhaps reflecting the various niches, free living and in planta, in which exopolysaccharides function. In some cases, exopolysaccharide synthesis is regulated coordinately with other virulence factors, and in other cases separately. Regulatory genes that have homology to the two-component sensor and transcriptional effect or systems are a common motif. In Rhizobium species, exopolysaccharide synthesis is regulated by transcriptional as well as posttranslational mechanisms. Exopolysaccharides function differently in the root-nodule symbiosis versus plant pathogenesis. Specific Rhizobium exopolysaccharide structures promote nodule development and invasion inlegumes that form in determinate nodules. In plant pathogenesis, less specific mechanisms of pathogenesis occur: exopolysaccharides cause wilting by blocking xylem vessels, are partly responsible for water-soaked lesions, and may also aid in invasion, growth, and survival in plant tissues.},
   Keywords = {capsular polysaccharide
extracellular polysaccharide
plant pathogen
Rhizobium
root nodule},
   Year = {1992} }




@article{
Leigh85,
   Author = {Leigh, J. A. and Signer, E. R. and Walker, G. C.},
   Title = {Exopolysaccharide-deficient mutants of Rhizobium meliloti that form ineffective nodules},
   Journal = {Proceedings of the National Academy of Sciences of the United States of America},
   Volume = {82},
   Number = {18},
   Pages = {6231-6235},
   Abstract = {By screening with the fluorescent stain Calcofluor, we have isolated 26 independent transposon Tn5 insertion mutants of Rhizobium meliloti that are deficient in the production of a known extracellular polysaccharide (Exo-). The mutants belonged to six distinct genetic groups based on the ability of their Exo- phenotype to be complemented by different recombinant plasmids from a R. meliloti clone bank. With few exceptions, all of the mutants formed ineffective (non-nitrogen-fixing) nodules on alfalfa. For all but one group, the complementing plasmids restored effective nodulation. These results establish a firm and extensive correlation between the ability of Rhizobium to produce a particular polysaccharide and symbiotic proficiency. The ineffective nodules appeared to contain no bacteroids and to form without shepherds' crooks or infection threads; this symbiotic phenotype matches that described for a set of independently isolated mutants that belong phenotypically and genetically to the group B exopolysaccharide mutants described previously. Apparently the exopolysaccharide, although not required for nodule formation, is involved in wild-type nodule invasion.},
      Year = {1985} }




@article{
Lerouge90,
   Author = {Lerouge, P. and Roche, P. and Faucher, C. and Maillet, F. and Truchet, G. and Prome, J. C. and Denarie, J.},
   Title = {Symbiotic host-specificity of \emph{Rhizobium meliloti} is determined by a sulphated and acylated glucosamine oligosaccharide signal},
   Journal = {Nature},
   Volume = {344},
   Number = {6268},
   Pages = {781-784},
   Abstract = {Rhizobia are symbiotic bacteria that elicit the formation on leguminous plants of specialized organs, root nodules, in which they fix nitrogen. In various Rhizobium species, such as R. leguminosarum and R. meliloti, common and host-specific nodulation (nod) genes have been identified which determine infection and nodulation of specific hosts. Common nodABC genes as well as host-specific nodH and nodQ genes were shown recently, using bioassays, to be involved in the production of extracellular Nod signals. Using R. meliloti strains overproducing symbiotic Nod factors, we have purified the major alfalfa-specific signal, NodRm-1, by gel permeation, ion exchange and C18 reverse-phase high performance liquid chromatography. From mass spectrometry, nuclear magnetic resonance, 35S-labelling and chemical modification studies, NodRm-1 was shown to be a sulphated ?-1,4-tetrasaccharide of D-glucosamine (M(r) 1,102) in which three amino groups were acetylated and one was acylated with a C16 bisunsaturated fatty acid. This purified Nod signal specifically elicited root hair deformation on the homologous host when added in nanomolar concentration.},
      Year = {1990} }




@article{
Levin00,
   Author = {Levin, Bruce R. and Bergstrom, Carl T.},
   Title = {Bacteria are different: Observations, interpretations, speculations, and opinions about the mechanisms of adaptive evolution in prokaryotes},
   Journal = {Proceedings of the National Academy of Sciences of the United States of America},
   Volume = {97},
   Number = {13},
   Pages = {6981-6985},
      Year = {2000} }




@article{
Lewis00,
   Author = {Lewis, Kim},
   Title = {Programmed Death in Bacteria},
   Journal = {Microbiology and Molecular Biology Reviews},
   Volume = {64},
   Number = {3},
   Pages = {503-514},
   Abstract = {Programmed cell death (PCD) in bacteria plays an important role in developmental processes, such as lysis of the mother cell during sporulation of Bacillus subtilis and lysis of vegetative cells in fruiting body formation of Myxococcus xanthus. The signal transduction pathway leading to autolysis of the mother cell includes the terminal sporulation sigma factor E[sigma]K, which induces the synthesis of autolysins CwlC and CwlH. An activator of autolysin in this and other PCD processes is yet to be identified. Autolysis plays a role in genetic exchange in Streptococcus pneumoniae, and the gene for the major autolysin, lytA, is located in the same operon with recA. DNA from lysed cells is picked up by their neighbors and recombined into the chromosome by RecA. LytA requires an unknown activator controlled by a sensory kinase, VncS. Deletion of vncS inhibits autolysis and also decreases killing by unrelated antibiotics. This observation suggests that PCD in bacteria serves to eliminate damaged cells, similar to apoptosis of defective cells in metazoa. The presence of genes affecting survival without changing growth sensitivity to antibiotics (vncS, lytA, hipAB, sulA, and mar) indicates that bacteria are able to control their fate. Elimination of defective cells could limit the spread of a viral infection and donate nutrients to healthy kin cells. An altruistic suicide would be challenged by the appearance of asocial mutants without PCD and by the possibility of maladaptive total suicide in response to a uniformly present lethal factor or nutrient depletion. It is proposed that a low rate of mutation serves to decrease the probability that asocial mutants without PCD will take over the population. It is suggested that PCD is disabled in persistors, rare cells that are resistant to killing, to ensure population survival. It is suggested that lack of nutrients leads to the stringent response that suppresses PCD, producing a state of tolerance to antibiotics, allowing cells to discriminate between nutrient deprivation and unrepairable damage. High levels of persistors are apparently responsible for the extraordinary survival properties of bacterial biofilms, and genes affecting persistence appear to be promising targets for development of drugs aimed at eradicating recalcitrant infections. PCD in unicellular eukaryotes is also considered, including aging in Saccharomyces cerevisiae. Apoptosis-like elimination of defective cells in S. cerevisiae and protozoa suggests that all unicellular life forms evolved altruistic programmed death that serves a variety of useful functions.},
      Year = {2000} }




@article{
Li00,
   Author = {Li, P.-L. and Farrand, S. K.},
   Title = {The replicator of the nopaline-type Ti plasmid pTiC58 is a member of the repABC family and is influenced by the TraR-dependent quorum-sensing regulatory system},
   Journal = {Journal of Bacteriology},
   Volume = {182},
   Number = {1},
   Pages = {179-188},
   Abstract = {The replicator (rep) of the nopaline-type Ti plasmid pTiC58 is located adjacent to the trb operon of this conjugal element. Previous genetic studies of this region (D. R. Gallie, M. Hagiya, and C. I. Kado, J. Bacteriol. 161:1034-1041, 1985) identified functions involved in partitioning, origin of replication and incompatibility, and copy number control. In this study, we determined the nucleotide sequence of a 6,146-bp segment that encompasses the rep locus of pTiC58. The region contained four full open reading frames (ORFs) and one partial ORF. The first three ORFs, oriented divergently from the traI-trb operon, are closely related to the repA, repB, and repC genes of the octopine-type Ti plasmid pTiB6S3 as well as to other repA, -B, and -C genes from the Ri plasmid pRiA4b and three large plasmids from Rhizobium spp. The fourth ORF and the partial ORF are similar to y4CG and y4CF, respectively, of the Sym plasmid pNGR234a. The 363-bp intergenic region between traI and repA contained two copies of the tra box which is the cis promoter recognition site for TraR, the quorum-sensing activator of Ti plasmid conjugal transfer. Expression of the traI-trb operon from the tra box II-associated promoter mediated by TraR and its acyl-homoserine lactone ligand, AAI, was negatively influenced by an intact tra box III. On the other hand, the region containing the two tra boxes was required for maximal expression of repA, and this expression was enhanced slightly by TraR and AAI. Copy number of a minimal rep plasmid increased five- to sevenfold in strains expressing traR but only when AAI also was provided. Consistent with this effect, constitutive expression of the quorum-sensing system resulted in an apparent increase in Ti plasmid copy number. We conclude that Ti plasmid copy number is influenced by the quorum-sensing system, suggesting a connection between conjugal transfer and vegetative replication of these virulence elements.},
      Year = {2000} }




@article{
Li99,
   Author = {Li, Y. and Bai, Y. and Chen, W.},
   Title = {Studies on DNA-DNA hybridization and 16S rDNA sequence of rhizobia isolated from Shapotou desert soil in Ningxia autonomous region of China},
   Journal = {Wei sheng wu xue bao = Acta microbiologica Sinica},
   Volume = {39},
   Number = {2},
   Pages = {95-99},
   Abstract = {Based on the previous studies on numerical taxonomy and multilocus enzymes electrophoresis patterns of the 12 rhizobial strains isolated from Shapotou region, the contents of G + C mol%, DNA-DNA relatedness and 16SrDNA sequence of the representative strain were tested. The DNA G + C content of the members of this group ranged from 56.4 to 62.2. The values of DNA-DNA hybridization within the group were above 70%, and relatendness between representative strains of this group and known rhizobial species was below 66.6%. The full-length of 16S rDNA sequence of representative strain N220 was compared with the type strains of all known rhizobia species and related bacteria by the PHLIP version 3.572c composed a unrooted phylogenetic tree, the strain N220, R. galegea, two unnamed rhizobial strains(SH19312, SH22623) and three A-grobacterium strains constituted a branch in this tree. The similarity values of 16S rDNA sequence between strain N220 and other strains in this branch were above 95%.},
      Year = {1999} }




@article{
Liang05,
   Author = {Liang, Y. and Harris, J. M.},
   Title = {Response of root branching to abscisic acid is correlated with nodule formation both in legumes and nonlegumes},
   Journal = {American Journal of Botany},
   Volume = {92},
   Number = {10},
   Pages = {1675-1683},
   Abstract = {Legumes are unique among higher plants in forming a symbiosis with Rhizobium. Phylogenetic studies indicate this symbiosis may have evolved as many as three times within the Fabaceae; alternatively, a predisposition for nodulation evolved early in the history of the legume lineage. We have identified a physiological trait - increased lateral root formation in response to abscisic acid (ABA) - that marks all nodulating and non-nodulating legume species in our study set with the exception of Chamaecrista fasciculata and Cercis occidentalis. In contrast, nonlegume species tested decrease lateral root formation in response to ABA. Cercis is not a descendant of any common ancestor hypothesized to have evolved Rhizobium nodulation and has an intermediate response to ABA, partway between that of nonlegumes and legumes. We suggest that acquisition of altered responsiveness of roots to ABA is coincident with the appearance of a predisposition for nodulation within the legumes, followed by a loss in Chamaecrista. In addition, we demonstrate that altered ABA responsiveness of lateral root formation characterizes roots of the actinorhizal nodulator, Casuarina glauca, but not the closely related, nonactinorhizal species, Betula papyrifera. Thus our data provide evidence for a physiological root trait associated with nodulation both in legumes and in an actinorhizal plant.},
   Keywords = {Abscisic acid
Actinorhizal
Arabidopsis thaliana
Fabaceae
Lateral root
Medicago truncatula
Nodulation
Rhizobium},
   Year = {2005} }




@article{
Lieven97,
   Author = {Lieven-Antoniou, C. A. and Whittam, T. S.},
   Title = {Specificity in the symbiotic association of Lotus corniculatus and Rhizobium loti from natural populations},
   Journal = {Molecular Ecology},
   Volume = {6},
   Number = {7},
   Pages = {629-639},
   Abstract = {To test whether Rhizobium loti are coadapted to nodulate local plant genotypes, we competed R. Ioti strains in a common environment with clonally propagated Lotus corniculatus. Both the plants and bacterial strains were originally collected from natural populations in three localities and the R. loti strains used were distinguishable by enzyme electrophoretic markers and differed in geographical origin relative to host plant origin. The proportions of nodules occupied by symbiont strains varied widely and depended on both host plant and symbiont genotype. Nonrandom nodulation patterns resulted primarily from preferential nodulation of host genotypes by the symbiont strain that had been associated with the host in the natural environment. Symbionts nodulating their original hosts were preferentially found in nodules on adventitious tap roots as opposed to the younger, lateral roots (for one host-symbiont pair) or in large nodules, independent of location on the root system (for a second host-symbiont pair). The proportion of nodules occupied by a symbiont on novel host genotypes varied, ranging from nearly random expectation to a significant reduction in the proportion of nodules occupied. The analysis of the bacteria recovered from 994 nodules by multilocus enzyme electrophoresis revealed that 952 (95.8%) nodules were occupied by one of the four inoculant strains and 11 (1.1%) were co-occupied by two inoculant strains. A total of 31 (3.1%) nodules were occupied by strains that did not match the electrophoretic profiles of the original inoculant strains. Based on the comparison of multilocus profiles for 23 enzyme loci, we concluded that these bacteria were foreign strains and not recombinants of the original inoculant strains. Our findings indicate a strong host genotype by strain interaction underlying the outcome of rhizobial competition for nodulation sites and suggest there are distinct mechanisms leading to differential recognition of compatible host and symbiont genotypes.},
   Keywords = {Coadaptation
Competition
Ecological genetics
Genetic diversity
Host specificity
Rhizobium-legume symbiosis},
   Year = {1997} }




@article{
Limpens03,
   Author = {Limpens, Erik and Bisseling, Ton},
   Title = {Signaling in symbiosis},
   Journal = {Current Opinion in Plant Biology},
   Volume = {6},
   Number = {4},
   Pages = {343-350},
   Abstract = {In recent years, the major focus in nodulation research has been on the genetic dissection of Nod-factor signaling. Components of this pathway appear to be shared with signaling processes that are induced during the formation of mycorrhiza. With the cloning of orthologs of the NIN and DMI2 genes from several legumes, the molecular characteristics of components of the Nod-factor-signaling pathway are now starting to be revealed. Orthologs of HAR1, a key player in the systemic autoregulatory mechanism controlling nodule numbers, have also been cloned recently. The mechanism by which nodulation is autoregulated is related to that by which fixed nitrogen inhibits nodulation. Genes that are involved in Nod-factor signaling may be targets for mechanisms that suppress nodulation. If this is the case, it would bring two fascinating areas of symbiosis together.},
      Year = {2003} }




@article{
Limpens05,
   Author = {Limpens, E. and Mirabella, R. and Fedorova, E. and Franken, C. and Franssen, H. and Bisseling, T. and Geurts, R.},
   Title = {Formation of organelle-like N2-fixing symbiosomes in legume root nodules is controlled by DMI2},
   Journal = {Proceedings of the National Academy of Sciences of the United States of America},
   Volume = {102},
   Number = {29},
   Pages = {10375-10380},
   Abstract = {In most legume nodules, the N2-fixing rhizobia are present as organelle-like structures inside their host cells. These structures, named symbiosomes, contain one or a few rhizobia surrounded by a plant membrane. Symbiosome formation requires the release of bacteria from cell-wall-bound infection threads. In primitive legumes, rhizobia are hosted in intracellular infection threads that, in contrast to symbiosomes, are bound by a cell wall. The formation of symbiosomes is presumed to represent a major step in the evolution of legume-nodule symbiosis, because symbiosomes facilitate the exchange of metabolites between the two symbionts. Here, we show that the genes, which are essential for initiating nodule formation, are also actively transcribed in mature Medicago truncatula nodules in the region where symbiosome formation occurs. At least one of these genes, encoding the receptor kinase DOES NOT MAKE INFECTIONS 2 (DMI2) is essential for symbiosome formation. The protein locates to the host cell plasma membrane and to the membrane surrounding the infection threads. A partial reduction of DMI2 expression causes a phenotype that resembles the infection structures found in primitive legume nodules, because infected cells are occupied by large intracellular infection threads instead of by organelle-like symbiosomes. © 2005 by The National Academy of Sciences of the USA.},
   Keywords = {Infection
Medicago
Nod factor
Rhizobium},
   Year = {2005} }




@book{
Lindley25,
   Author = {Lindley, J.},
   Title = {Botanical Register 11},
   Publisher = {t. 912 (publication page)},
      Year = {1825} }




@article{
Lindstrom89,
   Author = {Lindstr\"om, K.},
   Title = {\emph{Rhizobium galegae}, a new species of legume root nodule bacteria},
   Journal = {International Journal of Systematic Bacteriology},
   Volume = {39},
   Number = {3},
   Pages = {365-367},
   Keywords = {bacterial flora
plant root
rhizobium},
   Year = {1989} }




@article{
Lindstrom91,
   Author = {Lindstr\"om, K. and Kaijalainen, S.},
   Title = {Genetic Relatedness of Bacteriophage Infecting Rhizobium-Galegae Strains},
   Journal = {Fems Microbiology Letters},
   Volume = {82},
   Number = {3},
   Pages = {241-246},
   Abstract = {Seven bacteriophage (PHI-1R, PHI-1OW, PHI-3R, PHI-3OW, PHI-1261 M, PHI-1261 V and PHI-gor3V), specific for the Rhizobium galegae species and representing three morphotypes, were isolated from different locations in Finland and in New Zealand. DNA was isolated from these phage and from phage PHI-1R-3 and PHI-1R', which were derived from PHI-1R in the laboratory, and analyzed by restriction endonuclease digestion and dot blot DNA hybridization. The sizes of the phage DNAs were estimated to range from 45.1-114.6 kb. The restriction patterns revealed four different phage genotypes, which correlated with the isolation hosts. DNA hybridization showed that the four genotypes were distantly related. The genotypes were distinguished when purified phage protein was analyzed in SDS-PAGE gels.},
   Keywords = {bacteriophage; dna homology; rhizobium-galegae; taxonomy
legume},
   Year = {1991} }




@article{
Lindstrom05,
   Author = {Lindstr\"om, K. and Mart\'inez-Romero, M. E.},
   Title = {International Committee on Systematics of Prokaryotes. Subcommittee on the taxonomy of Agrobacterium and Rhizobium},
   Journal = {International Journal of Systematic and Evolutionary Microbiology},
   Volume = {55},
   Number = {3},
   Pages = {1383},
      Year = {2005} }




@article{
Lindstrom85,
   Author = {Lindstr\"om, K. and Sarsa, M. and Polkunen, J. and Kansanen, P.},
   Title = {Symbiotic nitrogen fixation of Rhizobium (Galega) in acid soils, and its survival in soil under acid and cold stress.},
   Journal = {Plant and Soil},
   Volume = {87},
   Number = {2},
   Pages = {293-302},
   Abstract = {Goat's rue Galega orientalis, its symbiotic nitrogen fixation and R. (Galega) are tolerant of moderately acid agricultural soils, but harsh winters may reduce bacterial numbers in the soil. -from Authors},
   Keywords = {Galega orientalis
goat's rue},
   Year = {1985} }




@article{
Lindstrom02,
   Author = {Lindstr\"om, K. and Terefework, Z. and Suominen, L. and Lortet, G.},
   Title = {Signalling and development of Rhizobium-legume symbioses},
   Journal = {Biology and Environment: Proceedings of the Royal Irish Academy, Section B},
   Volume = {102},
   Number = {1},
   Abstract = {This paper discusses the signal exchange between rhizobia and legumes and the processes leading to a nitrogen-fixing symbiosis, viz., infection, nodule formation and nitrogen fixation. The taxonomy and evolution of the root nodule bacteria are also discussed.},
      Year = {2002} }




@article{
Lira05,
   Author = {Lira, M. D. and Lima, A. S. T. and Arruda, J. R. F. and Smith, D. L.},
   Title = {Effect of root temperature on nodule development of bean, lentil and pea},
   Journal = {Soil Biology and Biochemistry},
   Volume = {37},
   Number = {2},
   Pages = {235-239},
   Abstract = {The rhizobia-legume symbiosis is the main source of fixed nitrogen for many agricultural systems. However, it is inhibited by low soil temperature. To date, research on nodulation has involved either qualitative or destructive analyses. The use of computer-based image analysis potentially allows nodules to be followed during the course of development. Seedlings of bean (Phaseolus vulgaris L.), lentil (Lens culinaris Medik.) and pea (Pisum sativum L.) were transplanted into plastic growth pouches suspended in water baths maintained at 10, 15, 20 or 25 degreesC. Two days after transplanting, all plants were inoculated with appropriate rhizobial strains. Seven days after inoculation, plant roots were scanned;, this was repeated weekly for 7 weeks. Data on nodule length were collected through image analysis. Nodule length was correlated with nodule size and development. There were increases in the precision of estimates of environmental effects through observation of individual nodule development, as opposed to averages for populations of nodules. The effects of root temperature on nodulation and nodule development were observed both in the delayed onset of nodulation and in reduced subsequent nodule growth rate, resulting in effects on final nodule size. (C) 2004 Published by Elsevier Ltd.},
      Year = {2005} }




@article{
Liston94,
   Author = {Liston, A. and Wheeler, J. A.},
   Title = {The phylogenetic position of the genus Astragalus (Fabaceae): Evidence from the chloroplast genes rpoC1 and rpoC2},
   Journal = {Biochemical Systematics and Ecology},
   Volume = {22},
   Number = {4},
   Pages = {377-388},
      Year = {1994} }




@article{
Lui05,
   Author = {Liu, J. and Wang, E. T. and Chen, W. X.},
   Title = {Diverse rhizobia associated with woody legumes \emph{Wisteria sinensis}, \emph{Cercis racemosa} and \emph{Amorpha fruticosa} grown in the temperate zone of China},
   Journal = {Systematic and Applied Microbiology},
   Volume = {28},
   Number = {5},
   Pages = {465-477},
   Abstract = {Fifty-nine bacterial isolates from root nodules of the woody legumes Wisteria sinensis, Cercis racemosa and Amorpha fruticosa grown in the central and eastern regions of China were characterized with phenotypic analysis, PCR-based 16S and 23S rRNA gene RFLP, Box PCR and 16S rRNA gene sequencing. Seven main phena were defined in numerical taxonomy, which corresponded to distinct groups within the genera Agrobacterium, Bradyrhizobium, Mesorhizobium and Rhizobium in 16S and 23S rRNA gene PCR-RFLP. The phylogenetic relationships of the 16S rRNA genes supported the grouping results of PCR-RFLP. Most of the isolates from Amorpha fruticosa were classified into two groups closely related to Mesorhizobium amorphae. Seventeen of the 21 isolates from Wisteria sinensis were identified as two groups related to Rhizobium and Agrobacterium. Six out of 10 isolates from Cercis racemosa were identified as a group related to Bradyrhizobium. Our results indicated that each of the investigated legumes nodulated mainly with one or two rhizobial groups, although isolates from different plants intermingled in some small bacterial groups. In addition, correlation between geographic origin and grouping results was found in the isolates from Amorpha fruticosa. These results revealed that the symbiotic bacteria might have been selected by both the legume hosts and the geographic factors. © 2005 Elsevier GmbH. All rights reserved.},
   Keywords = {Amorpha
Cercis
Diversity
Phylogeny
Rhizobia
Wisteria},
   Year = {2005} }




@article{
Lobin88,
   Author = {Lobin, W. and Barthlott, W.},
   Title = {Sophora toromiro (Leguminosae); the lost tree of Easter Island},
   Journal = {Bot. Gard. Conserv. News},
   Volume = {1},
   Number = {3},
   Pages = {32-34},
      Year = {1988} }




@article{
Lodwig03,
   Author = {Lodwig, E. M. and Poole, P. S.},
   Title = {Metabolism of \emph{Rhizobium} bacteroids},
   Journal = {Critical reviews in plant sciences},
   Volume = {22},
   Number = {1},
   Pages = {37-38},
      Year = {2003} }




@article{
Loh01a,
   Author = {Loh, J. T. and Stacey, G.},
   Title = {Feedback regulation of the \emph{Bradyrhizobium japonicum} nodulation genes},
   Journal = {Molecular Microbiology},
   Volume = {41},
   Number = {6},
   Pages = {1357-64},
   Abstract = {Lipochitin Nod signals are produced by rhizobia and are required for the establishment of a nitrogen-fixing symbiosis with a legume host. The nodulation genes encode products required for the synthesis of this signal and are induced in response to plant-produced flavonoid compounds. The addition of chitin and lipo-chitin oligomers to Bradyrhizobium japonicum cultures resulted in a significant reduction in the expression of a nod-lacZ fusion. Intracellular expression of NodC, encoding a chitin synthase, also reduced nod gene expression. In contrast, expression of the ChiB chitinase increased nod gene expression. The chain length of the oligosaccharide was important in feedback regulation, with chitotetraose molecules the best modulators of nod gene expression. Feedback regulation is mediated by the induction of nolA by chitin, resulting in elevated levels of the repressor protein, NodD2.},
   Keywords = {Bacterial Proteins
genetics
metabolism
Base Sequence
Bradyrhizobium
Chitin
Chitin Synthase
Chitinase
DNA Primers
Fabaceae
microbiology
Feedback
Gene Expression Regulation
Bacterial
Genes
Nitrogen Fixation
Lipopolysaccharides
chemistry
Models
Biological
N-Acetylglucosaminyltransferases
Oligosaccharides
Plant Proteins
Signal Transduction
Support
U.S.Gov't
Non-P.H.S.
Symbiosis},
   Year = {2001} }




@article{
Loh01b,
   Author = {Loh, J. T. and Yuen-Tsai, J. P. Y. and Stacey, M. G. and Lohar, D. and Welborn, A. and Stacey, G.},
   Title = {Population density-dependent regulation of the Bradyrhizobium japonicum nodulation genes},
   Journal = {Molecular Microbiology},
   Volume = {42},
   Number = {1},
   Pages = {37-46},
   Abstract = {The nodulation genes of Bradyrhizobium japonicum are essential for infection and establishment of a nitrogen-fixing symbiosis. Here, we demonstrate that plant-produced isoflavones induce nodulation gene expression in a population density-dependent fashion. Nodulation gene induction is highest at a low population density and significantly reduced in more dense cultures. A quorum signal molecule in the conditioned medium of B. japonicum cultures mediates this repression. Repression in response to the quorum signal results from the induction of NolA which, in turn, induces NodD2 leading to inhibition of nod gene expression. Consistent with this, nolA-lacZ and nodD2-lacZ expression increased with increasing population density. Unlike the wild type, the ability to induce nodY-lacZ expression did not decline with population density in a NolA mutant. Normally, nod gene expression is repressed in planta (i.e. within nodules). However, expression of a nodY-GUS fusion was not repressed in a NolA mutant, suggesting that quorum-sensing control may mediate in planta repression of the nod genes. Addition of conditioned medium to cultures significantly reduced nod gene expression. Treatment of inoculant cultures with conditioned medium also reduced the ability of B. japonicum to nodulate soybean plants.},
      Year = {2001} }




@article{
Lohar05,
   Author = {Lohar, D. P. and VandenBosch, K. A.},
   Title = {Grafting between model legumes demonstrates roles for roots and shoots in determining nodule type and host/rhizobia specificity},
   Journal = {Journal of Experimental Botany},
   Volume = {56},
   Number = {416},
   Pages = {1643-1650},
   Abstract = {Previous grafting experiments have demonstrated that legume shoots play a critical role in symbiotic development of nitrogen-fixing root nodules by regulating nodule number. Here, reciprocal grafting experiments between the model legumes Lotus japonicus and Medicago truncatula were carried out to investigate the role of the shoot in the host-specificity of legume-rhizobia symbiosis and nodule type. Lotus japonicus is nodulated by Mesorhizobium loti and makes determinate nodules, whereas M. truncatula is nodulated by Sinorhizobium meliloti and makes indeterminate nodules. When inoculated with M. loti, L. japonicus roots grafted on M. truncatula shoots produced determinate nodules identical in appearance to those produced on L. japonicus self-grafted roots. Moreover, the hypernodulation phenotype of L. japonicus har1-1 roots grafted on wild-type M. truncatula shoots was restored to wild type when nodulated with M. loti. Thus, L. japonicus shoots appeared to be interchangeable with M. truncatula shoots in the L. japonicus root/M. loti symbiosis. However, M. truncatula roots grafted on L. japonicus shoots failed to induce nodules after inoculation with S. meliloti or a mixture of S. meliloti and M. loti. Instead, only early responses to S. meliloti such as root hair tip swelling and deformation, plus induction of the early nodulation reporter gene MtENOD11:GUS were observed. The results indicate that the L. japonicus shoot does not support normal symbiosis between the M. truncatula root and its microsymbiont S. meliloti, suggesting that an unidentified shoot-derived factor may be required for symbiotic progression in indeterminate nodules. © The Author [2005]. Published by Oxford University Press. All rights reserved.},
   Keywords = {Host specificity
Lotus
Medicago
Nod factor
Nodule type
Root
Shoot},
   Year = {2005} }




@article{
Long89,
   Author = {Long, S.R.},
   Title = {Rhizobium-legume nodulation: life together in the underground.},
   Journal = {Cell},
   Volume = {56},
   Number = {2},
   Pages = {203-214},
      Year = {1989} }




@article{
Long96,
   Author = {Long, S.R.},
   Title = {Rhizobium symbiosis: Nod factors in perspective},
   Journal = {Plant Cell},
   Volume = {8},
   Number = {10},
   Pages = {1885-1898},
      Year = {1996} }




@article{
Lopez-Garcia02,
   Author = {Lopez-Garcia, S. L. and Vazquez, T. E. and Favelukes, G. and Lodeiro, A. R.},
   Title = {Rhizobial position as a main determinant in the problem of competition for nodulation in soybean},
   Journal = {Environ Microbiol},
   Volume = {4},
   Number = {4},
   Pages = {216-24},
   Abstract = {Selected Bradyrhizobium japonicum strains inoculated on soybean seeds often fail to occupy a significant proportion of nodules when a competitor rhizobial population is established in the soil. This competition problem could result from a genetic/ physiological advantage of the adapted soil population over the introduced inoculant or from a positional advantage, as the soil population already occupies the soil profile where the roots will penetrate, whereas the inoculant remains concentrated around the seeds. Here, we have assessed the contribution of these factors with a laboratory model in which a rhizobial population is established in sterile vermiculite. We observed that the wild-type strain B. japonicum LP 3004 was able to grow in pots with N-free plant nutrient solution-watered vermiculite for six or seven generations with a duplication rate of at least 0.7 day(-1). In addition, the rhizobial population persisted for 3 months with 10(6)-10(7) colony-forming units ml(-1) of the vermiculite-retained solution. N-starved, young rhizobial cultures are more efficient in performing several steps along their early association with soybean roots. However, N starvation during growth of rhizobia used for seed inoculation did not enhance their competitiveness against a 1 month vermiculite-established rhizobial population, which occupied more than 72% of the nodules. When a similarly established rhizobial population was recovered from the vermiculite and homogeneously suspended in plant nutrient solution, these cells were significantly less competitive (29% of nodules occupied) than rhizobia obtained from a fresh, logarithmic culture in a N-poor minimal medium, thus indicating that cell position rather than intrinsic competitiveness was the determinant for nodule occupation.},
   Keywords = {Aluminum Silicates
*Antibiosis
Bradyrhizobium/*physiology
Plant Roots/microbiology
Rhizobium/*physiology
Soil Microbiology
Soybeans/*microbiology
Support, Non-U.S. Gov't
Symbiosis},
   Year = {2002} }




@article{
Lopez-Lara96,
   Author = {Lopez-Lara, I. M.  and Blok-Tip, L.  and Quinto, C.  and Garcia, M. L.  and Stacey, G.  and Bloemberg, G. V.  and Lamers, G. E.  and Lugtenberg, B. J. and Thomas-Oates, J. E. and Spaink, H. P.},
   Title = {\emph{NodZ} of \emph{Bradyrhizobium} extends the nodulation host range of \emph{Rhizobium} by adding a fucosyl residue to nodulation signals.},
   Journal = {Molecular Microbiology},
   Volume = {21},
   Number = {2},
   Pages = {397-408},
   Abstract = {The nodulation genes of rhizobia are involved in the production of the lipo-chitin oligosaccharides (LCO), which are signal molecules required for nodule formation. A mutation in nodZ of Bradyrhizobium japonicum results in the synthesis of nodulation signals lacking the wild-type 2-O-methylfucose residue at the reducting-terminal N-acetylglucosamine. This phenotype is correlated with a defective nodulation of siratro (Macroptilium atropurpureum). Here we show that transfer of nodZ to Rhizobium leguminosarum blovar (bv) viciae, which produces LCOs that are not modified at the reducing-terminal N-acetylglucosamine, results in production of LCOs with a fucosyl residue on C-6 of the reducing-terminal N-acetylglucosamine. This finding, together with in vitro enzymatic assays, indicates that the product of nodZ functions as a fucosyltransferase. The transconjugant R. leguminosarum strain producing fucosylated LCOs acquires the capacity to nodulate M. atropurpureum, Glycine soja, Vigna unguiculate and Leucaena leucocephala. Therefore, nodZ extends the narrow host range of R. leguminosarum bv. viciae to include various tropical legumes. However, microscopic analysis of nodules induced on siratro shows that these nodules do not contain bacteroids, showing that transfer of nodZ does not allow R. leguminosarum to engage in a nitrogen-fixing symbiosis with this plant.},
      Year = {1996} }




@article{
Lopez-Lara00,
   Author = {Lopez-Lara, I. M. and Geiger, O.},
   Title = {Expression and purification of four different rhizobial acyl carrier proteins},
   Journal = {Microbiology},
   Volume = {146 ( Pt 4)},
   Pages = {839-49},
   Abstract = {In rhizobia, besides the constitutive acyl carrier protein (AcpP) involved in the biosynthesis and transfer of common fatty acids, there are at least three specialized acyl carrier proteins (ACPs): (1) the flavonoid-inducible nodulation protein NodF; (2) the RkpF protein, which is required for the biosynthesis of rhizobial capsular polysaccharides; and (3) AcpXL, which transfers 27-hydroxyoctacosanoic acid to a sugar backbone during lipid A biosynthesis. Whereas the nucleotide sequences encoding the three specialized ACPs are known, only the amino acid sequence of the AcpP of Sinorhizobium meliloti was available. In this study, using reverse genetics, the genes for the constitutive AcpPs of S. meliloti and of Rhizobium leguminosarum were cloned and sequenced. Previously, it had been shown that NodF and RkpF can be overproduced in Escherichia coli using the T7 polymerase expression system. Using the same system, the constitutive AcpPs of S. meliloti and of R. leguminosarum, together with the specialized ACP AcpXL, were overproduced and purified. All the known ACPs of rhizobia can be labelled in vivo during expression in E. coli with radioactive beta-alanine added to the growth medium due to their modification with a 4'-phosphopantetheine prosthetic group. The availability of all functionally different ACPs should help to unravel how different fatty acids are targeted towards different biosynthetic pathways in one organism.},
   Keywords = {Acyl Carrier Protein
genetics
metabolism
Amino Acid Sequence
Bacterial Proteins
Base Sequence
Cloning
Molecular
Molecular Sequence Data
Rhizobium
Support
Non-U.S.Gov't},
   Year = {2000} }




@article{
Lorkiewicz97,
   Author = {Lorkiewicz, Z.},
   Title = {Nodulation genes in the Rhizobium--plant signal exchange},
   Journal = {Acta Biochimica Polonica},
   Volume = {44},
   Number = {1},
   Pages = {1-12},
   Abstract = {The process of the host-plant recognition by rhizobia is complex and multi-step. The interaction between legumes and microorganisms results in the induction of the root nodule. This symbiotic interaction is highly host-specific. Bacteria within nodules fix atmospheric nitrogen. This process is of immense ecological and economic significance. The subject of this presentation is the molecular mechanism by which the bacterium determines its host-specific characteristics. First flavonoids secreted by the plant roots induce the transcription of bacterial genes involved in nodulation, the so-called nod genes. This leads to the next step of the signalling system, i.e. the production and secretion of lipo-oligosaccharide molecules by rhizobia. These signal molecules have various discernible effects on the roots of the host leguminous plants. The bacterial nodulation factors were isolated and structurally identified as substituted and N-acylated chitin oligosaccharides. These prokaryotic signals play a key role in the symbiosis by controlling the host specificity of the bacteria. They constitute a new class of signalling molecules able to elicit nodule organogenesis in leguminous plants in the absence of bacteria. More recent studies implicate involvement of root cell membrane depolarization and ion selective channels in the communication processes that initiate nodule formation.},
   Keywords = {Gene Expression Regulation, Bacterial
Gene Expression Regulation, Plant
*Genes, Bacterial
*Genes, Plant
Rhizobium/*genetics
*Signal Transduction
Symbiosis/*genetics},
   Year = {1997} }




@article{
Lowther95,
   Author = {Lowther, W. L. and Patrick, H. N.},
   Title = {\emph{Rhizobium} strain requirements for improved nodulation of \emph{Lotus corniculatus}},
   Journal = {Soil Biology \& Biochemistry},
   Volume = {27},
   Number = {4-5},
   Pages = {721-724},
   Abstract = {Farmers in New Zealand have reported seedling establishment problems with Lotus corniculatus. Field trials have indicated that partial or complete nodulation failures can occur due to the rapid death of rhizobia on the seed. Fifteen strains of Rhizobium loti, prepared as peat inoculant, were evaluated for survival on inoculated seed of L. corniculatus, and for ability to nodulate such seed when oversewn into native grassland. Survival of rhizobia after 24 h varied from 1 to 89%. There were significant differences between strains in the percentage of seedlings nodulated. The currently recommended New Zealand strain (ICMP 9005) performed poorly, with only 1% of rhizobia surviving on the seed and 7% of plants nodulated. The results indicate that nodulation problems with L. corniculatus in New Zealand can be overcome by selecting strains with better survival and nodulation characteristics. Determination of survival rates on the seed offers a rapid laboratory screening method for initial evaluation of rhizobia for inoculant use.},
   Keywords = {seed},
   Year = {1995} }




@article{
Lowther02,
   Author = {Lowther, W. L. and Pryor, H. N. and Littlejohn, R. P. and Hussain, S. W. and Willliams, W. M.},
   Title = {\emph{Rhizobium} specificity of \emph{Trifolium ambiguum} M. Bieb x \emph{T.~repens} L. hybrid clovers},
   Journal = {Euphytica},
   Volume = {127},
   Number = {3},
   Pages = {309-315},
   Abstract = {Growth of full-sib families of an F-1 interspecific hybrid between Trifolium ambiguum M. Bieb and T. repens L, and two generations of backcross hybrids (BC1F2 and BC2F1) with T. repens as the recurrent parent, were compared to their parental species. Plants were grown in a N-free medium and inoculated with Rhizobium leguminosarum biovar trifolii rhizobia effective on T. ambiguum or T. repens. Hybridisation produced progeny that nodulated with rhizobia from either T. ambiguum or T. repens, but plant growth varied. Mean weights of T. repens and hybrids, particularly F-1 and BC1F2, were higher when inoculated with a mixture of strains isolated from field grown T. repens than with the New Zealand inoculant strain for T. repens. When inoculated with the mix of rhizobia from T. repens, mean weights were 242, 189, 132, 125, and 100 mg/plant for T. repens, BC2F1, BC1F2, F-1 and T. ambiguum, respectively. However, although the mean weight of BC2F1 lines was significantly less than T. repens, there was considerable variation in individual full-sib families indicating the potential to select within BC2F1 hybrids for high plant growth/symbiotic nitrogen fixation. The weight of T. ambiguum plants inoculated with the New Zealand inoculant strain for hexaploid T. ambiguum was similar to T. repens inoculated with the mix of rhizobia from T. repens (253 and 242 mg/plant, respectively). Mean fresh weights of F-1 hybrid plants were similar when inoculated with rhizobia for T. ambiguum or T. repens (125 and 130 mg/plant, respectively). However, weight of T. repens, BC1F2 and BC2F1 hybrids inoculated with rhizobia for T. ambiguum were all less than 90 mg/plant. There was a significant relationship between plant fresh weight and ethylene production. The results indicate that measuring weights of inoculated plants growing in N-free media is a rapid initial method of screening a range of plant germplasm for plant growth/symbiotic nitrogen fixation rates.},
   Keywords = {interspecific hybrids; nitrogen fixation; nodulation; rhizobia;
Trifolium ambiguum; Trifolium repens
caucasian clover; white clover; registration; germplasm; fixation;
strain},
   Year = {2002} }




@article{
Luckow05,
   Author = {Luckow, M. and Doyle, J. J. and Jobson, R. and Pfeil, B. and Hughes, C. and Harris, S. and Schrire, B. and Rico, L. and Lock, M. and MacKinder, B. and Winter, P. and Smith, G. F. and Willis, C. K. and Fagg, C. and Fortunato, R. and Hurter, J. and Breteler, F. J. and Van Der Maesen, J. G. and Wieringa, J. J. and Bruneau, A. and Caccavari, M. and Craven, L. and Crisp, M. and Alfonso Delgado, S. and Hern\'andez, H. M. and Sousa S., M. and Demissew, S. and Grether, R. and Herendeen, P.S. and Hirsch, A. M. and Klitgaard, B. B. and Labat, J.-N. and Simpson, B. B. and Timberlake, J. and Van Wyk, A. E. and Vorster, P. and Wojciechowski, M. F.},
   Title = {\emph{Acacia}: The case against moving the type to Australia},
   Journal = {Taxon},
   Volume = {54},
   Number = {2},
   Pages = {513-519},
   Abstract = {Recent studies have shown that Acacia is polyphyletic and must be split into five genera. Proposal 1584 would retypify Acacia: the type of the Australian taxon A. penninervis would be conserved over the current lectotype (A. scorpioides) of an African taxon. We disagree with the recommendation of the Spermatophyte Committee to endorse this proposal. Contrary to Article 14.12 of the ICBN, no detailed case against conservation was presented in Proposal 1584. We maintain that there are strong arguments against conservation, such as the large number of countries that would be affected, the economic importance of the extra-Australian species, and the economic burden placed on developing countries. Acceptance of this proposal would also violate the guidelines for conservation which clearly state that the principle of priority should prevail when conservation for one part of the world would create disadvantageous change in another part of the world.},
   Keywords = {Acacia
Conservation
Leguminosae
Nomenclature
Retypification},
   Year = {2005} }




@article{
Ludwig77,
   Author = {Ludwig, R. A. and Signer, E. R.},
   Title = {Glutamine synthetase control of nitrogen fixation in Rhizobia},
   Journal = {Basic Life Sci},
   Volume = {9},
   Pages = {419-20},
   Keywords = {Glutamate-Ammonia Ligase/*metabolism
Mutation
*Nitrogen Fixation
Nitrogenase/metabolism
Phenotype
Rhizobium/*enzymology},
   Year = {1977} }




@article{
Ludwig98,
   Author = {Ludwig, W. and Amann, R. and Mart\'inez-Romero, E. and Schonhuber, W. and Bauer, S. and Neef, A. and Schleifer, K. H.},
   Title = {rRNA based identification and detection systems for rhizobia and other bacteria},
   Journal = {Plant and Soil},
   Volume = {204},
   Number = {1},
   Pages = {1-19},
   Abstract = {Ribosomal ribonucleic acids are excellent marker molecules for the elucidation of bacterial phylogeny; they also provide useful target sites for identification and detection with nucleic acid probes. Based on the currently available 16S rRNA sequence data, bacteria of the rhizobial phenotype (plant nodulation, nitrogen fixation) are members of three moderately related phylogenetic sub-groups of the alpha-subclass of the Proteobacteria : i.e. the rhizobia group, the bradyrhizobia group, and the azorhizobia group. Ail rhizobia, azo-, brady-, meso- and sinorhizobia are closely related to and in some cases phylogenetically intermixed with, non-symbiotic and/or non-nitrogen-fixing bacteria. Especially in the case of Bradyrhizobium japonicum strains, the 16S rRNA sequence data indicate substantial heterogeneity. Specific probe design and evaluation are discussed. A multiprobe concept for resolving specificity problems with group specific probes is presented. In situ identification with group specific probes of rhizobia in cultures as well as rhizobia and cyanobacteria within plant material is shown.},
      Year = {1998} }




@article{
Luyindula75,
   Author = {Luyindula, N. and Tshitenge, G. and Lurquin, P. and Ledoux, L.},
   Title = {Rhizobium japonicum plasmids
[ETUDE DES PLASMIDES DE RHIZOBIUM JAPONICUM]},
   Journal = {Archives Internationales de Physiologie et de Biochimie},
   Volume = {83},
   Number = {1},
   Pages = {199-200},
      Year = {1975} }




@article{
Lyons97,
   Author = {Lyons-Weiler, J. and Hoelzer, G.A.},
   Title = {Escaping from the Felsenstein Zone by Detecting Long Branches in Phylogenetic Data},
   Journal = {Molecular Phylogenetics and Evolution},
   Volume = {8},
   Number = {3},
   Pages = {375-384},
   Abstract = {Long branches in a true phylogeny tend to disrupt hierarchical character covariation (phylogenetic signal) in the distribution of traits among organisms. The distortion of hierarchical structure in character-state matrices can lead to errors in the estimation of phylogenetic relationships and inconsistency of methods of phylogenetic inference. Examination of trees distorted by long-branch attraction will not reveal the identities of problematic taxa, in part because the distortion can mask long branches by reducing inferred branch lengths and through errors in branching order. Here we present a simple method for the detection of taxa whose placement in evolutionary trees is made difficult by the effects of long-branch attraction. The method is an extension of a tree-independent conceptual framework of phylogenetic data exploration (RASA). Taxa that are likely to attract are revealed because long branches leave distinct footprints in the distribution of character states among taxa, and these traces can be directly observed in the error structure of the RASA regression. Problematic taxa are identified using a new diagnostic plot called the taxon variance plot, in which the apparent cladistic and phenetic variances contributed by individual taxa are compared. The procedure for identifying long edges employs algorithms solved in polynomial time and can be applied to morphological, molecular, and mixed characters. The efficacy of the method is demonstrated using simulated evolution and empirical evidence of long branches in a set of recently published sequences. We show that the accuracy of evolutionary trees can be improved by detecting and combating the potentially misleading influences of long-branch taxa. © 1997 Academic Press.},
      Year = {1997} }




@article{
Ma90,
   Author = {Ma, S.-W. and Iyer, V. N.},
   Title = {New field isolates of Rhizobium leguminosarum biovar viciae that nodulate the primitive pea cultivar Afghanistan in addition to modern cultivars},
   Journal = {Applied and Environmental Microbiology},
   Volume = {56},
   Number = {7},
   Pages = {2206-2212},
   Abstract = {A collection of 13 field isolates of Rhizobium leguminosarum bv. viciae that have the ability to nodulate the roots of current North American cultivars of peas as well as a 'primitive' cultivar, Afghanistan, was examined. These isolates originated in diverse geographical regions of the world, which indicates that this phenotype is not restricted to isolates from any one region. When subclones of the nodulation region from one plasmid were used to examine EcoRI-fragment-length polymorphism in this collection of strains as well as in a collection comprising strains that do not modulate the primitive cultivar, polymorphism was found in both collections. With one exception, Ris?A6, all strains that nodulated cv. Afghanistan pea contained a region called nodX as an extension to the nodA BCIJ operon that has been observed in all R. leguminosarum bv. viciae strains, including those that do not nodulate cv. Afghanistan pea. Ris?A6 was also the only strain in which nodulating ability could not be associated with a conjugative plasmid.},
   Keywords = {geographic distribution
rhizobium leguminosarum},
   Year = {1990} }




@article{
Ma02,
   Author = {Ma, W. and Penrose, D. M. and Glick, B. R.},
   Title = {Strategies used by rhizobia to lower plant ethylene levels and increase nodulation},
   Journal = {Canadian Journal of Botany},
   Volume = {48},
   Number = {11},
   Pages = {947-54},
   Abstract = {Agriculture depends heavily on biologically fixed nitrogen from the symbiotic association between rhizobia and plants. Molecular nitrogen is fixed by differentiated forms of rhizobia in nodules located on plant roots. The phytohormone, ethylene, acts as a negative factor in the nodulation process. Recent discoveries suggest several strategies used by rhizobia to reduce the amount of ethylene synthesized by their legume symbionts, decreasing the negative effect of ethylene on nodulation. At least one strain of rhizobia produces rhizobitoxine, an inhibitor of ethylene synthesis. Active 1-aminocyclopropane-1-carboxylate (ACC) deaminase has been detected in a number of other rhizobial strains. This enzyme catalyzes the cleavage of ACC to alpha-ketobutyrate and ammonia. It has been shown that the inhibitory effect of ethylene on plant root elongation can be reduced by the activity of ACC deaminase.},
   Keywords = {Carbon-Carbon Lyases/antagonists \& inhibitors
Ethylenes/analysis/*metabolism
Nitrogen Fixation/*physiology
Plant Roots/*metabolism
Propanolamines/antagonists \& inhibitors/metabolism
Rhizobiaceae/genetics/metabolism/*physiology
Support, Non-U.S. Gov't
Symbiosis},
   Year = {2002} }




@article{
Ma96,
   Author = {Ma, X. and Margolin, W. and Ehrhardt, D.W.},
   Title = {Colocalization of cell division proteins FtsZ and FtsA to cytoskeletal structures in living Escherichia coli cells by using green fluorescent protein},
   Journal = {Proceedings of the National Academy of Sciences of the United States of America},
   Volume = {93},
   Number = {23},
   Pages = {12998-13003},
   Abstract = {In the current model for bacterial cell division. FtsZ protein forms a ring that marks the division plane, creating a cytoskeletal framework for the subsequent action of other proteins such as FtsA. This putative protein complex ultimately generates the division septum. Herein we report that FtsZ and FtsA proteins tagged with green fluorescent protein (GFP) colocalize to division-site ring-like structures in living bacterial cells in a visible space between the segregated nucleoids. Cells with higher levels of FtsZ-GFP or with FtsA-GFP plus excess wild-type FtsZ were inhibited for cell division and often exhibited bright fluorescent spiral tubules that spanned the length of the filamentous cells. This suggests that FtsZ may switch from a septation-competent localized ring to an unlocalized spiral under some conditions and that FtsA can bind to FtsZ in both conformations. FtsZ-GFP also formed nonproductive but localized aggregates at a higher concentration that could represent FtsZ nucleation sites. The general domain structure of FtsZ-GFP resembles that of tubulin, since the C terminus of FtsZ is not required for polymerization but may regulate polymerization state. The N- terminal portion of Rhizobium FtsZ polymerized in Escherichia coli and appeared to copolymerize with E. coli FtsZ, suggesting a degree of interspecies functional conservation. Analysis of several deletions of FtsA- GFP suggests that multiple segments of FtsA are important for its localization to the FtsZ ring.},
      Year = {1996} }




@article{
Malek99,
   Author = {Ma{\l}ek, W. and Sajnaga, E.},
   Title = {Current taxonomy of the rhizobia},
   Journal = {Acta Microbiologica Polonica},
   Volume = {48},
   Number = {2},
   Pages = {109-122},
   Abstract = {Rhizobia are soil bacteria that are capable of forming nitrogen-fixing nodules on
leguminous plants. For many years the taxonomy of nodule bacteria was based on their
selective interaction with the host plant. This principle of classification has recently been
de-emphasised and abandoned after the demonstration that in fast-growing rhizobia the
genes coding for nodulation and nitrogen fixation are located on transmissible symbiotic
plasmids. Currently, the host range is still an important criterion for rhizobium taxonomy but
for the description of a new bacterial genus and species the following of minimal standards
(proposed by the International Subcommittee for the taxonomy of Rhizobium and
Agrobacterium) are also required: rate of growth on laboratory media, carbohydrate
utilization patterns, metabolic capacities, antibiotic sensitivity, total protein fingerprinting,
multilocus enzyme electrophoresis, fatty acid analysis, DNA G+C content (rnol\%), DNADNA
and DNA-rRNA hybridization as well as 165 rDNA sequencing (Graham et at.,
1991). The basic unit of bacterial taxonomy is species, defined as a group of strains
showing 70\% or greater DNA-DNA relatedness and 5oC or less .Tm [.Tm is the difference
in melting temperature (Tm)] between the homologous and heterologous hybrids formed
under standard conditions (Wayne et at., 1987). In addition, the strains comprising a single
species should exhibit less than 5 mol\% differences in DNA G+C content and over 97\% of
16S rDNA sequence similarity (Goodfellow and O.Donnel, 1993). Species determined
this way should be supported by similar phenotypic properties of the bacteria. In spite of
the application in bacterial taxonomy of many new methods, especially those involving
molecular analysis of DNA, there is still no .golden standard. for the identification of
bacterial species. Integration of a wide range of data on microorganisms, together with
their numerical analysis seems to be the best solution at present (Vandamme et at.,
1996).},
   Keywords = {rhizobiaceae
taxonomy},
   Year = {1999} }




@article{
Malek05,
   Author = {Ma{\l}ek, W. and Sajnaga, E. and Wdowiak-Wr\'obel, S. and Studzin\'ska, B. and Nosalewicz, I. and S{\l}omka, M. and Tatara, A. and S\'wi{\c e}icka, I. and Gawron, A.},
   Title = {Characterization of phages virulent for \emph{Sarothamnus scoparius} bradyrhizobia},
   Journal = {Current Microbiology},
   Volume = {51},
   Number = {4},
   Pages = {244-249},
   Abstract = {Four virulent phages-?Dl, ?Tl, ?CYT21, and ?OS6, infective on Sarothamnus scoparius rhizobia-were isolated from the soil and characterized for morphology, host range, rate of adsorption to bacterial cells, and genome size. New phages were separated into two morphological families: Siphoviridae with long, noncontractile tails (?Dl, ?Tl) and Myoviridae with long, contractile tails (?CYT21, ?OS6). They were also classified into two groups by a host specificity. One of them included viruses (?Dl and ?Tl) that lysed S. scoparius bradyrhizobia and Bradyrhizobium sp. (Lupinus) strain Dl, and the second one comprised phages (?CYT21 and ?OS6) that parasitized only Scotch broom native microsymbionts. Phages specific for S. scoparius rhizobia were differentiated not only by morphology and host range but also by a genome size that was in the range from 47,583 to 60,098 b.p. © Springer Science+Business Media, Inc. 2005.},
      Year = {2005} }




@article{
MacKenzie79,
   Author = {MacKenzie, S. L. and Lapp, M. S. and Child, J. J.},
   Title = {Fatty acid composition of \emph{Rhizobium} spp},
   Journal = {Canadian Journal of Microbiology},
   Volume = {25},
   Number = {1},
   Pages = {68-74},
   Abstract = {The fatty acid composition of 42 isolates belonging to the major plant affinity groups of Rhizobium has been determined and found to vary reproducible with culture age. Numerical taxonomic techniques applied to the 15 major fatty acid components of log-phase cultures of comparable physiological age showed that the rhizobia constitute a uniform group. However, two clusters comprising soybean-cowpea isolates and pea-bean isolates were evident. These observations, based on a simple analysis of only one group of chemical components, indicate relationships among rhizobia which differ from the conventional plant-affinity groupings but which are consistent with other proposed relationships established using a variety of biochemical and physiological criteria.},
   Keywords = {Fabaceae/microbiology
Fatty Acids/*analysis
Plants, Medicinal
Rhizobium/*analysis/classification/growth \& development
Species Specificity},
   Year = {1979} }




@article{
Macphail97,
   Author = {Macphail, M. K.},
   Title = {Comment on M. Pole (1994): The New Zealand flora - Entirely long-distance dispersal?},
   Journal = {Journal of Biogeography},
   Volume = {24},
   Pages = {113-117},
      Year = {1997} }




@article{
Maiden98,
   Author = {Maiden, M. C. J. and Urwin, R. and Zhou, J. and Spratt, B.  G. and Bygraves, J. A. and Russell, J. E. and Feavers, I. M. and Feil, E. and Zhang, Q. and Morelli, G. and Zurth, K. and Achtman, M. and Caugant, D. A.},
   Title = {Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms},
   Journal = {Proceedings of the National Academy of Sciences of the United States of America},
   Volume = {95},
   Number = {6},
   Pages = {3140-3145},
   Abstract = {Traditional and molecular typing schemes for the characterization of pathogenic microorganisms are poorly portable because they index variation that is difficult to compare among laboratories. To overcome these problems, we propose multilocus sequence typing (MLST), which exploits the unambiguous nature and electronic portability of nucleotide sequence data for the characterization of microorganisms. To evaluate MLST, we determined the sequences of ?470-bp fragments from 11 housekeeping genes in a reference set of 107 isolates of Neisseria meningitidis from invasive disease and healthy carriers. For each locus, alleles were assigned arbitrary numbers and dendrograms were constructed from the pairwise differences in multilocus allelic profiles by cluster analysis. The strain associations obtained were consistent with clonal groupings previously determined by multilocus enzyme electrophoresis. A subset of six gene fragments was chosen that retained the resolution and congruence achieved by using all 11 loci. Most isolates from hyper-virulent lineages of serogroups A, B, and C meningococci were identical for all loci or differed from the majority type at only a single locus. MLST using six loci therefore reliably identified the major meningococcal lineages associated with invasive disease. MLST can be applied to almost all bacterial species and other haploid organisms, including those that are difficult to cultivate. The overwhelming advantage of MLST over other molecular typing methods is that sequence data are truly portable between laboratories, permitting one expanding global database per species to be placed on a World- Wide Web site, thus enabling exchange of molecular typing data for global epidemiology via the Internet.},
   Keywords = {Housekeeping genes
Hyper-virulent clones
Molecular typing
Neisseria meningitidis
World-Wide Web},
   Year = {1998} }




@article{
Mao94,
   Author = {Mao, C. and Downie, J. A. and Hong, G.},
   Title = {Two inverted repeats in the nodD promoter region are involved in nodD regulation in Rhizobium leguminosarum},
   Journal = {Gene},
   Volume = {145},
   Number = {1},
   Pages = {87-90},
   Abstract = {In Rhizobium leguminosarum (R.l.) biovar viciae, the nodulation gene nodD encodes a transcriptional activator (NodD) which binds to highly conserved DNA sequences (nod-boxes) in the promoters of other nod operons. In addition, NodD represses nodD transcription and this occurs at the divergent and overlapping nodA-nodD promoters. We mutagenised this region with hydroxylamine, and by cloning the mutagenised DNA into a Vector carrying the lacZ reporter gene downstream from the cloning site identified mutations affecting nodD expression and repression. The resulting plasmids were transferred to R.l. viciae strains containing or lacking nodD. Two classes of promoter mutants were identified: those in which nodD transcription was altered and those in which NodD-dependent repression was altered. The nucleotide (nt) changes in the promoter region were found to be located within two inverted repeat sequences (A2 and A3) which are about 70 bp apart. A2 is important for nodD transcription and A3 (which is upstream from A2) is involved in NodD-dependent repression. The nt sequence at A3 shows some homology to the nod-box region of the nodA promoter. It is proposed that the NodD-dependent repression occurs as a result of NodD binding to both A3 and the nodA nod-box, forming a loop which prevents transcription of nodD from its promoter, A2, which lies between A3 and the nod-bar. This model is supported by the observation that there are at least three sites for NodD binding in the nodA-nodD promoter region.},
   Keywords = {NodD protein
Regulation
Repression
RNA polymerase
Transcription},
   Year = {1994} }




@article{
Marie01,
   Author = {Marie, Corinne and Broughton, William J. and Deakin, William J.},
   Title = {Rhizobium type III secretion systems: legume charmers or alarmers?},
   Journal = {Current Opinion in Plant Biology},
   Volume = {4},
   Number = {4},
   Pages = {336-342},
   Abstract = {Mutagenesis and sequence analyses of rhizobial genomes have revealed the presence of genes encoding type III secretion systems. Considered as a machine used by plant and animal pathogens to deliver virulence factors into their hosts, this secretion apparatus has recently been proven to play a role in symbiotic bacteria-leguminous plant interactions.},
      Year = {2001} }




@article{
Marin03,
   Author = {Marin, V. A. and Teixeira, K. R. S. and Baldani, J. I.},
   Title = {Characterization of amplified polymerase chain reaction glnB and nifH gene fragments of nitrogen-fixing Burkholderia species},
   Journal = {Letters in Applied Microbiology},
   Volume = {36},
   Number = {2},
   Pages = {77-82},
   Abstract = {Aims: To clone and sequence polymerase chain reaction (PCR)-amplified glnB and nifH genes of the nitrogen-fixing bacteria Burkholderia brasilensis strain M130, B. tropicalis strain PPe8 and B. kururiensis strain KP23. Methods and Results: The glnB and nifH gene fragments were amplified by PCR using universal degenerated primers. A very high percentage of similarity for the nifH (100%) and glnB (96%) genes was observed between strains M130 and KP23. A similarity of 100% for the nifH gene was also observed between strains M130 and PPe8. However, the identity for the glnB gene was 98% and the similarity 88%. The phylogenetic tree of the nifH gene showed a very high degree of similarity to the 16S rDNA gene. Conclusions: The nitrogen-fixing bacteria of the Burkholderia genus formed a cluster separated from the other species of the genus mainly when the nifH rather than the glnB gene was used to construct the phylogenetic tree. Significance and Impact of the Study: Knowledge of the nifH and glnB gene sequences of B. brasilensis , B. tropicalis and B. kururiensis will support new studies on the diversity of these diazotrophs in natural environments.},
      Year = {2003} }




@article{
Markham72,
   Author = {Markham, K. R. and Godley, E. J.},
   Title = {Chemotaxonomic studies in \emph{Sophora} 1. An evaluation of \emph{Sophora microphylla} Aiton.},
   Journal = {New Zealand Journal of Botany},
   Volume = {10},
   Pages = {627-640},
      Year = {1972} }




@article{
Marsudi99,
   Author = {Marsudi, N. D. S. and Glenn, A. R. and Dilworth, M. J.},
   Title = {Identification and characterization of fast- and slow-growing root nodule bacteria from South-Western Australian soils able to nodulate \emph{Acacia saligna}},
   Journal = {Soil Biology and Biochemistry},
   Volume = {31},
   Number = {9},
   Pages = {1229-1238},
   Abstract = {A total of 133 root nodule bacterial strains were isolated from nodules of Acacia saligna growing in soils from nine geographically separate locations in South-Western Australia; 40 were characterized on the basis of their growth and physiology and 20 by 16 S rRNA sequence analysis. Thirty-nine strains were fast-growing rhizobia, and 94 slow-growing bradyrhizobia. The latter were essentially acid-tolerant, alkali-sensitive and salt-sensitive, while the former varied in acid-tolerance and were alkali- and salt-tolerant. In addition many of the rhizobia grew at 37C whereas few of the bradyrhizobia could. The fastgrowing strains utilized disaccharides whereas the slow-growing bradyrhizobia did not. Using PCR a 260-264 bp segment of the 16 S rRNA gene was amplified and then sequenced. The fast-growing rhizobia can be divided into at least two groups - one showing similarity to Rhizobium leguminosarum biovar phaseoli and the other to R. tropici. The slow-growers showed relationships to either Bradyrhizobium japonicum or Bradyrhizobium spp. (Lupinus).},
   Keywords = {Acacia saligna
Fast- and slow-growing
Root nodule bacteria
SW Australia},
   Year = {1999} }




@article{
Martinez87,
   Author = {Mart\'inez, E. and Palacios, R. and S\'anchez, F.},
   Title = {Nitrogen-fixing nodules induced by \emph{Agrobacterium tumefaciens} harboring \emph{Rhizobium phaseoli} plasmids.},
   Journal = {Journal of Bacteriology},
   Volume = {169},
   Number = {6},
   Pages = {2828-2834},
   Abstract = {Rhizobium phaseoli CFN299 forms nitrogen-fixing nodules in Phaseolus vulgaris (bean) and in Leucaena esculenta. It has three plasmids of 185, 225, and 410 kilobases. The 410-kilobase plasmid contains the nitrogenase structural genes. We have transferred these plasmids to the plasmid-free strain Agrobacterium tumefaciens GMI9023. Transconjugants containing different combinations of the R. phaseoli plasmids were obtained, and they were exhaustively purified before nodulation was assayed. Only transconjugants harboring the 410-kilobase plasmid nodulate P. vulgaris and L. esculenta. Nodules formed by all such transconjugants are able to reduce acetylene. Transconjugants containing the whole set of plasmids from CFN299 nodulate better and fix more nitrogen than the transconjugants carrying only the Sym plasmid. Microscopic analysis of nodules induced by A. tumefaciens transconjugants reveals infected cells and vascular bundles. None of the A. tumefaciens transconjugants, not even the one with the whole set of plasmids from CFN299, behaves in symbiosis like the original R. phaseoli strain; the transconjugants produce fewer nodules and have lower acetylene reduction (25% as compared to the original R. phaseoli strain) and more amyloplasts per nodule. More than 2,000 bacterial isolates from nodules of P. vulgaris and L. esculenta formed by the transconjugants were analyzed by different criteria. Not a single rhizobium could be detected. Our results show that R. phaseoli plasmids may be expressed in the A. tumefaciens background and direct the formation of effective, differentiated nodules.},
      Year = {1987} }




@article{
Martinez94,
   Author = {Mart\'inez-Romero, E.},
   Title = {Recent Developments in Rhizobium Taxonomy},
   Journal = {Plant and Soil},
   Volume = {161},
   Number = {1},
   Pages = {11-20},
   Abstract = {Recent developments in Rhizobium taxonomy are presented from a molecular and evolutionary point of view. Analyses of ribosomal RNA gene sequences provide a solid basis to infer phylogenies in the Rhizobiaceae family. These studies confirmed that Rhizobium and Bradyrhizobium are only distantly related and showed that Rhizobium and Bradyrhizobium are related to other groups of bacteria that are not plant symbionts. Rhizobium and Agrobacterium species are intermixed. Differences in plasmid content may explain to a good extent the different behavior of Rhizobium and Agrobacterium as symbionts or pathogens. Other approaches to identify and classify bacteria such as DNA-DNA hybridization, fatty acid analysis, RFLP and RPD-PCR techniques and phylogenies derived from other genes are in general agreement to the groupings derived by ribosomal sequences. Only a small proportion of nodulated legumes have been sampled for their symbionts and more knowledge is required on the systematics and taxonomy of Rhizobium and Bradyrhizobium species.},
      Year = {1994} }




@article{
Martinez03,
   Author = {Mart\'inez-Romero, E.},
   Title = {Diversity of Rhizobium-Phaseolus vulgaris symbiosis: overview and perspectives},
   Journal = {Plant and Soil},
   Volume = {252},
   Number = {1},
   Pages = {11-23},
   Abstract = {Common bean ( Phaseolus vulgaris) has become a cosmopolitan crop, but was originally domesticated in the Americas and has been grown in Latin America for several thousand years. Consequently an enormous diversity of bean nodulating bacteria have developed and in the centers of origin the predominant species in bean nodules is R. etli. In some areas of Latin America, inoculation, which normally promotes nodulation and nitrogen fixation is hampered by the prevalence of native strains. Many other species in addition to R. etli have been found in bean nodules in regions where bean has been introduced. Some of these species such as R. leguminosarum bv. phaseoli, R. gallicum bv. phaseoli and R. giardinii bv. phaseoli might have arisen by acquiring the phaseoli plasmid from R. etli. Others, like R. tropici, are well adapted to acid soils and high temperatures and are good inoculants for bean under these conditions. The large number of rhizobia species capable of nodulating bean supports that bean is a promiscuous host and a diversity of bean-rhizobia interactions exists. Large ranges of dinitrogen fixing capabilities have been documented among bean cultivars and commercial beans have the lowest values among legume crops. Knowledge on bean symbiosis is still incipient but could help to improve bean biological nitrogen fixation.},
      Year = {2003} }




@article{
Martinez96,
   Author = {Mart\'inez-Romero, E. and Caballero-Mellado, J.},
   Title = {\emph{Rhizobium} phylogenies and bacterial genetic diversity},
   Journal = {Critical Reviews in Plant Sciences},
   Volume = {15},
   Number = {2},
   Pages = {113-140},
   Abstract = {The Leguminosae is one of the largest families of plants. It has a broad geographical distribution, The principal legume species have defined sites of origin and these coincide with the diversification centers for their ''specific'' symbiotic bacteria. These nitrogen-fixing bacteria, which form nodules in the roots or stems of the plants, belong to different bacterial lineages (Rhizobium, Bradyrhizobium, and Azorhizobium) related to other nonsymbiotic bacteria. A remarkable characteristic of these bacteria is their large genetic diversity. The genetic relationships among the different bacterial groups are being defined based mainly on the analysis of the sequences of the ribosomal genes. Recent results point out the need to have a broader genomic scope. Gene maps, genome sizes, and sequence of metabolic genes would serve to validate the present Rhizobium and Bradyrhizobium phylogenies. More realistic phylogenies should perhaps consider lateral transfer between clusters of bacteria. A compilation of records of bacterial genetic diversity, including enterobacteria and pathogens, is presented and compared with Rhizobium diversity. It is proposed that human activities are having important effects on microbe diversity.},
      Year = {1996} }




@article{
Martinez93,
   Author = {Mart\'inez-Romero, E. and Jarvis, B. D. W.},
   Title = {International committee on systematic bacteriology subcommittee on the taxonomy of Agrobacterium and Rhizobium},
   Journal = {International Journal of Systematic Bacteriology},
   Pages = {622},
   Keywords = {agrobacterium
rhizobium},
   Year = {1993} }




@article{
Martinez91,
   Author = {Mart\'inez-Romero, E. and Segovia, L. and Mercante, F. M. and Franco, A. A. and Graham, P. and Pardo, M. A.},
   Title = {\emph{Rhizobium tropici}, a novel species nodulating \emph{Phaseolus vulgaris} L. beans and \emph{Leucaena} sp. trees},
   Journal = {International Journal of Systematic Bacteriology},
   Volume = {41},
   Number = {3},
   Pages = {417-426},
   Abstract = {A new Rhizobium species that nodulates Phaseolus vulgaris L. and Leucaena spp. is proposed on the basis of the results of multilocus enzyme electrophoresis, DNA-DNA hybridization, an analysis of ribosomal DNA organization, a sequence analysis of 16S rDNA, and an analysis of phenotypic characteristics. This taxon, Rhizobium tropici sp. nov., was previously named Rhizobium leguminosarum biovar phaseoli (type II strains) and was recognized by its host range (which includes Leucaena spp.) and nif gene organization. In contrast to R. leguminosarum biovar phaseoli, R. tropici strains tolerate high temperatures and high levels of acidity in culture and are symbiotically more stable. We identified two subgroups within R. tropici and describe them in this paper.},
   Keywords = {ribosome rna
rhizobium
Plants, Medicinal},
   Year = {1991} }




@article{
Martinez90,
   Author = {Martinez-Romero, E. and Rosenblueth, M.},
   Title = {Increased bean (Phaseolus vulgaris L.) nodulation competitiveness of genetically modified Rhizobium strains},
   Journal = {Applied and Environmental Microbiology},
   Volume = {56},
   Number = {8},
   Pages = {2384-2388},
   Abstract = {Rhizobium leguminosarum bv. phaseoli strain collections harbor heterogeneous groups of bacteria in which two main types of strains may be distinguished, differing both in the symbiotic plasmid and in the chromosome. We have analyzed under laboratory conditions the competitive abilities of the different types of Rhizobium strains capable of nodulating Phaseolus vulgaris L. bean. R. leguminosarum bv. phaseoli type I strains (characterized by nif gene reiterations and a narrow host range) are more competitive than type II strains (that have a broad host range), and both types are more competitive than the promiscuous rhizobia isolated from other tropical legumes able to nodulate beans. Type I strains become even more competitive by the transfer of a non-Sym, 225-kilobase plasmid from type II strain CFN299. This plasmid has been previously shown to enhance the nodulation and nitrogen fixation capabilities of Agrobacterium tumefaciens transconjugants carrying the Sym plasmid of strain CFN299. Other type I R. leguminosarum bv. phaseoli transconjugants carrying two symbiotic plasmids (type I and type II) have been constructed. These strains have a diminished competitive ability. The increase of competitiveness obtained in some transconjugants seems to be a transient property.},
      Year = {1990} }




@article{
Martyniuk00,
   Author = {Martyniuk, S. and Wo\'zniakowska, A. and Martyniuk, M. and Oro\'n, J.},
   Title = {A new sand pouch-plant infection technique for enumeration of rhizobia in soil},
   Journal = {Acta Societatis Botanicorum Poloniae},
   Volume = {69},
   Number = {4},
   Pages = {257-261},
   Abstract = {A sand pouch-plant infection technique for counting most probable numbers of rhizobia in soil is. described. Populations of Rhizobium leguminosanim bv. trifoli detected by the plant infection method performed in enclosed glass tubes or in sand pouches did not differ significantly. The described method was used to assess numbers of A. leguminosanim bv. trifoli (R.l.t.) and bv. viciae (R.l.v.) in 20 soils of Poland. Logarithms of the populations of R.l.t. in the tested sous ranged from not detectable level to 4.76 and those of R.l.v. from 2.23 to 5.84 in g-1 of soil dry mass. Numbers of R.l.t. were significantly correlated with soil clay, C org. and total N contents but not with the soil pH (in KCl), while numbers of R.l.v. showed significant correlation only with the soil pH.},
   Keywords = {Assessment
Nodulation
Pisum arvense
Rhizobium leguminosarum
Soil
Trifolium repens},
   Year = {2000} }




@article{
Marvel87,
   Author = {Marvel, D. J. and Torrey, J. G. and Ausubel, F. M.},
   Title = {Rhizobium symbiotic genes required for nodulation of legume and nonlegume hosts},
   Journal = {Proceedings of the National Academy of Sciences of the United States of America},
   Volume = {84},
   Number = {5},
   Pages = {1319-1323},
   Abstract = {Parasponia, a woody member of the elm family, is the only nonlegume genus whose members are known to form an effective nitrogen-fixing symbiosis with Bradyrhizobium or Rhizobium species. The Bradyrhizobium strain Rp501, isolated from Parasponia nodules, also nodulates the legumes siratro (Macroptilium atropurpureum) and cowpea (Vigna unguiculata). To test whether some of the same genes are involved in the early stages of legume and nonlegume nodulation, we generated transposon Tn5 insertions in the region of three evolutionarily conserved genes (nodA, nodB, and nodC) required for legume nodulation in several Rhizobium and Bradyrhizobium species. Assays of these mutant Rp501 strains on legume hosts and Parasponia seedlings established that nodABC are required for nodulation of legume and nonlegume hosts, indicating that nonlegumes and legumes can respond to the same bacterial signal(s). In addition, a strain carrying a Tn5 insertion adjacent to the nodABC genes vigorously nodulated Rp501 legume hosts but was incapable of nodulating Parasponia, possibly identifying a nonlegume-specific nodulation function.},
      Year = {1987} }




@article{
Mathesius03,
   Author = {Mathesius, U.},
   Title = {Conservation and divergence of signalling pathways between roots and soil microbes - The Rhizobium-legume symbiosis compared to the development of lateral roots, mycorrhizal interactions and nematode-induced galls},
   Journal = {Plant and Soil},
   Volume = {255},
   Number = {1},
   Pages = {105-119},
   Abstract = {This review compares endophytic symbiotic and pathogenic root-microbe interactions and examines how the development of root structures elicited by various micro-organisms could have evolved by recruitment of existing plant developmental pathways. Plants are exposed to a multitude of soil micro-organisms which affect root development and performance. Their interactions can be of symbiotic and pathogenic nature, both of which can result in the formation of new root structures - how does the plant regulate the different outcomes of interactions with microbes? The idea that pathways activated in plant by micro-organisms could have been 'hijacked' from plant developmental pathways is not new, it was essentially proposed by P. S. Nutman in 1948, but at that time, the molecular evidence to support that hypothesis was missing. Genetic evidence for overlaps between different plant-microbe interactions have previously been examined. This review compares the physiological and molecular plant responses to symbiotic rhizobia with those to arbuscular mycorrhizal fungi, pathogenic nematodes and the development of lateral roots and summarises evidence from both molecular and cellular studies for substantial overlaps in the signalling pathways underlying root-micro-organism interactions. A more difficult question has been why plant responses to micro-organisms are so similar, even though the outcomes are very different. Possible hypotheses for divergence of signalling pathways and future approaches to test these ideas are presented.},
   Keywords = {Arbuscular mycorrhiza
Auxin
Flavonoids
Lateral root formation
Nematode galls
Nodulation},
   Year = {2003} }




@article{
Mathis05,
   Author = {Mathis, R. and de Rycke, R. and D'Haeze, W. and Van Maelsaeke, E. and Anthonio, E. and Van Montagu, M. and Holsters, M. and Vereecke, D. and Van Gijsegem, F.},
   Title = {Lipopolysaccharides as a communication signal for progression of legume endosymbiosis},
   Journal = {Proceedings of the National Academy of Sciences of the United States of America},
   Volume = {102},
   Number = {7},
   Pages = {2655-2660},
   Abstract = {Establishment of a successful symbiosis between rhizobia and legumes results from an elaborate molecular dialogue between both partners. Bacterial nodulation (Nod) factors are indispensable for initiating plant responses, whereas bacterial surface polysaccharides are important for infection progression and nodule development. The mutant ORS571-oac2 of Azorhizobium caulinodans, affected in its surface polysaccharides, provokes a defective interaction with its host Sesbania rostrata. ORS571-oac2 induced structures with retarded development and continued generation of infection centers and organ primordia, leading to multilobed ineffective nodules. Bacterial development throughout the interaction occurred without major defects. A functional bidirectional complementation was obtained upon coinfection of ORS571-oac2 and a Nod factor-deficient mutant, indicating that the Fix<sup>-</sup> phenotype of ORS571-oac2-induced nodules resulted from the absence of a positive signal from ORS571-oac2. Indeed, the Fix<sup>-</sup> phenotype could be complemented by coinoculation of ORS571-oac2 with lipopolysaccharides (LPSs) purified from A. caulinodans. Our data show that Nod factors and LPSs are consecutive signals in symbiosis. Nod factors act first to trigger the onset of the nodulation and invasion program; LPSs inform the plant to proceed with the symbiotic interaction and to develop a functional fixation zone.},
   Keywords = {Nodulation
Plant-bacterium interaction
Polysaccharides},
   Year = {2005} }




@article{
Maunder99,
   Author = {Maunder, M. and Culham, A. and Maunder, M. and Bordeu, A. and Allainguillaume, J. and Wilkinson, M.},
   Title = {Genetic diversity and pedigree for Sophora toromiro (Leguminosae): A tree extinct in the wild},
   Journal = {Molecular Ecology},
   Volume = {8},
   Number = {5},
   Pages = {725-738},
   Abstract = {Sophora toromiro was endemic to the Pacific island of Rapa Nui (Easter Island) and is extinct in the wild. The species has survived in private and botanic gardens. The species is the subject of an international study to support its conservation ex situ and eventual reintroduction. As a contribution to this study the genetic diversity of the surviving stocks and herbarium samples has been assessed by means of random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (inter-SSR) analysis. The analysis indicated low levels of genetic diversity suggesting a very small number of founders. In addition, misidentified trees were identified allowing their removal from the conservation project.},
   Keywords = {Ancient DNA
Ex situ conservation
Genetic variation
Inter-SSR
RAPD
Sophora
genetic diversity
Sophora toromiro},
   Year = {1999} }




@phdthesis{
McCallum96,
   Author = {McCallum, N. G.},
   Title = {Genetic diversity and phylogeny of native New Zealand rhizobia},
   School = {Department of Microbiology, University of Otago},
   Type = {Honours Dissertation},
      Year = {1996} }




@article{
McDougall81,
   Author = {McDougall, I. and Embleton, B. J. J. and Stone, D. B.},
   Title = {Origin and evolution of Lord Howe Island, southwest Pacific Ocean},
   Journal = {Journal of the Geological Society of Australia},
   Volume = {28},
   Pages = {155-176},
      Year = {1981} }




@article{
McGlone01,
   Author = {McGlone, M. S. and Duncan, R. P. and Heenan, P. B.},
   Title = {Endemism, species selection and the origin and distribution of the vascular plant flora of New Zealand},
   Journal = {Journal of Biogeography},
   Volume = {28},
   Number = {2},
   Pages = {199-216},
   Abstract = {Aim: To evaluate competing views on the origin and distribution of the New Zealand flora by testing the hypothesis that the geographical distribution of species is unrelated to ecological traits such as habitat requirements and dispersal capabilities. Location: The New Zealand archipelago. Methods: An analysis of the factors correlated with distribution and endemism for alpine plants within New Zealand, and for the New Zealand biota as a whole. Results: Woody plants are highly endemic; nonendemic plants tend to be herbaceous and are concentrated among the highly dispersible ferns and fern allies, orchids and wetland plants. These groups make up 32% of the total flora but contribute 78% of nonendemics. Alpine plants with wide spatial distribution tend to have greater altitudinal ranges, a broader habitat preference and better dispersal ability. Main conclusions: Most vascular plants reached New Zealand by long-distance transoceanic dispersal, probably during the Late Miocene to early Pleistocene period. During the Miocene and Pliocene, similar climates and landscapes to those of Australia and northern island groups, and highly invasible terrain, permitted dispersal of woody plants. Cooling climates and formation of a more mountainous, more compact landscape after that time reduced dispersal of woody plants and favoured herbaceous, wetland and highly dispersible plant groups. The prominence of dispersal has led to intense selective immigration, and is responsible for many characteristic features of the flora. Species selection by glacial-interglacial cycles has restricted acquisition or retention of cool or arid climate adaptations, particularly in the lowland flora. Endemic and range disjunction patterns in the New Zealand mainland are not, in general, directly caused by Pliocene inundations or the faulting and associated horizontal displacement of terrain that has continued since the Miocene. They have arisen mainly through Pleistocene extinctions, speciation and dispersal, and some patterns are strongly linked to repeated glaciation. Endemic centres are associated with differentiated terrain and climates providing isolation, distinctive environments, and habitat continuity conducive to speciation.},
   Keywords = {Alpine plants
Biogeography
Dispersal
Endemism
New Zealand
Vascular plants},
   Year = {2001} }




@article{
McGowan05,
   Author = {McGowan, H. A. and Kamber, B and Mctainsh, G. H. and Marx, S. K.},
   Title = {High resolution provenancing of long travelled dust deposited on the Southern Alps, New Zealand},
   Journal = {Geomorphology},
   Volume = {69},
   Number = {1-4},
   Pages = {208-221},
   Abstract = {On 7 February 2000 an atypical orange discolouration of snowfields in the central Southern Alps, New Zealand occurred following the passage of a cold front. Analysis of snow samples identified fine orangey-brown dust mixed with much coarser grey dust. Air parcel forward trajectories from dust sources in southern and central Australia, where dust storms were reported on 4 February 2000, were computed to identify the deposits source. Geochemical analyses of the dust deposit using 26 trace elements, unaffected by regional air pollution and gravitational sorting, indicate that 20% of the dust was sourced from western New South Wales, with 45% from the eastern Eyre Peninsula of South Australia and the remaining 35% was local New Zealand dust. This provenancing approach provides a spatial resolution of long travelled dust sourcing not previously achieved.

Keywords: Dust deposition; Geochemical provenance; Air parcel trajectories; New Zealand; Australia},
      Year = {2005} }




@article{
McGrath95,
   Author = {McGrath, S. P. and Chaudri, A. M. and Giller, K. E.},
   Title = {Long-term effects of metals in sewage sludge on soils, microorganisms and plants},
   Journal = {Journal of Industrial Microbiology},
   Volume = {14},
   Number = {2},
   Pages = {94-104},
   Abstract = {This paper reviews the evidence for impacts of metals on the growth of selected plants and on the effects of metals on soil microbial activity and soil fertility in the long-term. Less is known about adverse long-term effects of metals on soil microorganisms than on crop yields and metal uptake. This is not surprising, since the effects of metals added to soils in sewage sludge are difficult to assess, and few long-term experiments exist. Controlled field experiments with sewage sludges exist in the UK, Sweden, Germany and the USA and the data presented here are from these long-term field experiments only. Microbial activity and populations of cyanobacteria, Rhizobium leguminosarum bv. trifolii, mycorrhizae and the total microbial biomass have been adversely affected by metal concentrations which, in some cases, are below the European Community's maximum allowable concentration limits for metals in sludge-treated soils. For example, N2 fixation by free living heterotrophic bacteria was found to be inhibited at soil metal concentrations of (mg kg-1): 127 Zn, 37 Cu, 21 Ni, 3.4 Cd, 52 Cr and 71 Pb. N2-fixation by free-living cyanobacteria was reduced by 50% at metal concentrations of (mg kg-1): 114 Zn, 33 Cu, 17 Ni, 2.9 Cd, 80 Cr and 40 Pb. Rhizobium leguminosarum bv. trifolii numbers decreased by several orders of magnitude at soil metal concentrations of (mg kg-1): 130-200 Zn, 27-48 Cu, 11-15 Ni, and 0.8-1.0 Cd. Soil texture and pH were found to influence the concentrations at which toxicity occurred to both microorganisms and plants. Higher pH, and increased contents of clay and organic carbon reduced metal toxicity considerably. The evidence suggests that adverse effects on soil microbial parameters were generally found at surpringly modest concentrations of metals in soils. It is concluded that prevention of adverse effects on soil microbial processes and ultimately soil fertility, should be a factor which influences soil protection legislation.},
   Keywords = {Cyanobacteria
Metal toxicity
Mycorrhiza
Nitrogen fixation
Rhozobia
Soil microbial biomass},
   Year = {1995} }




@article{
McInroy99,
   Author = {McInroy, S. G. and Campbell, C. D. and Haukka, K. E. and Odee, D. W. and Sprent, J. I. and Wang, W. J. and Young, J. P. W. and Sutherland, J. M.},
   Title = {Characterisation of rhizobia from African acacias and other tropical woody legumes using Biolog (TM) and partial 16S rRNA sequencing},
   Journal = {FEMS Microbiology Letters},
   Volume = {170},
   Number = {1},
   Pages = {111-117},
   Abstract = {A Biolog(TM) (sole carbon source utilisation) user database of tropical and temperature rhizobial strains was created and used in conjunction with the partial 16S rRNA sequencing method to characterise 12 rhizobial isolates from African acacias and other tropical woody legumes. There was close agreement between the two methods but also some significant discrepancies. A high degree of diversity was shown in the relatively small sample of isolates, with 4 out of 5 of the currently proposed rhizobial genera represented. This is the first time Biolog has shown congruence with genotypic fingerprinting: using a wide selection of rhizobial reference and test strains. (C) 1999 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.},
      Year = {1999} }




@article{
McIver89,
   Author = {McIver, J.  and Djordjevic, M. A. and Weinman, J. J. and Bender, G. L. and Rolfe, B. G.},
   Title = {Extension of host range of \emph{Rhizobium leguminosarum} bv. \emph{trifolii} caused by point mutations in \emph{nodD} that result in alterations in regulatory function and recognition of inducer molecules.},
   Journal = {Molecular Plant Microbe Interactions},
   Volume = {2},
   Number = {3},
   Pages = {97-106},
   Abstract = {The positive activation of several nodulation genes in strain ANU843 of Rhizobium leguminosarum biovar trifolii is mediated by the product of the nodD gene and by the interaction of NodD with plant-secreted inducer and anti-inducer compounds. We have mutagenized the nodD gene of strain ANU843 with nitrosoguanidine and have found that the ability of the mutated nodD products to interact with inducer and anti-inducer compounds is affected by the amino acid sequence in at least two key regions, including a novel area between amino acids 77 and 123. Several novel classes of mutants were recognized by phenotypic and molecular analysis of the mutant nodD genes. Classes 1 and 4 mutants were able to induce nodA expression independently of the addition of inducer and anti-inducer compounds and were unable to mediate autoregulation of the nodD gene. Classes 2 and 3 mutants retained several properties of the wild-type nodD, including the ability to interact with inducer and anti-inducer compounds and the capacity to autoregulate nodD expression. In addition, class 2 mutants showed an inducer-independent ability to mediate nodA expression to 10-fold higher levels over control strains. The class 3 mutant showed reactivity to compounds that had little or no inducing ability with the wild-type nodD. An alteration in NodD function was demonstrated with classes 2 and 3 mutants, which showed greatly enhanced ability to complement a Tn5-induced mutation in the nodD1 gene of strain NGR234 and to restore nodulation ability on the tropical legume siratro. Mutants of nodD possessing inducer-independent ability to activate nod gene expression (classes 1, 2, and 4) were capable of extending the host range of R. l. bv. trifolii to the nonlegume Parasponia. DNA sequence analysis showed that single base changes were responsible for the altered phenotypic properties of five of six mutants examined. Four of the six mutations affected amino acid residues in a putative receiver domain in the N-terminal end of the nodD protein.},
      Year = {1989} }




@article{
McKenzie95,
   Author = {McKenzie, B. A. and Hill, G. D.},
   Title = {Growth and yield of two chickpea (Cicer arietinum L) varieties in Canterbury, New Zealand},
   Journal = {New Zealand Journal of Crop and Horticultural Science},
   Volume = {23},
   Number = {4},
   Pages = {467-474},
   Abstract = {Growth and yield of chickpeas (Cicer arietinum L.) was examined over two growing seasons (1990-91 and 1991-92) in Canterbury, New Zealand. The 1990-91 season was very suitable for chickpea growth and the seed yield was high at 345 g/m(2). The 1991-92 season was less suitable and seed yield was lower at only 187 g/m(2). In both growing seasons the application of nitrogen (N) fertiliser increased seed yields, with 50 kg N/ha giving a 17% increase in 1990-91 and 100 kg N/ha giving a 43% yield increase in 1991-92. Inoculation with Rhizobium had no effect on yield. There was no benefit from increasing plant population, even though higher plant populations intercepted more solar radiation. This was primarily because of a reduced number of pods/plant at the higher plant populations. Response to sowing date suggests that spring sowings will be the highest yielding. Crops sown in winter yielded up to 700 g dry matter (DM)/m(2), but harvest index (HI) was low at only 0.25. The spring sowing produced 210 g seed/m(2), from only 410 g of DM/m(2) giving a HI of 0.51.},
   Keywords = {radiation interception; population; density; sowing date; nitrogen;
'Kabuli'; 'desi'
winter; syria; crop},
   Year = {1995} }




@article{
McLaughlin00,
   Author = {McLaughlin, M. J. and Hamon, R. E. and McLaren, R. G. and Speir, T. W. and Rogers, S. L.},
   Title = {Review: A bioavailability-based rationale for controlling metal and metalloid contamination of agricultural land in Australia and New Zealand},
   Journal = {Australian Journal of Soil Research},
   Volume = {38},
   Number = {6},
   Pages = {1037-1086},
   Abstract = {Metal pollution of agricultural land in Australia and New Zealand is less severe than that documented in many European countries, due to the lower density of urban developments and a lower level of industrialisation. However, Australia and New Zealand are highly dependent on plant production systems based on plant-microbial symbioses (e.g. Rhizobium, mycorrhizae) and other natural biogeochemical processes for maintaining nutrient status in soils that are generally low in nutrients and, in Australia, also low in organic matter. Data linking metal concentrations in soil to agricultural and ecological effects are sparse for Australia and New Zealand, and regulatory frameworks and guidelines to control metal contamination of soils rely heavily on data generated in countries of the northern hemisphere. Adoption of benchmark concentrations for metal contaminants from these countries has led to inappropriate levels being chosen for several elements. These problems could be avoided and metal contamination of soils could be more effectively controlled if instead of relying on total concentrations of metals in soil and soil amendments, regulations and guidelines considered the biologically active fractions. This review considers the advantages and disadvantages of a bioavailability-based approach to the control of metal contamination of soils and suggests improvements needed to avoid both over- and under-protective measures.},
   Keywords = {heavy metal; pollution; regulation
leguminosarum biovar trifolii; plant-available cadmium; dtpa soil test;
sewage-sludge; trace-elements; heavy-metals; swiss-chard; urease
activity; wheat-grain; pasture contamination},
   Year = {2000} }




@article{
Mears59,
   Author = {Mears, A. D.},
   Title = {Cotyledon colour: A useful measure for nodulation effectiveness},
   Journal = {Rhizobium Newsletter},
   Volume = {4},
   Number = {1},
   Pages = {43-45},
      Year = {1959} }




@article{
Medrano04,
   Author = {Medrano-Soto, A. and Moreno-Hagelsieb, G. and Vinuesa, P. and Christen, J. A. and Collado-Vides, J.},
   Title = {Successful Lateral Transfer Requires Codon Usage Compatibility Between Foreign Genes and Recipient Genomes},
   Journal = {Mol Biol Evol},
   Volume = {21},
   Number = {10},
   Pages = {1884-1894},
   Abstract = {We present evidence supporting the notion that codon usage (CU) compatibility between foreign genes and recipient genomes is an important prerequisite to assess the selective advantage of imported functions, and therefore to increase the fixation probability of horizontal gene transfer (HGT) events. This contrasts with the current tendency in research to predict recent HGTs in prokaryotes by assuming that acquired genes generally display poor CU. By looking at the CU level (poor, typical, or rich) exhibited by putative xenologs still resembling their original CU, we found that most alien genes predominantly present typical CU immediately upon introgression, thereby suggesting that the role of CU amelioration in HGT has been overemphasized. In our strategy, we first scanned a representative set of 103 complete prokaryotic genomes for all pairs of candidate xenologs (exported/imported genes) displaying similar CU. We applied additional filtering criteria, including phylogenetic validations, to enhance the reliability of our predictions. Our approach makes no assumptions about the CU of foreign genes being typical or atypical within the recipient genome, thus providing a novel unbiased framework to study the evolutionary dynamics of HGT.},
      Year = {2004} }




@article{
Meinhardt93,
   Author = {Meinhardt, L.W. and Krishnan, H.B. and Balatti, P.A. and Pueppke, S.G.},
   Title = {Molecular cloning and characterization of a sym plasmid locus that regulates cultivar-specific nodulation of soybean by Rhizobium fredii USDA257},
   Journal = {Molecular Microbiology},
   Volume = {9},
   Number = {1},
   Pages = {17-29},
   Abstract = {Rhizobium fredii strain USDA257 produces nitrogen-fixing nodules on primitive soybean cultivars such as peking but tails to nodulate agronomically improved cultivars such as McCall. Transposon-mutant 257DH4 has two new phenotypes: it nodulates McCall, and its ability to do so is sensitive to the presence of parental strain USDA257, i.e. it is subject to competitive nodulation blocking. We have isolated a cosmid containing DNA that corresponds to the site of transposon insertion in 257DH4 and have localized Tn5 on an 8.0 kb EcoRI tragment. The 5596 bp DNA sequence that surrounds the insertion site contains seven open reading frames. Five of these, designated nolBTU, ORF4, and nolV, are closely spaced and of the same polarity. nolW and nolX are of the opposite polarity. The initiation codon for nolW lies 155 bp upstream from that of nolB, and it is separated from nolX by 281 bp. The predicted NolT and NolW proteins have putative membrane-spanning regions. The N-terminus of the hypothetical NolW protein also has limited homology to NodH of Rhizobium meliloti, buf none of the deduced protein sequences has significant homology to known nodulation gene products. Site-directed mutagenesis with mudII1734 confirms that inactivation of nolB, nolT, nolU, nolV, nolW, or nolX extends host range for nodulation to McCall soybean. This phenotype could not be genetically dissected from sensitivity to competitive nodulation blocking. Expression of nolBTU and nolX is induced as much as 30-fold by flavonoid signal molecules, even though these genes lack nod-box promoters. Histochemical staining of McCall roots inoculated with nolB-, nolU-, or nolX-lacZ fusions verifies that these genes are expressed continuously from preinfection to the stage of the functional nodule. Although a nolU-ORF4-nolV clone hybridizes to a single 8.0 kb EcoRI fragment from 10 strains of R. fredii and broad-host-range Rhizobium sp. NGR234, hybridizing sequences are not detectable in other rhizobia.},
      Year = {1993} }




@inproceedings{
Mendel65,
   Author = {Mendel, Gregor},
   Title = {Experiments in Plant Hybridization},
   BookTitle = {Natural History Society of Brunn in Bohemia},
      Year = {1865} }




@article{
Mercante98,
   Author = {Mercante, F. M. and Cunha, C. D. and Straliotto, R. and Ribeiro, Jr., W. Q. and Vanderleyden, J. and Franco, A. A.},
   Title = {\emph{Leucaena leucocephala} as a trap-host for \emph{Rhizobium tropici} strains from the Brazilian ``Cerrado'' region},
   Journal = {Revista de Microbiologia},
   Volume = {29},
   Number = {1},
   Pages = {49-58},
   Abstract = {Using Leucaena leucocephala as a trap-host, 422 strains of rhizobia were isolated from the bean (Phaseolus vulgaris L.) rhizosphere in the Cerrado region of Brazil. Traditional bean-producing areas with no history of rhizobial inoculation were sampled. Colony DNA hybridizations with gene-specific probes were used to identify strains that could be grouped as R. tropici, type I strains (R. leguminosarum by. phaseoli or R. etli), or as other Rhizobium species. The same typing procedure was applied to 61 isolates from a large collection of strains isolated from bean plants inoculated with the same soil samples. Rhizobium tropici was present at all sites. The population of rhizobia isolated from bean plants was more heterogeneous than rhizobial population isolated from Leucaena. More than 90% of Leucaena isolates could be typed as R. tropici. Strains typed as R. tropici hybridized with R. leguminosarum hup structural genes, but not with R. leguminosarum by. phaseoli ORF3, and the majority of them had a relative efficiency above 0.75. All the Leucaena strains were found to effectively nodulate beans and most of them yielded higher shoot dry weight than R. tropici strain CIAT899.},
      Year = {1998} }




@article{
Mergaert97,
   Author = {Mergaert, P. and Van Montagu, M. and Holsters, M.},
   Title = {Molecular mechanisms of Nod factor diversity},
   Journal = {Mol Microbiol},
   Volume = {25},
   Number = {5},
   Pages = {811-7},
   Abstract = {The rhizobia-legume symbiosis is highly specific. Major host specificity determinants are the bacterial Nod factor signals that trigger the nodulation programme in a compatible host. Nod factors are lipo-chitooligosaccharides (LCOs) varying in the oligosaccharide chain length, the nature of the fatty acids and substitutions on the oligosaccharide. The nod genotype of rhizobia, which forms the genetic basis for this structural variety, includes a set of nodulation genes encoding the enzymes that synthesize LCOs. Allelic and non-allelic variation in these genes ensures the synthesis of different LCO structures by the different rhizobia. The nod genotypes co-evolved with host plant divergence in contrast to the rhizobia, which followed a different evolution. Horizontal gene transfer probably played an important role during evolution of symbiosis. The nod genotypes are particularly well equipped for horizontal gene transfer because of their location on transmissible plasmids and/or on 'symbiosis islands', which are symbiotic regions associated with movable elements.},
   Keywords = {Evolution, Molecular
Genes, Structural, Bacterial
Genotype
Lipopolysaccharides/*biosynthesis/*chemistry
Rhizobium/chemistry/classification/genetics
Support, Non-U.S. Gov't
Variation (Genetics)},
   Year = {1997} }




@article{
Michiels98,
   Author = {Michiels, J. and Dombrecht, B. and Vermeiren, N. and Xi, C. W. and Luyten, E. and Vanderleyden, J.},
   Title = {Phaseolus vulgaris is a non-selective host for nodulation},
   Journal = {FEMS Microbiology Ecology},
   Volume = {26},
   Number = {3},
   Pages = {193-205},
   Abstract = {A systematic analysis of the symbiotic phenotype on Phaseolus vulgaris of tropical rhizobia isolated from a variety of leguminous plant species and of classified type strains from the genera Rhizobium, Sinorhizobium, Mesorhizobium, Bradyrhizobium and Azorhizobium was performed. Depending on the bean cultivar, between 80 and 90% of the tested rhizobia were able to nodulate. A minority of these nodules were also nitrogen-fixing. A detailed microscopic analysis of the induced nodules or nodular structures revealed that the interaction between these strains and P. vulgaris was arrested at different stages of the interaction. Our results show that P. vulgaris is able to perceive signals for nodulation from many rhizobia although most of the interactions are not effective. (C) 1995 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.},
      Year = {1998} }




@article{
Mildenhall72,
   Author = {Mildenhall, D. C.},
   Title = {Fossil pollen of \emph{Acacia} type from New Zealand},
   Journal = {New Zealand Journal of Botany},
   Volume = {10},
   Number = {3},
   Pages = {485-494},
   Abstract = {Numerous specimens of a pollen grain polyad similar to tose of present day \it{Acacia} have been found in a Castlecliffian (Middle Pleistocene) sample from the north of New Zealand. Their abundance suggests that the genus Acacia  was represented in the  Quaternary flora of New Zealand. It may have become extinct during the ``last glaciation''. Fossil localities where \it{Acacia} has been found are listed.},
      Year = {1972} }




@article{
Mildenhall84,
   Author = {Mildenhall, D. C. and Pocknall, D. T.},
   Title = {Palaeobotanical evidence for changes in Miocene and Pliocene climates in New Zealand},
      Year = {1984} }




@article{
Mildenhall89,
   Author = {Mildenhall, D. C. and Pocknall, D. T.},
   Title = {Miocene-Pleistocene spores and pollen from Central Otago, South Island, New Zealand},
   Journal = {New Zealand Geological Survey Paleontological Bulletin},
   Volume = {59},
   Pages = {1-128},
      Year = {1989} }




@article{
Miller01b,
   Author = {Miller, Joseph T. and Bayer, Randall J.},
   Title = {Molecular phylogenetics of Acacia (Fabaceae: Mimosoideae) based on the chloroplast MATK coding sequence and flanking  TRNK intron spacer regions},
   Journal = {American Journal of Botany},
   Volume = {88},
   Number = {4},
   Pages = {697-705},
   Abstract = {The tribe Acacieae (Fabaceae: Mimosoideae) contains two genera, the monotypic African Faidherbia and the pantropical Acacia, which comprise about 1200 species with over 950 confined to Australia. As currently recognized, the genus Acacia is subdivided into three subgenera: subg. Acacia, subg. Aculeiferum, and the predominantly Australian subg. Phyllodineae. Morphological studies have suggested the tribe Acacieae and genus Acacia are artificial and have a close affinity to the tribe Ingeae. Based on available data there is no consensus on whether Acacia should be subdivided. Sequence analysis of the chloroplast trnK intron, including the matK coding region and flanking noncoding regions, indicate that neither the tribe Acacieae nor the genus Acacia are monophyletic. Two subgenera are monophyletic; section Filicinae of subgenus Aculeiferum does not group with taxa of the subgenus. Section Filicinae, eight Ingeae genera, and Faidherbia form a weakly supported paraphyletic grade with respect to subg. Phyllodineae. Acacia subg. Aculeiferum (s. s.) is sister to the grade. These data suggest that characters currently used to differentiate taxa at the tribal, generic, and subgeneric levels are polymorphic and homoplasious in cladistic analyses.},
      Year = {2001} }




@article{
Miller96,
   Author = {Miller, Karen J. and Wood, Janet M.},
   Title = {Osmoadaptation by Rhizosphere Bacteria},
   Journal = {Annual Review of Microbiology},
   Volume = {50},
   Number = {1},
   Pages = {101-136},
   Abstract = {The osmolality of rhizosphere soil water is expected to be elevated in relation to bulk-soil water osmolality as a result of the exclusion of solutes by plant roots during water uptake, the release of plant root exudates, and the production of exopolymers by plant roots and rhizobacteria. In contrast, the osmolality of water within highly hydrated bulk soil is low (less than 50 Osm/kg); thus the ability to adapt to elevated osmolality is likely to be important for successful rhizosphere colonization by rhizobacteria. The present review focuses on the osmoadaptive responses of three gram-negative rhizobacterial genera: Rhizobium, Azospirillum, and Pseudomonas. Specifically, we examine the compatible solutes and osmoprotectants utilized by various species within these genera. The adaptation of rhizobacteria to hypoosmotic environments is also examined in the present review. In particular, we focus on the biosynthesis and accumulation of periplasmic glucans by rhizobacteria. Finally, the relationship between rhizobacterial osmoadaptation and selected plant-microbe interactions is considered.},
      Year = {1996} }




@article{
Miller01a,
   Author = {Miller, Melissa B. and Bassler, Bonnie L.},
   Title = {Quorum Sensing in Bacteria},
   Journal = {Annual Review of Microbiology},
   Volume = {55},
   Number = {1},
   Pages = {165-199},
   Abstract = {Quorum sensing is the regulation of gene expression in response to fluctuations in cell-population density. Quorum sensing bacteria produce and release chemical signal molecules called autoinducers that increase in concentration as a function of cell density. The detection of a minimal threshold stimulatory concentration of an autoinducer leads to an alteration in gene expression. Gram-positive and Gram-negative bacteria use quorum sensing communication circuits to regulate a diverse array of physiological activities. These processes include symbiosis, virulence, competence, conjugation, antibiotic production, motility, sporulation, and biofilm formation. In general, Gram-negative bacteria use acylated homoserine lactones as autoinducers, and Gram-positive bacteria use processed oligo-peptides to communicate. Recent advances in the field indicate that cell-cell communication via autoinducers occurs both within and between bacterial species. Furthermore, there is mounting data suggesting that bacterial autoinducers elicit specific responses from host organisms. Although the nature of the chemical signals, the signal relay mechanisms, and the target genes controlled by bacterial quorum sensing systems differ, in every case the ability to communicate with one another allows bacteria to coordinate the gene expression, and therefore the behavior, of the entire community. Presumably, this process bestows upon bacteria some of the qualities of higher organisms. The evolution of quorum sensing systems in bacteria could, therefore, have been one of the early steps in the development of multicellularity.},
      Year = {2001} }




@article{
Miller02,
   Author = {Miller, R. E. and Buckley, T. R. and Manos, P. S.},
   Title = {An examination of the monophyly of morning glory taxa using Bayesian phylogenetic inference},
   Journal = {Systematic Biology},
   Volume = {51},
   Number = {5},
   Pages = {740-753},
   Abstract = {The objective of this study was to obtain a quantitative assessment of the monophyly of morning glory taxa, specifically the genus Ipomoea and the tribe Argyreieae. Previous systematic studies of morning glories intimated the paraphyly of Ipomoea by suggesting that the genera within the tribe Argyreieae are derived from within Ipomoea; however, no quantitative estimates of statistical support were developed to address these questions. We applied a Bayesian analysis to provide quantitative estimates of monophyly in an investigation of morning glory relationships using DNA sequence data. We also explored various approaches for examining convergence of the Markov chain Monte Carlo (MCMC) simulation of the Bayesian analysis by running 18 separate analyses varying in length. We found convergence of the important components of the phylogenetic model (the tree with the maximum posterior probability, branch lengths, the parameter values from the DNA substitution model, and the posterior probabilities for clade support) for these data after one million generations of the MCMC simulations. In the process, we identified a run where the parameter values obtained were often outside the range of values obtained from the other runs, suggesting an aberrant result. In addition, we compared the Bayesian method of phylogenetic analysis to maximum likelihood and maximum parsimony. The results from the Bayesian analysis and the maximum likelihood analysis were similar for topology, branch lengths, and parameters of the DNA substitution model. Topologies also were similar in the comparison between the Bayesian analysis and maximum parsimony, although the posterior probabilities and the bootstrap proportions exhibited some striking differences. In a Bayesian analysis of three data sets (ITS sequences, waxy sequences, and ITS + waxy sequences) no supoort for the monophyly of the genus Ipomoea, or for the tribe Argyreieae, was observed, with the estimate of the probability of the monophyly of these taxa being less than 3.4 × 10-7.},
   Keywords = {Bayesian statistics
Convergence
Ipomoea
ITS
Markov chain Monte Carlo
Maximum likelihood
Maximum parsimony
Waxy},
   Year = {2002} }




@article{
Mills85,
   Author = {Mills, K. K. and Bauer, W. D.},
   Title = {Rhizobium attachment to clover roots},
   Journal = {J Cell Sci Suppl},
   Volume = {2},
   Pages = {333-45},
   Abstract = {The adhesion of rhizobia to surfaces of clover roots was examined by an indirect plate-counting assay and phase-contrast microscopy. The number of Rhizobium trifolii cells attached to clover root segments increased in approximately linear fashion during the first hour of incubation, but did not change appreciably thereafter. The addition of 30 mM-2-deoxy-D-glucose, which effectively inhibits binding of clover root lectin, did not promote the release of previously attached bacteria nor inhibit subsequent attachment to either root segments or root hairs. Rhizobia of several heterologous species attached to clover roots in numbers comparable to those of strains of R. trifolii, the homologous species. These results indicate that rhizobia have effective mechanisms of adhesion to non-host roots and that clover lectin contributed little or nothing to attachment under the conditions examined.},
   Keywords = {Cell Adhesion/drug effects
Cell Wall/physiology
Deoxyglucose/pharmacology
Fertilization
Microscopy, Phase-Contrast
*Plant Physiology
Rhizobium/*physiology
Support, Non-U.S. Gov't
*Symbiosis
Time Factors},
   Year = {1985} }




@article{
Milovidov28,
   Author = {Milovidov, P. F.},
   Title = {Ein neuer Leguminosen-kn\"ollchenmikrob (\emph{Bacterium radicicola}
forma \emph{carmichaeliana})},
   Journal = {Centralblatt f\"ur Bakteriologie},
   Volume = {2},
   Number = {68},
   Pages = {333-345},
      Year = {1928} }




@article{
Mindell96,
   Author = {Mindell, D. P. and Thacker, C. E.},
   Title = {Rates of molecular evolution: Phylogenetic issues and applications},
   Journal = {Annual Review of Ecology and Systematics},
   Volume = {27},
   Pages = {279-303},
      Year = {1996} }




@article{
Misof02,
   Author = {Misof, B. and Anderson, C. L. and Buckley, T. R. and Erpenbeck, D. and Rickert, A. and Misof, K.},
   Title = {An empirical analysis of mt 16S rRNA covarion-like evolution in insects: Site-specific rate variation is clustered and frequently detected},
   Journal = {Journal of Molecular Evolution},
   Volume = {55},
   Number = {4},
   Pages = {460-469},
   Abstract = {The structural and functional analysis of rRNA molecules has attracted considerable scientific interest. Empirical studies have demonstrated that sequence variation is not directly translated into modifications of rRNA secondary structure. Obviously, the maintenance of secondary structure and sequence variation are in part governed by different selection regimes. The nature of those selection regimes still remains quite elusive. The analysis of individual bacterial models cannot adequately explore this topic. Therefore, we used primary sequence data and secondary structures of a mitochondrial 16S rRNA fragment of 558 insect species from 15 monophyletic groups to study patterns of sequence variation, and variation of secondary structure. Using simulation studies to establish significance levels of change, we found that despite conservation of secondary structure, the location of sequence variation within the conserved rRNA structure changes significantly between groups of insects. Despite our conservative estimation procedure we found significant site-specific rate changes at 56 sites out of 184. Additionally, site-specific rate variation is somewhat clustered in certain helices. Both results confirm what has been predicted from an application of non-stationary maximum likelihood models to rRNA sequences. Clearly, constraints on sequence variation evolve and leave footprints in the form of evolutionary plasticity in rRNA sequences. Here, we show that a better understanding of the evolution of rRNA sequences can be obtained by integrating both phylogenetic and structural information.},
   Keywords = {Covarion
Evolutionary plasticity
mt 16S rRNA
Secondary structure
Site-specific rate variation},
   Year = {2002} }




@article{
Mitchell02,
   Author = {Mitchell, A. D. and Heenan, P. B.},
   Title = {\emph{Sophora} sect.~\emph{Edwardsia} (Fabaceae): further evidence from nrDNA sequence data of a recent and rapid radiation around the Southern Oceans},
   Journal = {Botanical Journal of the Linnean Society},
   Volume = {140},
   Number = {4},
   Pages = {435-441},
   Abstract = {Phylogenetic relationships are inferred from nuclear ribosomal internal transcribed spacer sequences for species belonging to Sophora sect. Edwardsia from South America, New Zealand, Lord Howe Island, Hawai'i, La Reunion, Easter Island, and Raivavae Island (French Polynesia). Results support the monophyly of sect. Edwardsia, but relationships among the species from this section are poorly resolved due to most species having identical sequences. The origin of Sophora sect. Edwardsia is discussed, as competing hypotheses have proposed the group originated in South America from a North American ancestor, or in the north-west Pacific. We suggest sect. Edwardsia may have arisen in the north-west Pacific from a Eurasian ancestor.c The Linnean Society of London, Botanical Journal of the Linnean Society, 2002, 140, 435-441.},
      Year = {2002} }




@article{
Mithofer02,
   Author = {Mithofer, A.},
   Title = {Suppression of plant defence in rhizobia--legume symbiosis},
   Journal = {Trends in Plant Science},
   Volume = {7},
   Number = {10},
   Pages = {440-4},
   Abstract = {The symbiosis between rhizobia and legumes is characterized by the formation of dinitrogen-fixing root nodules. Although rhizobia colonize roots in a way that is reminiscent of pathogenic microorganisms, no host plant defence reactions are triggered during successful symbioses. Nevertheless, the plants obviously control the invading bacteria; failure in effective nodule formation or infections with rhizobia defective in surface polysaccharides often result in pathogenic responses. This article focuses on whether and how defence responses in effective symbiosis might be suppressed. Recent results suggest a central role for rhizobial polysaccharides acting as antagonists in the negative regulation of defence induction.},
   Keywords = {Carbohydrate Sequence
Fabaceae/genetics/*growth \& development/microbiology
Immunity, Natural/genetics
Molecular Sequence Data
Molecular Structure
Oligosaccharides/chemistry/metabolism
Plant Diseases/genetics/microbiology
Plant Roots/genetics/growth \& development/microbiology
Polysaccharides, Bacterial/chemistry/metabolism
Rhizobiaceae/genetics/*growth \& development/metabolism
Support, Non-U.S. Gov't
Symbiosis/genetics/*physiology},
   Year = {2002} }




@article{
Mitra04,
   Author = {Mitra, R. M. and Shaw, S. L. and Long, S. R.},
   Title = {Six nonnodulating plant mutants defective for Nod factor-induced transcriptional changes associated with the legume-rhizobia symbiosis},
   Journal = {Proceedings of the National Academy of Sciences of the United States of America},
   Volume = {101},
   Number = {27},
   Pages = {10217-10222},
   Abstract = {As the legume-rhizobia symbiosis is established, the plant recognizes bacterial-signaling molecules, Nod factors (NFs), and initiates transcriptional and developmental changes within the root to allow bacterial invasion and the construction of a novel organ, the nodule. Plant mutants defective in nodule initiation (Nod(-)) are thought to have defects in NF-signal transduction. However, it is unknown whether WT plants respond to NF-independent bacterial-derived signals or whether Nod- plant mutants show defects in global symbiosis-associated gene expression. To characterize plant gene expression in the establishment of the symbiosis, we used an Affymetrix oligonucleotide microarray representing 9,935 Medicago truncatula expressed sequences. We identified 46 sequences that are differentially expressed in plants exposed for 24 h to WT Sinorhizobium meliloti or to the invasion defective S. meliloti mutant, exoA. Eight of these genes encode nucleolar proteins, which are implicated in ribosome biogenesis. We also identified differentially expressed transcription factors, signaling components, defense response proteins, stress response proteins, and several previously uncharacterized genes. NF appears both necessary and sufficient to induce most changes. Six of seven Nod(-) M. truncatula mutants (nfp, dmi1, dmi2, dmi3, nsp1, and nsp2) showed no transcriptional response to S. meliloti, suggesting that the encoded proteins are required for initiating new transcription. The Nod- mutant hcl, however, exhibits a reduced transcriptional response to S. meliloti, indicating that the machinery responsible for initiating new transcription is at least partially functional in this mutant.},
      Year = {2004} }




@article{
Molouba99,
   Author = {Molouba, Flore and Lorquin, Jean and Willems, Anne and Hoste, Bart and Giraud, Eric and Dreyfus, Bernard and Gillis, Monique and de Lajudie, Philippe and Masson-Boivin, Catherine},
   Title = {Photosynthetic Bradyrhizobia from Aeschynomene spp. Are Specific to Stem-Nodulated Species and Form a Separate 16S Ribosomal DNA Restriction Fragment Length Polymorphism Group},
   Journal = {Applied and Environmental Microbiology},
   Volume = {65},
   Number = {7},
   Pages = {3084-1427},
   Abstract = {We obtained nine bacterial isolates from root or collar nodules of the non-stem-nodulated Aeschynomene species A. elaphroxylon, A. uniflora, or A. schimperi and 69 root or stem nodule isolates from the stem-nodulated Aeschynomene species A. afraspera, A. ciliata, A. indica, A. nilotica, A. sensitiva, and A. tambacoundensis from various places in Senegal. These isolates, together with 45 previous isolates from various Aeschynomene species, were studied for host-specific nodulation within the genus Aeschynomene, also revisiting cross-inoculation groups described previously by D. Alazard (Appl. Environ. Microbiol. 50:732-734, 1985). The whole collection of Aeschynomene nodule isolates was screened for synthesis of photosynthetic pigments by spectrometry, high-pressure liquid chromatography, and thin-layer chromatography analyses. The presence of puf genes in photosynthetic Aeschynomene isolates was evidenced both by Southern hybridization with a Rhodobacter capsulatus photosynthetic gene probe and by DNA amplification with primers defined from photosynthetic genes. In addition, amplified 16S ribosomal DNA restriction analysis was performed on 45 Aeschynomene isolates, including strain BTAi1, and 19 reference strains from Bradyrhizobium japonicum, Bradyrhizobium elkanii, and other Bradyrhizobium sp. strains of uncertain taxonomic positions. The 16S rRNA gene sequence of the photosynthetic strain ORS278 (LMG 12187) was determined and compared to sequences from databases. Our main conclusion is that photosynthetic Aeschynomene nodule isolates share the ability to nodulate particular stem-nodulated species and form a separate subbranch on the Bradyrhizobium rRNA lineage, distinct from B. japonicum and B. elkanii.},
      Year = {1999} }




@article{
Moreira98,
   Author = {Moreira, F. M. S. and Haukka, K. and Young, J. P. W.},
   Title = {Biodiversity of rhizobia isolated from a wide range of forest legumes in Brazil},
   Journal = {Molecular Ecology},
   Volume = {7},
   Number = {7},
   Pages = {889-895},
   Abstract = {Tropical forests have a high diversity of plant species; are they associated with a correspondingly rich microbial flora? We addressed this question by examining the symbiotic rhizobium bacteria that nodulate a diverse pool of forest legume species in Brazil. The 44 strains studied had been isolated from 29 legume tree species representing 13 tribes including all three subfamilies of the Leguminosae, and were chosen to represent major groups from a larger sample that had previously been characterized by SDS-PAGE of total proteins. Partial 16S rRNA gene sequence was determined, corresponding to positions 44-303 in the Escherichia coli sequence. Fifteen sequences were found, including six novel ones. However, all but one of them could be assigned to a genus because they grouped closely with sequences from previously described rhizobial species. Fast-growing strains had sequences similar to Rhizobium spp., Sinorhizobium spp. or Mesorhizobium spp., while the slow-growing strains had sequences similar to Bradyrhizobium spp. One strain with an intermediate growth rate had a unique sequence which indicated that the strain might belong to the genus Azorhizobium. Although the strains showed a variety of sequences, it was surprising that these strains isolated from taxonomically very diverse host plants in previously unexplored environments were mostly very similar to strains described previously, largely from agricultural systems.},
      Year = {1998} }




@article{
Morris02,
   Author = {Morris, C. E. and Bardin, M. and Girardin, H. and Guinebreti\`ere, M.-H. and Berge, O. and Frey-Klett, P. and Lebaron, P. and Thi\'ery, J. M. and Troussellier, M. and Fromin, N.},
   Title = {Microbial biodiversity: Approaches to experimental design and hypothesis testing in primary scientific literature from 1975 to 1999},
   Journal = {Microbiology and Molecular Biology Reviews},
   Volume = {66},
   Number = {4},
   Pages = {592-616},
   Abstract = {Research interest in microbial biodiversity over the past 25 years has increased markedly as microbiologists have become interested in the significance of biodiversity for ecological processes and as the industrial, medical, and agricultural applications of this diversity have evolved. One major challenge for studies of microbial habitats is how to account for the diversity of extremely large and heterogeneous populations with samples that represent only a very small fraction of these populations. This review presents an analysis of the way in which the field of microbial biodiversity has exploited sampling, experimental design, and the process of hypothesis testing to meet this challenge. This review is based on a systematic analysis of 753 publications randomly sampled from the primary scientific literature from 1975 to 1999 concerning the microbial biodiversity of eight habitats related to water, soil, plants, and food. These publications illustrate a dominant and growing interest in questions concerning the effect of specific environmental factors on microbial biodiversity, the spatial and temporal heterogeneity of this biodiversity, and quantitative measures of population structure for most of the habitats covered here. Nevertheless, our analysis reveals that descriptions of sampling strategies or other information concerning the representativeness of the sample are often missing from publications, that there is very limited use of statistical tests of hypotheses, and that only a very few publications report the results of multiple independent tests of hypotheses. Examples are cited of different approaches and constraints to experimental design and hypothesis testing in studies of microbial biodiversity. To prompt a more rigorous approach to unambiguous evaluation of the impact of microbial biodiversity on ecological processes, we present guidelines for reporting information about experimental design, sampling strategies, and analyses of results in publications concerning microbial biodiversity.},
      Year = {2002} }




@article{
Moulin04,
   Author = {Moulin, Lionel and Bena, Gilles and Boivin-Masson, Catherine and St{\c e}pkowski , Tomasz},
   Title = {Phylogenetic analyses of symbiotic nodulation genes support vertical and lateral gene co-transfer within the \emph{Bradyrhizobium} genus},
   Journal = {Molecular Phylogenetics and Evolution},
   Volume = {30},
   Number = {3},
   Pages = {720-732},
   Abstract = {Symbiotic nitrogen fixing bacteria--known as rhizobia--harbour a set of nodulation (nod) genes that control the synthesis of modified lipo-chitooligosaccharides, called Nod factors that are required for legume nodulation. The nodA gene, which is essential for symbiosis, is responsible for the attachment of the fatty acid group to the oligosaccharide backbone. The nodZ, nolL, and noeI genes are involved in specific modifications of Nod factors common to bradyrhizobia, i.e., the transfer of a fucosyl group on the Nod factor core, fucose acetylation and fucose methylation, respectively. PCR amplification, sequencing and phylogenetic analysis of nodA gene sequences from a collection of diverse Bradyrhizobium strains revealed the monophyletic character with the possible exception of photosynthetic Bradyrhizobium, despite high sequence diversity. The distribution of the nodZ, nolL, and noeI genes in the studied strains, as assessed by gene amplification, hybridization or sequencing, was found to correlate with the nodA tree topology. Moreover, the nodA, nodZ, and noeI phylogenies were largely congruent, but did not closely follow the taxonomy of the strains shown by the housekeeping 16S rRNA and dnaK genes. Additionally, the distribution of nodZ, noeI, and nolL genes suggested that their presence may be related to the requirements of their legume hosts. These data indicated that the spread and maintenance of nodulation genes within the Bradyrhizobium genus occurred through vertical transmission, although lateral gene transfer also played a significant role.},
      Year = {2004} }




@article{
Moulin01,
   Author = {Moulin, L. and Munive, A. and Dreyfus, B. and Boivin-Masson, C.},
   Title = {Nodulation of legumes by members of the beta-subclass of Proteobacteria},
   Journal = {Nature},
   Volume = {411},
   Number = {6840},
   Pages = {948-50},
   Abstract = {Members of the Leguminosae form the largest plant family on Earth, with around 18,000 species. The success of legumes can largely be attributed to their ability to form a nitrogen-fixing symbiosis with specific bacteria known as rhizobia, manifested by the development of nodules on the plant roots in which the bacteria fix atmospheric nitrogen, a major contributor to the global nitrogen cycle. Rhizobia described so far belong exclusively to the alpha-subclass of Proteobacteria, where they are distributed in four distinct phylogenetic branches. Although nitrogen-fixing bacteria exist in other proteobacterial subclasses, for example Herbaspirillum and Azoarcus from the phylogenetically distant beta-subclass, none has been found to harbour the nod genes essential for establishing rhizobial symbiosis. Here we report the identification of proteobacteria from the beta-subclass that nodulate legumes. This finding shows that the ability to establish a symbiosis with legumes is more widespread in bacteria than anticipated to date.},
   Keywords = {Burkholderia
classification
genetics
DNA
Bacterial
Ribosomal
Fabaceae
microbiology
Genes
Molecular Sequence Data
Mutagenesis
Nitrogen Fixation
Phylogeny
Plant Roots
Plants
Medicinal
RNA
16S
Symbiosis
beta Proteobacteria
isolation \& purification
physiology},
   Year = {2001} }




@article{
Mukhopadhyay95,
   Author = {Mukhopadhyay, D. and Tsiokas, L. and Zhou, X.-M. and Foster, D. and Brugge, J. S. and Sukhatme, V. P.},
   Title = {Hypoxic induction of human vascular endothelial growth factor expression through c-Src activation},
   Journal = {Nature},
   Volume = {375},
   Number = {6532},
   Pages = {577-581},
   Abstract = {Angiogenesis, the formation of new microvasculature by capillary sprouting, is crucial for tumour development. Hypoxic regions of solid tumours produce the powerful and directly acting angiogenic protein VEGF/VPF (vascular endothelial growth factor/vascular permeability factor). We now investigate the signal transduction pathway involved in hypoxic induction of VEGF expression. Hypoxia is known to induce a tyrosine kinase cascade that results in the activation of nitrogen-fixation genes in Rhizobium meliloti, and activation of tyrosine kinases is critical in signalling triggered by growth factors and ultraviolet light. We show here that genistein, an inhibitor of protein tyrosine kinases, blocks VEGF induction. Hypoxia increases the kinase activity of pp60(c-src) and its phosphorylation on tyrosine 416 but does not activate Fyn or Yes. Expression of either a dominant-negative mutant form of c-Src or of Raf-1 markedly reduces VEGF induction, VEGF induction by hypoxia in c-src(-) cells is impaired, although there is a compensatory activation of Fyn. Our results provide an insight into hypoxia-triggered intracellular signalling, define VEGF as a new downstream target for c-Src, and suggest a role for c-Src in promoting angiogenesis.},
      Year = {1995} }




@article{
Mullin87,
   Author = {Mullin, D. and Minnich, S. and Chen, L. S. and Newton, A.},
   Title = {A set of positively regulated flagellar gene promoters in Caulobacter crescentus with sequence homology to the nif gene promoters of Klebsiella pneumoniae.},
   Journal = {Journal of Molecular Biology},
   Volume = {195},
   Number = {4},
   Pages = {939-943},
   Abstract = {The study reported here describes nuclease S1 mapping of the in-vivo transcription start sites of transcription units I and III of the hook gene cluster of Caulobacter crescentus. We show that transcription units I and II of this flagellar (fla) gene cluster, which have divergent promoters with transcription start sites separated by 218 nucleotides, are under positive transcriptional control by genes in transcription unit III. The promoters of transcription units I, II, and III were compared with flagellin gene promoters P25, P27 and P29 recently identified in C. crescentus. Promoters PII, P25, and P27, which are under positive regulation by transcription units III to V have strongly conserved sequence elements at -13 and -24 with the consensus sequence (C/T)TGGC(C/G)C-N5-TTGC. The -13, -24 sequence elements are not well conserved in promoter PI, but the promoter does contain a copy of the -13 and -24 consensus sequence 23 base-pairs upstream (PI). The C. crescentus fla gene promoters are not homologous to the canonical Escherichia coli -10, -35 promoter sequence, but they are very similar to the -12, -24 nif gene promoter sequence reported for Klebsiella pneumoniae and Rhizobium sp. The four positively regulated fla gene promoters examined here also share a third conserved element designated II-1, with the consensus sequence C-C-CGGC--AAA--GC-G, located at approximately -100. We speculate that the conserved sequence elements mapping at -13, -24 and -100 are cis-acting regulatory elements required for the transcription and periodic regulation of these fla genes in the C. crescentus cell cycle.},
   Keywords = {bacterial gene
promoter region
Genes, Bacterial
Promoter Regions (Genetics)},
   Year = {1987} }




@article{
Murphy87,
   Author = {Murphy, P.J. and Heycke, N. and Banfalvi, Z.},
   Title = {Genes for the catabolism and synthesis of an opine-like compound in Rhizobium meliloti are closely linked and on the Sym plasmid},
   Journal = {Proceedings of the National Academy of Sciences of the United States of America},
   Volume = {84},
   Number = {2},
   Pages = {493-497},
   Abstract = {In alfalfa nodules induced by Rhizobium meliloti strain L5-30 the compound L-3-O-methyl-scyllo-inosamine (3-O-MSI) is synthesized. This compound is also catabolized specifically by this strain. Its biological properties are therefore similar to the Agrobacterium opines. To answer the question whether opine-like compounds ('Rhizopines') play a role in a plant symbiotic interaction, we isolated the genes for the catabolism of 3-O-MSI (moc genes) and for the induction of its synthesis in the nodule [mos gene(s)]. moc and mos genes were shown to be closely linked and located on the Sym plasmid of L5-30, suggesting that they have co-evolved and may be important in symbiosis. These genes have been cloned into a broad host-range vector that can be mobilized into other R. meliloti strains where they are expressed. The location of the mos genes in the bacteria extends the opine concept, initially developed for a plant pathological interaction, to a symbiotic one.},
      Year = {1987} }




@article{
Murray86,
   Author = {Murray, D. R.},
   Title = {Seed dispersal by water},
   Journal = {Seed Dispersal},
   Pages = {49-85},
      Year = {1986} }




@article{
Musiyiwa05,
   Author = {Musiyiwa, K. and Mpepereki, S. and Giller, K. E. and Musiyiwa, K.},
   Title = {Symbiotic effectiveness and host ranges of indigenous rhizobia nodulating promiscuous soyabean varieties in Zimbabwean soils},
   Journal = {Soil Biology and Biochemistry},
   Volume = {37},
   Number = {6},
   Pages = {1169-1176},
   Abstract = {Presence of indigenous rhizobia nodulating promiscuous soyabean was determined in 92, mainly sandy soils, from wetter agro-ecological zones of Zimbabwe suited to soyabean production. A total of 129 isolates were obtained from nodules of promiscuous soyabean varieties, Magoye and Hernon 147, and a specific variety, Roan grown in potted soils. Magoye nodulated in 80%, Hernon 147 in 50% and Roan in only 25% of the 92 soils tested. Rhizobia populations ranged from undetectable to 2.4×10<sup>4</sup> cells g<sup>-1</sup> of soil. Twenty-one of these isolates were tested for symbiotic effectiveness on two varieties, promiscuous Magoye and specific Roan. Differences in parameters such as nodule numbers, nodule weights and total N fixed reflected diversity among the indigenous isolates. Three isolates had significantly higher N <sub>2</sub>-fixing potential in comparison with the commercial strain MAR 1491 on promiscuous Magoye. Host ranges of 34 isolates were evaluated on nine legume species: Arachis hypogaea, Cajanus cajan, Crotalaria juncea, Glycine max, Macroptilium atropurpureum, Phaseolus vulgaris, Sesbania sesbania, Vigna subterranea, Vigna unguiculata. Of these 34 isolates, 33 formed nodules with M. atropurpureum of which 61% were moderately effective to very effective while all nodulated V. unguiculata with 58% being moderately effective to very effective. Twenty-eight isolates nodulated V. subterranea and C. cajan (short season variety) with 76 and 36% of these being moderately to very effective, respectively. None of the isolates formed nodules on Phaseolus vulgaris, Arachis hypogaea or Sesbania sesban. Our results indicate that the ability of even specific varieties of soyabean to nodulate with indigenous isolates in African soils is greater than generally assumed. © 2005 Elsevier Ltd. All rights reserved.},
   Keywords = {Host range
Indigenous rhizobia
Promiscuous soyabean
Symbiotic effectiveness},
   Year = {2005} }




@article{
Mutch04,
   Author = {Mutch, L. A. and Young, J. P. W.},
   Title = {Diversity and specificity of Rhizobium leguminosarum biovar viciae on wild and cultivated legumes},
   Journal = {Molecular Ecology},
   Volume = {13},
   Number = {8},
   Pages = {2435-2444},
   Abstract = {The symbiotic partnerships between legumes and their root-nodule bacteria (rhizobia) vary widely in their degree of specificity, but the underlying reasons are not understood. To assess the potential for host-range evolution, we have investigated microheterogeneity among the shared symbionts of a group of related legume species. Host specificity and genetic diversity were characterized for a soil population of Rhizobium leguminosarum biovar viciae (Rlv) sampled using six wild Vicia and Lathyrus species and the crop plants pea (Pisum sativum) and broad bean (Vicia faba). Genetic variation among 625 isolates was assessed by restriction fragment length polymorphism (RFLP) of loci on the chromosome (ribosomal gene spacer) and symbiosis plasmid (nodD region). Broad bean strongly favoured a particular symbiotic genotype that formed a distinct phylogenetic subgroup of Rlv nodulation genotypes but was associated with a range of chromosomal backgrounds. Host range tests of 80 isolates demonstrated that only 34% of isolates were able to nodulate V. faba. By contrast, 89% were able to nodulate all the local wild hosts tested, so high genetic diversity of the rhizobial population cannot be ascribed directly to the diversity of host species at the site. Overall the picture is of a population of symbionts that is diversified by plasmid transfer and shared fairly indiscriminately by local wild legume hosts. The crop species are less promiscuous in their interaction with symbionts than the wild legumes.},
      Year = {2004} }




@article{
Mutch03,
   Author = {Mutch, L. A. and Young, J. P. W. and Tamimi, S. M.},
   Title = {Genotypic characterisation of rhizobia nodulating Vicia faba from the soils of Jordan: A comparison with UK isolates},
   Journal = {Soil Biology and Biochemistry},
   Volume = {35},
   Number = {5},
   Pages = {709-714},
   Abstract = {Seven isolates of Rhizobium leguminosarum bv. viciae (Rlv) that nodulate faba beans (Vicia faba) from six sites in Jordan were characterised for chromosomal (glnII) and symbiotic (nodD-F) genotypes using polymerase chain reaction-restriction fragment length polymorphism and sequencing methods. The results were compared to those obtained in a previous UK study, to determine whether or not the UK field population are indigenous or if they were dispersed during the radiation of V. faba domestication. All seven Jordanian isolates displayed novel chromosomal and symbiotic genotypes not identified in the UK population. © 2003 Elsevier Science Ltd. All rights reserved.},
   Keywords = {Genotype
Jordan
Polymerase chain reaction-restriction fragment length polymorphism
Rhizobia
United Kingdom
Vicia faba},
   Year = {2003} }




@inproceedings{
Nandasena05,
   Author = {Nandasena, K. G. and Tiwari, R. P. and O'Hara, G. W. and Howieson, J. G.},
   Title = {Why is it necessary to manage the \emph{in situ} development of poorly effective promiscuous rhizobia?},
   BookTitle = {14th Australian nitrogen fixation conference},
   Editor = {Brockwell, J.},
   Address= {Katoomba, Australia},
   Publisher = {The Australian Society for Nitrogen Fixation},
   Pages = {114-122},
      Year = {2005} }




@article{
Nazaret91,
   Author = {Nazaret, S. and Cournoyer, B. and Normand, P. and Simonet, P.},
   Title = {Phylogenetic relationships among Frankia genomic species determined by use of amplified 16S rDNA sequences},
   Journal = {Journal of Bacteriology},
   Volume = {173},
   Number = {13},
   Pages = {4072-4078},
   Abstract = {Actinomycetes of the genus Frankia establish a nitrogen-fixing symbiosis with a large number of woody dicotyledonous plants. Hundreds of strains isolated from various actinorhizal plants growing in different geographical areas have recently been classified into at least nine genomic species by use of the DNA-DNA hybridization technique (M. P. Fernandez, H. Meugnier, P. A. D. Grimont, and R. Bardin, Int. J. Syst. Bacteriol. 39:424-429, 1989). A protocol based on the amplification and sequencing of 16S ribosomal DNA segments was used to classify and estimate the phylogenetic relationships among eight different genomic species. A good correlation was established between the grouping of strains according to their 16S ribosomal DNA sequence homology and that based on total DNA homology, since most genomic species could be characterized by a specific sequence. The phylogenetic tree showed that strains belonging to the Alnus infectivity group are closely related to strains belonging to the Casuarina infectivity group and that strains of these two infectivity groups are well separated from strains of the Elaeagnus infectivity group, which also includes atypical strains isolated from the Casuarina group. This phylogenetic analysis was also very efficient for classifying previously unclassified pure cultures or unisolatable strains by using total DNA extracted directly from nodules.},
      Year = {1991} }




@article{
Neves97,
   Author = {Neves, M. C. P. and Rumjanek, N. G.},
   Title = {Diversity and adaptability of soybean and cowpea rhizobia in tropical soils},
   Journal = {Soil Biology and Biochemistry},
   Volume = {29},
   Number = {5-6},
   Pages = {889-895},
   Abstract = {The current interest on biodiversity, allied with the use of powerful molecular biology techniques, are revealing the nodulation abilities of tropical legumes, their preferences in terms of relationships with rhizobia, the dynamics of the rhizobia population, and data are accumulating on the cowpea group of tropical rhizobia. Studies on the ecology of cowpea-nodulating rhizobia in soils from the semi-arid region of Brazil, are providing an understanding of the ecology of soybean nodulating rhizobia in Brazilian soils and are revealing a large community of native strains capable of nodulating soybeans in soils where soybeans never have been planted. Many isolates showed a limited ability to nodulate soybean roots and formed nodule-like structures, or pseudo-nodules. Recent host range analysis of known rhizobia species has generated substantial data that is rapidly changing recognized patterns of symbiotic specificity. Cowpeas, soybeans and common beans nodulate with many different species of rhizobia, and the occurrence of both slow- and fast-growing strains in the same plant species has been reported for many genera of tropical legumes. This review will focus on recent data on the diversity of tropical rhizobia and their adaptability to tropical soils. Copyright (C) 1996 Elsevier Science Ltd.},
      Year = {1997} }




@article{
Ngom04,
   Author = {Ngom, A. and Nakagawa, Y. and Sawada, H. and Tsukahara, J. and Wakabayashi, S. and Uchiumi, T. and Nuntagij, A. and Kotepong, S. and Suzuki, A. and Higashi, S. and Abe, M.},
   Title = {A novel symbiotic nitrogen-fixing member of the Ochrobactrum clade isolated from root nodules of Acacia mangium},
   Journal = {Journal of General and Applied Microbiology},
   Volume = {50},
   Number = {1},
   Pages = {17-28},
   Abstract = {Ten strains of root nodule bacteria were isolated from the nodules of Acacia mangium grown in the Philippines and Thailand. Partial sequences (approx. 300 bp) of the 16 SrRNA gene of each isolate were analyzed. The nucleotide sequences of strain DASA 35030 indicated high homology (>99%) with members of the genus Ochrobactrum in Brucellaceae, although the sequences of other isolates were homologous to those of two distinct genera Bradyrhizobium and Rhizobium. The strain DASA 35030 was strongly suggested to be a strain of Ochrobactrum by full length sequences of the 16 SrRNA gene, fatty acids composition, G+C contents of the DNA, and other physiological characteristics. Strain DASA 35030 induced root nodules on A. mangium, A. albida and Paraserianthes falcataria. The nodules formed by strain DASA 35030 fixed nitrogen and the morphology of the nodules is the same as those of nodules formed by the other isolates. This is the first report that the strain of Ochrobactrum possesses complete symbiotic ability with Acacia.},
      Year = {2004} }




@article{
Nicholas97,
   Author = {Nicholas, K. B. and Nicholas, Jr., H. B. and Deerfield, II, D. W.},
   Title = {GeneDoc: Analysis and visualization of genetic variation},
   Journal = {EMBNEW News},
   Volume = {4},
   Pages = {14},
      Year = {1997} }




@article{
Nick99,
   Author = {Nick, G. and de Lajudie, P. and Eardly, B. D. and Suomalainen, S. and Paulin, L. and Zhang, X. P. and Gillis, M. and Lindstr\"om, K.},
   Title = {\emph{Sinorhizobium arboris} sp. nov. and \emph{Sinorhizobium kostiense} sp. nov., isolated from leguminous trees in Sudan and Kenya},
   Journal = {International Journal of Systematic Bacteriology},
   Volume = {49},
   Number = {4},
   Pages = {1359-1368},
   Abstract = {SDS-PAGE of total bacterial proteins was applied to the classification of 25 Sudanese and five Kenyan strains isolated from the root nodules of Acacia senegal and Prosopis chilensis. Twenty strains were also studied by multilocus enzyme electrophoresis (MLEE) and the whole 16S rRNA gene was sequenced from two strains representing the two major clusters. These results, together with the previously reported numerical taxonomy analysis, pulsed-field gel electrophoresis studies, DNA-DNA dot-blot hybridization, genomic fingerprinting using repetitive sequence-based PCR, DNA base composition analysis, DNA-DNA reassociation analysis, partial sequencing of the 16S rRNA gene and RFLP analysis of the amplified 16S rRNA gene, showed that all 30 strains belong to the genus Sinorhizobium. Two of the strains grouped with Sinorhizobium saheli and seven with Sinorhizobium terangae, while the rest did not cluster with any of the established species. The majority of the strains formed two phenotypically and genotypically distinct groups and we therefore propose that these strains should be classified as two new species. Sinorhizobium arboris sp. nov. and Sinorhizobium kostiense sp. nov.},
      Year = {1999} }




@article{
Nienaber01,
   Author = {Nienaber, A. and Hennecke, H. and Fischer, H. M.},
   Title = {Discovery of a haem uptake system in the soil bacterium Bradyrhizobium japonicum},
   Journal = {Molecular Microbiology},
   Volume = {41},
   Number = {4},
   Pages = {787-800},
   Abstract = {In Bradyrhizobium japonicum, the nitrogen-fixing symbiont of soybeans, we have identified a haem uptake system, Hmu, that comprises a cluster of nine open reading frames. Predicted products of these genes include: HmuR, a TonB-dependent haem receptor in the outer membrane; HmuT, a periplasmic haem-binding protein; and HmuUV, an ABC transporter in the inner membrane. Furthermore, we identified homologues of ExbBD and TonB, that are required for energy transduction from the inner to the outer membrane. Mutant analysis and complementation tests indicated that HmuR and the ExbBD-TonB system, but not the HmuTUV transporter, are essential for haem uptake or haem acquisition from haemoglobin and leghaemoglobin. The TonB system seems to be specific for haem uptake as it is dispensable for siderophore uptake. Therefore, we propose the existence of a second TonB homologue functioning in the uptake of Fe-chelates. When tested on soybean host plants, hmuT-hmuR and exbD-tonB mutants exhibited wild-type symbiotic properties. Thus, haem uptake is not essential for symbiotic nitrogen fixation but it may enable B. japonicum to have access to alternative iron sources in its non-symbiotic state. Transcript analysis and expression studies with lacZ fusions showed that expression of hmuT and hmuR is induced under low iron supply. The same was observed in fur and irr mutant backgrounds although maximal induction levels were decreased. We conclude either that both regulators, Fur and Irr, independently mediate transcriptional control by iron or that a yet unknown iron regulatory system activates gene expression under iron deprivation. An A/T-rich cis-acting element, located in the promoter region of the divergently transcribed hmuTUV and hmuR genes, is possibly required for this type of iron control.},
      Year = {2001} }




@article{
Nishimura02,
   Author = {Nishimura, R. and Ohmori, M. and Fujita, H. and Kawaguchi, M.},
   Title = {A Lotus basic leucine zipper protein with a RING-finger motif negatively regulates the developmental program of nodulation},
   Journal = {Proceedings of the National Academy of Sciences of the United States of America},
   Volume = {99},
   Number = {23},
   Pages = {15206-10},
   Abstract = {The developmental program of nodulation is regulated systemically in leguminous host species. A mutant astray (Ljsym77) in Lotus japonicus has lost some sort of its ability to regulate this symtem, and shows enhanced and early nodulation. In the absence of rhizobia, this mutant exhibits characteristics associated with defects in light and gravity responses. These nonsymbiotic phenotypes of astray are very similar to those observed in photomorphogenic Arabidopsis mutant hy5. Based on this evidence, we predicted that astray might contain a mutation in the HY5 homologue of L. japonicus. The homologue, named LjBzf, encodes a basic leucine zipper protein in the C-terminal half that shows the highest level of identity with HY5 of all Arabidopsis proteins. It also encodes legume-characteristic combination of motifs, including a RING-finger motif and an acidic region in the N-terminal half. The astray phenotypes were cosegregated with LjBzf, and the failure to splice the intron was detected. Nonsymbiotic and symbiotic phenotypes of astray were complemented by introduction of CaMV35SLjBzf. It is noteworthy that although Arabidopsis hy5 showed an enhancement of lateral root initiation, Lotus astray showed an enhancement of nodule initiation but not of lateral root initiation. Legume-characteristic combination of motifs of ASTRAY may play specific roles in the regulation of nodule development.},
   Keywords = {Amino Acid Sequence
Base Sequence
DNA Primers
Gene Expression Regulation, Developmental
Gene Expression Regulation, Plant
Genetic Vectors
Glucuronidase/genetics
Hypocotyl/physiology
Leucine Zippers/*physiology
Lotus/growth \& development/*physiology
Molecular Sequence Data
Nuclear Proteins/*genetics
Plant Proteins/*genetics
Plant Roots/physiology
Plants, Genetically Modified
Polymorphism (Genetics)
Reverse Transcriptase Polymerase Chain Reaction
Sequence Alignment
Sequence Homology, Amino Acid
Support, Non-U.S. Gov't
Symbiosis},
   Year = {2002} }




@article{
Noreen03,
   Author = {Noreen, S. and Schlaman, H. R. M. and Bellog\'in, R. A. and Buendia-Claveria, A. M. and Espuny, M. R. and Harteveld, M. and Medina, C. and Ollero, F. J. and Olsthoorn, M. M. A. and Soria-Diaz, M. E. and Spaink, H. P. and Temprano, F. and Thomas-Oates, J. and Vinardell, J. M. and Yang, S. S. and Zhang, H. Y. and Ru\'iz-Sainz, J. E.},
   Title = {Alfalfa nodulation by Sinorhizobium fredii does not require sulfated Nod-factors},
   Journal = {Functional Plant Biology},
   Volume = {30},
   Number = {12},
   Pages = {1219-1232},
   Abstract = {Rhizobium strain 042B(s) is able to nodulate both soybean and alfalfa cultivars. We have demonstrated, by mass spectrometry, that the nodulation (Nod) factors produced by this strain are characteristic of those produced by Sinorhizobium fredii, which typically nodulates soybean; they have 3-5 N-acetylglucosamine (GlcNAc) residues, a mono-unsaturated or saturated C16, C18 or C20 fatty-acyl chain, and a (methyl) fucosyl residue on C6 of the reducing-terminal GlcNAc. In order to study Rhizobium strain 042B(s) and its nodulation behaviour further, we introduced an insertion mutation in the noeL gene, which is responsible for the presence of the (methyl) fucose residue on the reducing terminal GlcNAc of the Nod-factors, yielding mutant strain SVQ523. A plasmid (pHM500) carrying nodH, nodP and nodQ, the genes involved in sulfation of Nod-factors on C6 of the reducing-terminal GlcNAc, was introduced into SVQ523, generating SVQ523. pHM500. As expected, strain SVQ523 produces unfucosylated Nod-factors, while SVQ523. pHM500 produces both unfucosylated and unfucosylated sulfated Nod-factors. Plant tests showed that soybean nodulation was reduced if the inoculant (SVQ523.pHM500) produced sulfated Nod-factors. In the Asiatic alfalfa cultivar Baoding, SVQ523 (absence of a substitution at C6) failed to nodulate, but both 042B(s) (fucosyl at C6) and SVQ523. pHM500 (sulfate at C6) formed nodules. In contrast, SVQ523 showed enhanced nodulation capacity with the western alfalfa cultivars ORCA and ARC. These results indicate that Nod-factor sulfation is not a requisite for S. fredii to nodulate alfalfa.},
      Year = {2003} }




@article{
Normand95,
   Author = {Normand, P.},
   Title = {Utilisation des s\'equences 16S pour le positionnement phyl\'etique d'un organisme inconnu},
   Journal = {Oc\'eanis},
   Volume = {21},
   Pages = {31-56},
      Year = {1995} }




@article{
Normand92,
   Author = {Normand, P. and Cournoyer, B. and Simonet, P. and Nazaret, S.},
   Title = {Analysis of a ribosomal RNA operon in the actinomycete Frankia},
   Journal = {Gene},
   Volume = {111},
   Number = {1},
   Pages = {119-124},
   Abstract = {The organisation of ribosomal RNA-encoding (rrn) genes has been studied in Frankia sp. strain ORS020606. The two rrn clusters present in Frankia strain ORS020606 were isolated from genomic banks in phage ?EMBL3 by hybridization with oligodeoxyribonucleotide probes. The 5'-3' gene order is the usual one for bacteria: 16S-23S-5S. The two clusters are not distinguishable by restriction enzyme mapping inside the coding section, but vary considerably outside it. Sequencing showed that the 16S-rRNA-encoding gene of ORS020606 is very closely related to that of another Alnus-infective Frankia strain (Ag45/Mut15) and highly homologous to corresponding genes of Streptomyces spp. Two possible promoter sequences were detected upstream from the 16S gene, while no tRNA-encoding gene was detected in the whole operon. Regions with a high proportion of divergence for the study of phylogenetic relationships within the genus were looked for and found in the first intergenic spacer, in the 23S and in the 16S gene.},
   Keywords = {16S, 23S, 5S rRNA
actinomycetales
Casuarina
nitrogen-fixing
recombinant DNA},
   Year = {1992} }




@article{
Normand96,
   Author = {Normand, P. and Orso, S. and Cournoyer, B. and Jeannin, P. and Chapelon, C. and Dawson, J. and Evtushenko, L. and Misra, A. K.},
   Title = {Molecular phylogeny of the genus Frankia and related genera and emendation of the family Frankiaceae},
   Journal = {International Journal of Systematic Bacteriology},
   Volume = {46},
   Number = {1},
   Pages = {1-9},
   Abstract = {The members of the actinomycete genus Frankia are nitrogen-fixing symbionts of many species of woody dicotyledonous plants belonging to eight families. Several strains isolated from diverse actinorhizal plants growing in different geographical areas were used in this study. The phylogenetic relationships of these organisms and uncharacterized microsymbionts that are recalcitrant to isolation in pure culture were determined by comparing complete 16S ribosomal DNA sequences. The resulting phylogenetic tree revealed that there was greater diversity among the Alnus-infective strains than among the strains that infect other host plants. The four main subdivisions of the genus Frankia revealed by this phylogenetic analysis are (i) a very large group comprising Frankia alni and related organisms (including Alnus rugosa Sp+ microsymbionts that are seldom isolated in pure culture), to which Casuarina-infective strains, a Myrica nagi microsymbiont, and other effective Alnus-infective strains are related; (ii) unisolated microsymbionts of Dryas, Coriaria, and Datisca species; (iii) Elaeagnus- infective strains; and (iv) 'atypical' strains (a group which includes an Alnus-infective, non-nitrogen-fixing strain). Taxa that are related to this well-defined, coherent Frankia cluster are the genera Geodermatophilus, 'Blastococcus,' Sporichthya, Acidothermus, and Actinoplanes. However, the two genera whose members have multilocular sporangia (the genera Frankia and Geodermatophilus) did not form a coherent group. For this reason, we propose that the family Frankiaceae should be emended so that the genera Geodermatophilus and 'Blastococcus' are excluded and only the genus Frankia is retained.},
      Year = {1996} }




@article{
Norris56,
   Author = {Norris, D. O.},
   Title = {Legumes and the \emph{Rhizobium} symbiosis},
   Journal = {Empire Journal of Experimental Agriculture},
   Volume = {24},
   Pages = {247-270},
      Year = {1956} }




@inproceedings{
Norris65,
   Author = {Norris, D. O.},
   Title = {\emph{Rhizobium} relationships in legumes},
   BookTitle = {Proceedings of the 9th International Grasslands Congress},
   Address= {S\~ao Paulo},
   Volume = {2},
   Pages = {1087-1092},
      Year = {1965} }




@article{
Norton02,
   Author = {Norton, D. A. and Godley, E. J. and Heenan, P. B. and Ladley, J. J.},
   Title = {Germination of Sophora seeds after prolonged storage},
   Journal = {New Zealand Journal of Botany},
   Volume = {40},
   Number = {3},
   Abstract = {Germination of Sophora seeds 24-40 years old from New Zealand (8 species), Chile (2 species), Lord Howe Island, Australia (1 species), and Hawai'i (1 species), and of fresh seed from trees established using seeds from the same seed lots, was assessed. Germination was rapid for most seed lots, with, on average, fresh seed having high germination (77-94%) and stored seed low germination (0-40%). Exceptions to this were old S. chrysophylla seed, which had unusually high germination (84%), and fresh S. longicarinata seed, which had unusually low germination (24%). The results provide further support for the role of long-distance oceanic dispersal for the distribution of Sophora sect. Edwardsia around the Southern Hemisphere, and also suggest that long-term seed storage could be used for the ex situ management of Sophora populations. The results also highlight some intriguing ecological correlates of germination that warrant further study.},
      Year = {2002} }




@article{
Nour94b,
   Author = {Nour, S.M. and Cleyet-Marel, J.-C. and Beck, D. and Effosse, A. and Fernandez, M.P.},
   Title = {Genotypic and phenotypic diversity of \emph{Rhizobium} isolated from chickpea (\emph{Cicer arietinum} L.)},
   Journal = {Canadian Journal of Microbiology},
   Volume = {40},
   Number = {5},
   Pages = {345-354},
   Abstract = {The diversity of 16 strains of chickpea-infective rhizobia from various geographical origins was analysed using genotypic and phenotypic approaches. Multilocus enzyme electrophoresis was performed, and restriction fragment length polymorphisms of the amplified 16S+IGS (intergenic spacer) rRNA gene, assimilation of 147 carbon sources, antibiotic resistance, and tolerance to NaCl and extreme pH values and temperatures were tested. These approaches had different discriminating powers. Esterase polymorphisms gave a unique pattern for each strain, allowing this method to be used for strain fingerprinting. Genetic distances between strains were estimated. The three approaches used in this study yielded consistent results. They evidenced high heterogeneity among the strains, and made it possible to classify the strains into two clusters. Isozyme patterns for superoxide dismutase were particularly interesting, since they delineated the same two groups. The phenotypic tests clearly confirmed the existence of two genetic groups on the basis of 11 phenotypic characters. Owing to the large phylogenetic distance between the two groups of strains, the taxonomic strains of chickpea-infective strains is discussed.},
   Keywords = {genetic diversity
multilocus enzyme electrophoresis
phenotypic diversity
restriction fragment length polymorphisms
Rhizobium sp. (Cicer arietinum L.)
rhizobium
Plants, Medicinal},
   Year = {1994} }




@article{
Nour95,
   Author = {Nour, S. M. and Cleyet-Marel, J.-C. and Normand, P. and Fernandez, M. P.},
   Title = {Genomic heterogeneity of strains nodulating chickpeas (\emph{Cicer arietinum} L.) and description of \emph{Rhizobium mediterraneum} sp. nov.},
   Journal = {International Journal of Systematic Bacteriology},
   Volume = {45},
   Number = {4},
   Pages = {640-648},
   Abstract = {The genetic diversity of chickpea strains was studied by using 30 isolates obtained from nodules on chickpeas growing in uninoculated fields over a wide geographic range. The following taxonomic approaches were used: DNA-DNA relatedness analysis, restriction fragment length polymorphism analysis of the amplified 16S ribosomal DNA (rDNA) intergenic spacer (IGS), and total 16S rRNA sequence analysis. The division of chickpea-infective strains into two major phylogenetic groups (groups A and B) that has been described previously was confirmed by the polymorphism of the 16S IGS rDNA. We identified a total of five genomic species, including the previously described species Rhizobium ciceri. All of the group B strains except one were homogeneous and belonged to a single genomic species corresponding to R. ciceri. Group A was heterogeneous, containing three genomic species and five strains that remained unclassified, and its members had very different PCR restriction fragment length polymorphism profiles. The complete 16S rRNA sequences of strains representing the two major groups, R. ciceri UPM-Ca7(T) (T = type strain) and genomic species 2 strain UPM-Ca36(T), exhibited 19 mismatches. Both of these strains belonged to the Rhizobium loti-Rhizobium huakuii branch; R. ciceri UPM-Ca7(T) was closely related to R. loti, and strain UPM- Ca36(T) was clearly separated from R. ciceri and closely related to R. huakuii. Thus, genomic species 2 could be distinguished from R. ciceri by its 16S rRNA sequence, by DNA relatedness data, by the polymorphism of the 16S IGS rDNAs, and by previously described multilocus enzyme electrophoresis results and phenotypic characteristics. Therefore, we propose that strains belonging to genomic species 2 should be classified in a new species, Rhizobium mediterraneum, and that strain UPM-Ca36 should be the type strain.},
   Keywords = {pea
plant root
rhizobium},
   Year = {1995} }




@article{
Nour94a,
   Author = {Nour, S. M. and Fernandez, M. P. and Normand, P. and Cleyet-Marel, J.-C.},
   Title = {\emph{Rhizobium ciceri} sp. nov., consisting of strains that nodulate chickpeas (\emph{Cicer arietinum} L.)},
   Journal = {International Journal of Systematic Bacteriology},
   Volume = {44},
   Number = {3},
   Pages = {511-522},
   Abstract = {The taxonomic status of 16 collection strains of chickpea (Cicer arietinum L.) rhizobia which were previously determined to belong to two groups (groups A and B) were compared with reference strains belonging to different genera and species of the family Rhizobiaceae. We used the following taxonomic, phylogenetic, and phenotypic characteristics and approaches to study these organisms: DNA homology, guanine-plus-cytosine content, restriction fragment length polymorphism of the amplified 16S-intergenic spacer rRNA gene, partial 16S rRNA sequencing, and auxanographic tests performed with 147 carbon sources. Similar groups of chickpea strains were identified by the different approaches. The chickpea strains were found to belong to the genus Rhizobium regardless of the phylogenetic group to which they belonged (group A or B). All strains fell into a tight cluster which included Rhizobium loti and Rhizobium galegae, and the group B strains were closely related to R. loti. An analysis of partial 16S ribosomal DNA sequences revealed identical nucleotide sequences for the slowly growing strains and fast-growing strains that were used as representatives of groups A and B, respectively, and these organisms fell into the Rhizobium-Agrobacterium lineage. When the sequences of these organisms were compared with the partial sequences of Rhizobium huakuii and R. loti, one- and two-nucleotide mismatches were observed, respectively, indicating that the chickpea rhizobia are closely related to these two species. The DNA-DNA hybridization data revealed that the chickpea rhizobia exhibited low levels of homology (less than 17%) to previously described Rhizobium and Bradyrhizobium species. Moreover, when we compared chickpea strains to R. loti and R. huakuii, the most closely related species as determined by the partial 16S rRNA sequence analysis, the homology values ranged from 21 to 52% and the ?T(m) values were greater than 5°C (?T(m) is the difference between the denaturation temperatures of the heterologous and homologous duplexes). These results confirmed that the rhizobia that nodulate chickpeas cannot be assigned to a previously described species. Within the chickpea rhizobia, the DNA homology values obtained when members of groups A and B were compared were less than 38%, indicating that the group A and group B organisms belong to different species. Furthermore, these organisms can be distinguished from each other by the results of phenotypic tests. We propose that the group B chickpea rhizobia should be assigned to a new species, Rhizobium ciceri; UPM-Ca7 is the type strain of R. ciceri.},
   Keywords = {dna
ribosome rna
rhizobium
Plants, Medicinal},
   Year = {1994} }




@article{
Novikova96,
   Author = {Novikova, N. I.},
   Title = {Modern concepts of the phylogeny and taxonomy of nodule bacteria},
   Journal = {Microbiology},
   Volume = {65},
   Number = {4},
   Pages = {383-394},
   Abstract = {Data on the diversity of legume microsymbionts are considered. According to the modern taxonomic system, nodule bacteria are grouped into four genera: Rhizobium, Bradyrhizobium, Sinorhizobium, and Azorhizobium. The idea of a fifth genus, ''Mesorhizobium,'' is discussed. Phylogenetically, strains of different rhizobial genera are only distant relatives. The possibility of smoothing over the contradictions between the formal classification of nodule bacteria and data on their phylogeny is discussed.},
      Year = {1996} }




@article{
Nuti77,
   Author = {Nuti, M. P. and Ledeboer, A. M. and Lepidi, A. A. and Schilperoort, R. A.},
   Title = {Large plasmids in different rhizobium species},
   Journal = {Journal of General Microbiology},
   Volume = {100},
   Number = {2},
   Pages = {241-248},
      Year = {1977} }




@article{
Nutman87,
   Author = {Nutman, P. S.},
   Title = {A century of nitrogen fixation research: Present status and future},
   Journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences},
   Volume = {317},
   Number = {1184},
   Pages = {69-106},
   Abstract = {The discovery of symbiotic nitrogen fixation, announced a century ago in Berlin, and published in full two years later by Hellriegel & Wilfarth, ended 60 years of controversy and ushered in the modern era of intensive investigation, the extent of which was not then foreseen and which continues unabated. Hellriegel & Wilfarth's great contribution was in proving that legume nodules fixed atmospheric nitrogen. They also showed that the nodule-inducing `ferment' was to some degree specific, that it occurred in different abundancies in different soils, that it was killed by moderate heat and harmed by drought, that the nitrogen fixed by a nodulated legume was not immediately available to plants growing alongside and that small quantities of combined nitrogen did not affect nodulation, whereas larger amounts were inhibitory. This remarkable achievement does not detract from the historic work done much earlier by Boussingault, Lawes, Gilbert and others, who showed by meticulous experiment that neither legumes nor other plants could fix atmospheric nitrogen, in spite of the capacity of the former to enrich themselves, and the soil in which they grew, with combined nitrogen. Earlier workers were so concerned with the need to exclude from their experiments any chemical contamination with ammonia, dust, etc., that they also excluded microorganisms and thus failed to discover fixation. Hellriegel & Wilfarth worked with the light infertile soils of North Germany, where addition of nitrogen was essential. This probably contributed to their success; differences in growth between legumes with and without nodules were quickly seen. Advances in nitrogen fixation research over the past century encompassed many areas in chemistry, biology and agriculture. That nitrogen fixation is among the key processes sustaining life was established by this work, but many fundamental aspects remain obscure, especially in the genetics and physiology of the functioning symbiosis. The catalogue of nitrogen-fixing organisms and associations, and their detailed description, is still incomplete; some nitrogen-fixing systems are in urgent need of conservation. A deeper understanding of these matters will improve our ability to manage the cycling of nitrogen in agricultural and other ecosystems so as to increase protein yields of crops and avoid environmental and energy problems associated with intensive methods of production based wholly on fertilizer nitrogen.},
      Year = {1987} }




@article{
Nutman79,
   Author = {Nutman, P. S. and Hearne, R.},
   Title = {Persistence of nodule bacteria in soil under long-term cereal cultivation},
   Journal = {Rothamsted Raport for},
   Volume = {1979},
   Pages = {77-90},
      Year = {1979} }




@article{
Obaton02,
   Author = {Obaton, M. and Bouniols, A. and Piva, G. and Vadez, V.},
   Title = {Are Bradyrhizobium japonicum stable during a long stay in soil?},
   Journal = {Plant and Soil},
   Volume = {245},
   Number = {2},
   Pages = {315-326},
   Abstract = {Two strains of Bradyrhizobium japonicum, recognizable by their intrinsic resistance to high levels of antibiotics and their serological features were introduced into three calcareous soils under field conditions. These strains were re-isolated 16 or 20 years later and compared with the parental strains kept lyophilized. In the Dijon location, the survival was high although soybean was never grown in the field. But the B. japonicum completely disappeared in the Montpellier field after 10 years under vineyard. In the Toulouse field after the two initially introduced strains, inoculation of subsequent soybean crops with a new strain enabled this strain to occupy 70-80% of the nodules; these results suggest that under such conditions the problem of competition can be solved by repeated inoculation. In this field, the number of introduced B. japonicum remained high during 4 years without soybeans, but a new inoculation would be necessary after 5 years. In the two fields where the survival was high, the two strains remained at about the same relative level as at introduction, there was no detectable exchange of characters between them. With regards to agronomic characteristics, there were no important changes in the competitivity of the strains. Among the eight field isolates tested in a greenhouse for efficiency by comparison with eight lyophilized isolates, seven showed no significant difference for the total weight of soybean or seed yield but one field isolate showed a loss of efficiency corresponding to 27% less seed weight. This long-term experiment allowed us to conclude that the B. japonicum strains used were stable for many characters, but variations in efficiency may rarely occur.},
   Keywords = {Bradyrhizobium japonicum
Competition
Efficiency
Stability
Survival in soil},
   Year = {2002} }




@article{
Ocallahan97,
   Author = {O'Callahan, K. J. and Davey, Michael R. and Cocking, E. C.},
   Title = {Xylem colonization of the legume Sesbania rostrata by Azorhizobium caulinodans},
   Journal = {Proceedings of the Royal Society of London - Series B: Biological Sciences},
   Volume = {264},
   Pages = {1821-1826},
      Year = {1997} }




@article{
OGara76,
   Author = {O'Gara, F. and Shanmugam, K. T.},
   Title = {Regulation of nitrogen fixation by Rhizobia. Export of fixed N$_2$ as  NH$_4$$^+$},
   Journal = {Biochimica et Biophysica Acta},
   Volume = {437},
   Number = {2},
   Pages = {313-321},
   Abstract = {The metabolic fate of gaseous nitrogen (15N2) fixed by free-living cultures of Rhizobia (root nodule bacteria) induced for their N2-fixation system was followed. A majority of the fixed 15N2 was found to be exported into the cell supernatant. For example, as much as 94% of the 15N2 fixed by Rhizobium japonicum (soybean symbiont) was recovered as 15NH+4 from the cell supernatant following alkaline diffusion. Several species of root nodule bacteria also exported large quantities of NH+4 from L-histidine. Evidence is presented that overproduction and export of NH+4 by free-living Rhizobia may be closely linked to the control of several key enzymes of NH+4 assimilation. For instance, NH+4 was found to repress glutamine synthetase whereas L-glutamate repressed glutamate synthase. Assimilation of NH+4 as nitrogen source for growth of Rhizobia was inhibited by glutamate. The mechanism of regulation of NH+4 production by root nodule bacteria is discussed.},
   Keywords = {Ammonia/*metabolism
Glutamate-Ammonia Ligase/metabolism
Kinetics
Nitrogen/*metabolism
*Nitrogen Fixation
Nitrogenase/metabolism
Rhizobium/*metabolism
Species Specificity
Support, U.S. Gov't, Non-P.H.S.},
   Year = {1976} }




@article{
Ogasawara03,
   Author = {Ogasawara, M. and Suzuki, T. and Mutoh, I. and Annapurna, K. and Arora, N. K. and Nishimura, Y. and Maheshwari, D. K.},
   Title = {\emph{Sinorhizobium indiaense} sp. nov. and \emph{Sinorhizobium abri} sp. nov. isolated from tropical legumes, \emph{Sesbania rostrata} and \emph{Abrus precatorius}, respectively},
   Journal = {Symbiosis},
   Volume = {34},
   Number = {1},
   Pages = {53-68},
   Abstract = {Strains of root nodulating bacteria isolated from the leguminous plants Sesbania rostrata and Abrus precatorius growing in the sub Himalayan tract in the western Uttar Pradesh, a tropical region of India, were compared with the reference Strains of Sinorhizobium, Rhizobium, Azorhizobium and Agrobacterium. The phylogenetic analysis based on 16S rRNA gene sequences showed that the isolates from S. rostrata and strains from A. precatorius, were the members of the genus Sinorhizobium. The 16S rRNA gene sequence similarity values of representative strain Ra-3 (from S. rostrata) and HA-1 (from A. precatoritis) showed low values in species level, namely those of 97.1% to Sinorhizobium arboris and 96.1% to S. fredii and S. xinjiangense, respectively. Similarity values of both strains and other Sinorhizobium spp. were mostly lower than those of the above species. On the basis of the results, with the data of phenotypic characteristics, cellular fatty acid compositions (major, 18:1 acid), ubiquinone system (major, Q-10) and DNA-DNA relatedness, we propose the name Sinorhizobium indiaense for strains from S. rostrata and S. abri for strains from A. precatorius.},
      Year = {2003} }




@article{
Ogawa95,
   Author = {Ogawa, J. and Long, S. R.},
   Title = {The Rhizobium meliloti groELc locus is required for regulation of early nod genes by the transcription activator NodD},
   Journal = {Genes and Development},
   Volume = {9},
   Number = {6},
   Pages = {714-729},
   Abstract = {The molecular chaperones related to GroEL (hsp60, cpn60) interact with partially folded proteins and appear to assist them to attain active and correctly folded conformation. They are required for cell viability but are probably more important for some processes than for others. Through a random genetic search to find loci that are required for expression of the Rhizobium meliloti nod (nodulation) genes, we isolated a mutant (B4) defective in luteolin-dependent activation of nod gene expression, and found it carries a Tn5 insertion within a chromosomal groEL gene (groELc) located just downstream of a groESc gene. The groELc mutation affected activity of three related LysR-type activator proteins NodD1, NodD3, and SyrM; on plants, the mutants formed nodules late, and the nodules were Fix-. Hybridization and protein expression analysis show that a similar groESL locus (groESLa) maps to the Rm1021 megaplasmid pSyma. Southern blot analysis revealed additional, but less closely related sequences hybridizing to groELc and groESc probes elsewhere in the R. meliloti genome. Clones of groESLc and groESLa can each restore robust phage ? growth on an Escherichia coli groE mutant. Likewise each clone can complement all of the phenotypes observed for B4 mutants; thus, the two appear to be functionally equivalent if expression is controlled. We determined that groELc is required for normal DNA binding of the NodD target sequence in R. meliloti. GroEL coimmunopurifies with NodD1 from R. meliloti, which suggests a direct physical association between these proteins. GroEL is thus probably involved in the folding or assembly of transcriptionally active NodD.},
   Keywords = {GroEL
LysR
nod genes
NodD
Rhizobium meliloti
sym plasmid
transcriptional activation},
   Year = {1995} }




@article{
OHara98,
   Author = {O'Hara, G. W.},
   Title = {The Role of Nitrogen Fixation in Crop Production},
   Journal = {Journal of Crop Production},
   Volume = {1},
   Number = {2},
   Pages = {115-138},
   Abstract = {Biological nitrogen fixation is an important process for agricultural productivity in many cropping systems because of direct inputs of atmospheric nitrogen, and rotational effects such as disease control. Advances in molecular biology techniques provide new opportunities to understand the ecology of root nodule bacteria and may improve the selection of elite strains for inoculation. An understanding of the genetic basis of nodulation in grain and pasture legumes may improve inoculation technologies. Temperate and tropical pastures may be improved through effective inoculation, removal of nutritional constraints, and use of alternate legume species. Increases in nitrogen fixation in crop legumes may result from addressing problems in the legume host, the microsymbiont and the environment.},
   Keywords = {Fixation
Legumes
Nitrogen
Nodulation
Pasture
Pulses
Soybean},
   Year = {1998} }




@article{
Oke99,
   Author = {Oke, Valerie and Long, Sharon R.},
   Title = {Bacteroid formation in the  \emph{Rhizobium}--legume symbiosis},
   Journal = {Current Opinion in Microbiology},
   Volume = {2},
   Number = {6},
   Pages = {641-646},
   Abstract = {During the Rhizobium-legume symbiosis, bacteria enter the cells of host plants and differentiate into nitrogen-fixing bacteroids. Recent mutant screens and expression studies have revealed bacterial genes involved in the developmental pathway and demonstrate how the genetic requirements can vary from one host-microbe system to another. Whether bacteroids are terminally differentiated cells is an ongoing debate and new experimental systems are required to address this issue.},
      Year = {1999} }




@article{
Oldroyd04,
   Author = {Oldroyd, G. E. D. and Downie, J. A.},
   Title = {Calcium, kinases and nodulation signalling in legumes},
   Journal = {Nature Reviews Molecular Cell Biology},
   Volume = {5},
   Number = {7},
   Pages = {566-576},
   Abstract = {Several genes have recently been identified using legume mutants that are defective for nodulation signalling. The proteins they encode include novel types of receptor-like kinase that are predicted to recognize bacterial nodulation (Nod) factors, a leucine-rich-repeat receptor kinase, a putative ion channel and a predicted Ca2+/calmodulin-dependent protein kinase. The identification of these gene products provides new insights into the legume signalling responses to rhizobial signals.},
      Year = {2004} }




@article{
Oliver28,
   Author = {Oliver, W. R. B.},
   Title = {The flora of the Waipaoa Series (Late Pliocene) of New Zealand},
   Journal = {Transactions and Proceedings of the New Zealand Institute},
   Volume = {59},
   Pages = {287-303},
      Year = {1928} }




@article{
Olsthoorn98,
   Author = {Olsthoorn, M. M. and Lopez-Lara, I. M. and Petersen, B. O. and Bock, K. and Haverkamp, J. and Spaink, H. P. and Thomas-Oates, J. E.},
   Title = {Novel branched nod factor structure results from alpha-(1-->3) fucosyl transferase activity: the major lipo-chitin oligosaccharides from Mesorhizobium loti strain NZP2213 bear an alpha-(1-->3) fucosyl substituent on a nonterminal backbone residue},
   Journal = {Biochemistry},
   Volume = {37},
   Number = {25},
   Pages = {9024-32},
   Abstract = {Mesorhizobium loti has been described as a microsymbiont of plants of the genus Lotus. Lipo-chitin oligosaccharides (LCOs), or Nod factors, produced by several representative M. loti strains all have similar structures. Using fast-atom-bombardment tandem mass spectrometry and NMR spectroscopy, we have now examined the LCOs from the type strain NZP2213 and observed a much greater variety of structures than has been described for the strains of M.loti studied previously. Interestingly, we have identified as the major LCO a structure that bears a fucose residue alpha-1,3-linked to the GlcNAc residue proximal to the nonreducing terminal GlcNAc residue. This is the first time, to our knowledge, that substitution on an internal GlcNAc residue of the LCO backbone has been observed. This novel LCO structure suggests the presence of a novel fucosyltransferase activity in strain NZP2213. Since the presence of this extra structure does not have the effect of broadening the host range, we suggest that the modification of the LCOs with a fucose residue linked to a nonterminal GlcNAc residue might provide protection against degradation by a particular host plant enzyme (e.g., a chitinase) or alternatively represents adaptation to a particular host-specific receptor. The action of the alpha-(1-->3) fucosyltransferase seems to reduce significantly the activity of NodS, the methyltransferase involved in the addition of the N-methyl substituent to the nonreducing terminal GlcNAc residue. An additional novel LCO structure has been identified having only a GlcNAc2 backbone. This is to our knowledge the first description of such a minimal LCO structure.},
   Keywords = {Acetylglucosamine/chemistry
Bacterial Proteins/metabolism
Carbohydrate Conformation
Chitin/*chemistry/metabolism
Chromatography, High Pressure Liquid
Chromatography, Thin Layer
Fabaceae/*microbiology
Fucose/*metabolism
Fucosyltransferases/*chemistry/metabolism
Lipopolysaccharides/*chemistry/metabolism
Mass Fragmentography
Methyltransferases/metabolism
Nuclear Magnetic Resonance, Biomolecular
*Plants, Medicinal
Rhizobium/chemistry/*enzymology
Structure-Activity Relationship
Support, Non-U.S. Gov't},
   Year = {1998} }




@article{
Orchard05,
   Author = {Orchard, A. E. and Maslin, B. R.},
   Title = {The case for conserving \emph{Acacia}  with a new type},
   Journal = {Taxon},
   Volume = {54},
   Number = {2},
   Pages = {509-512},
      Year = {2005} }




@article{
Orgambide94,
   Author = {Orgambide, G. G. and Philip-Hollingsworth, S. and Hollingsworth, R. I. and Dazzo, F. B.},
   Title = {Flavone-enhanced accumulation and symbiosis-related biological activity of a diglycosyl diacylglycerol membrane glycolipid from Rhizobium leguminosarum biovar trifolii},
   Journal = {Journal of Bacteriology},
   Volume = {176},
   Number = {14},
   Pages = {4338-4347},
   Abstract = {Rhizobium leguminosarum bv. trifolii is the bacterial symbiont which induces nitrogen-fixing root nodules on the leguminous host, white clover (Trifolium repens L.). In this plant-microbe interaction, the host plant excretes a flavone, 4',7-dihydroxyflavone (DHF), which activates expression of nodulation genes, enabling the bacterial symbiont to elicit various symbiosis-related morphological changes in its roots. We have investigated the accumulation of a diglycosyl diacylglycerol (BF-7) in wild-type R. leguminosarum bv. trifolii ANU843 when grown with DHF and the biological activities of this glycolipid bacterial factor on host and nonhost legumes. In vivo labeling studies indicated that wild-type ANU843 cells accumulate BF- 7 in response to DHF, and this flavone-enhanced alteration in membrane glycolipid composition was suppressed in isogenic nodA::Tn5 and nodD::Tn5 mutant derivatives. Seedling bioassays performed under microbiologically controlled conditions indicated that subnanomolar concentrations of purified BF-7 elicit various symbiosis-related morphological responses on white clover roots, including thick short roots, root hair deformation, and foci of cortical cell divisions. Roots of the nonhost legumes alfalfa and vetch were much less responsive to BF-7 at these low concentrations. A structurally distinct diglycosyl diacylglycerol did not induce these responses on white clover, indicating structural constraints in the biological activity of BF-7 on this legume host. In bioassays using aminoethoxyvinylglycine to suppress plant production of ethylene, BF-7 elicited a meristematic rather than collaroid type of mitogenic response in the root cortex of white clover. These results indicate an involvement of flavone-activated nod expression in membrane accumulation of BF-7 and a potent ability of this diglycosyl diacylglycerol glycolipid to perform as a bacterial factor enabling R. leguminosarum bv. trifolii to activate segments of its host's symbiotic program during early development of the root nodule symbiosis.},
      Year = {1994} }




@article{
Orla09,
   Author = {Orla-Jensen, S.},
   Title = {Die Hauptlinien des nat\"urlichen Baktieren Systems},
   Journal = {Centralblatt f\"ur Bakteriologie, Abt. II},
   Volume = {22},
   Pages = {305-346},
      Year = {1909} }




@article{
Ott05,
   Author = {Ott, T. and van Dongen, J. T. and Gu Nther, C. and Krusell, L. and Desbrosses, G. and Vigeolas, H. and Bock, V. and Czechowski, T. and Geigenberger, P. and Udvardi, M. K.},
   Title = {Symbiotic leghemoglobins are crucial for nitrogen fixation in legume root nodules but not for general plant growth and development},
   Journal = {Current Biology},
   Volume = {15},
   Number = {6},
   Pages = {531-5},
   Abstract = {Hemoglobins are ubiquitous in nature and among the best-characterized proteins []. Genetics has revealed crucial roles for human hemoglobins [], but similar data are lacking for plants. Plants contain symbiotic and nonsymbiotic hemoglobins []; the former are thought to be important for symbiotic nitrogen fixation (SNF). In legumes, SNF occurs in specialized organs, called nodules, which contain millions of nitrogen-fixing rhizobia, called bacteroids []. The induction of nodule-specific plant genes, including those encoding symbiotic leghemoglobins (Lb), accompanies nodule development []. Leghemoglobins accumulate to millimolar concentrations in the cytoplasm of infected plant cells prior to nitrogen fixation and are thought to buffer free oxygen in the nanomolar range, avoiding inactivation of oxygen-labile nitrogenase while maintaining high oxygen flux for respiration []. Although widely accepted, this hypothesis has never been tested in planta. Using RNAi, we abolished symbiotic leghemoglobin synthesis in nodules of the model legume Lotus japonicus. This caused an increase in nodule free oxygen, a decrease in the ATP/ADP ratio, loss of bacterial nitrogenase protein, and absence of SNF. However, LbRNAi plants grew normally when fertilized with mineral nitrogen. These data indicate roles for leghemoglobins in oxygen transport and buffering and prove for the first time that plant hemoglobins are crucial for symbiotic nitrogen fixation.},
      Year = {2005} }




@article{
Perez03,
   Author = {P\'erez-Fern\'andez, M. A. and Lamont, B. B.},
   Title = {Nodulation and performance of exotic and native legumes in Australian soils},
   Journal = {Australian Journal of Botany},
   Volume = {51},
   Number = {5},
   Pages = {543-553},
   Abstract = {Six Spanish legumes, Cytisus balansae, C. multiflorus, C. scoparius, C. striatus, Genista hystrix and Retama sphaerocarpa, were able to form effective nodules when grown in six south-western Australian soils. Soils and nodules were collected from beneath natural stands of six native Australian legumes, Jacksonia floribunda, Gompholobium tomentosum, Bossiaea aquifolium, Daviesia horrida, Gastrolobium spinosum and Templetonia retusa. Four combinations of soils and bacterial treatments were used as the soil treatments: sterile soil ( S), sterile inoculated soils ( SI), non-treated soil (N) and non-treated inoculated soils ( NI). Seedlings of the Australian species were inoculated with rhizobia cultured from nodules of the same species, while seedlings of the Spanish species were inoculated with cultures from each of the Australian species. All Australian rhizobia infected all the Spanish species, suggesting a high degree of 'promiscuity' among the bacteria and plant species. The results from comparing six Spanish and six Australian species according to their biomass and total nitrogen in the presence ( NI) or absence ( S) of rhizobia showed that all species benefitted from nodulation (1.02 - 12.94 times), with R. sphaerocarpa and C. striatus benefiting more than the native species. Inoculation ( SI and NI) was just as effective as, or more effective than the non-treated soil (i.e. non-sterile) in inducing nodules. Nodules formed on the Spanish legumes were just as efficient at fixing N-2 as were those formed on the Australian legumes. Inoculation was less effective than non-treated soil at increasing biomass but just as effective as the soil at increasing nitrogen content. Promiscuity in the legume - bacteria symbiosis should increase the ability of legumes to spread into new habitats throughout the world.},
      Year = {2003} }




@article{
Pacios-Bras02,
   Author = {Pacios-Bras, C. and Van der Burgt, Y. E. M. and Deelder, A. M. and Vinuesa, P. and Werner, D. and Spaink, H. P.},
   Title = {Novel lipochitin oligosaccharide structures produced by Rhizobium etli KIM5s},
   Journal = {Carbohydrate Research},
   Volume = {337},
   Number = {13},
   Pages = {1191-1200},
   Abstract = {The novel lipochitin oligosaccharide (LCOs) structures produced by Rhizobium etli KIM5s were characterized using a nanoHPLC reverse-phase system coupled to an ion-trap mass spectrometer. This technique was shown to be more sensitive for structural elucidation of LCOs than previously used mass spectrometric methods. The structures of the LCOs of R. etli KIM5s, the majority containing six monosaccharide residues, differed from those synthesized by all other rhizobia analyzed to date. In addition, novel structures in which the chitin backbone was deacetylated at one or more GlcNAc moieties were found as minor compounds. The difference in host range of this strain compared to that of other known bean microsymbionts is discussed. © 2002 Elsevier Science Ltd. All rights reserved.},
   Keywords = {Ion-trap mass spectrometry
Lipochitin oligosaccharides (LCOs)
NanoHPLC system
Nodulation
Rhizobium etli},
   Year = {2002} }




@article{
Page96,
   Author = {Page, R. D. M.},
   Title = {TREEVIEW: An application to display phylogenetic trees on personal computers},
   Journal = {Computer Applications in the Biosciences},
   Volume = {12},
   Number = {4},
   Pages = {357-358},
      Year = {1996} }




@article{
Pai95,
   Author = {Pai, J. G. B. and Graves, W. R.},
   Title = {Seed source affects seedling development and nitrogen fixation of Maackia amurensis},
   Journal = {J Environ Hortic},
   Volume = {13},
   Pages = {142-146},
      Year = {1995} }




@article{
Pallen05,
   Author = {Pallen, M. J. and Beatson, S. A. and Bailey, C. M.},
   Title = {Bioinformatics, genomics and evolution of non-flagellar type-III secretion systems: A Darwinian perpective},
   Journal = {FEMS Microbiology Reviews},
   Volume = {29},
   Number = {2},
   Pages = {201-229},
   Abstract = {We review the biology of non-flagellar type-III secretion systems from a Darwinian perspective, highlighting the themes of evolution, conservation, variation and decay. The presence of these systems in environmental organisms such as Myxococcus, Desulfovibrio and Verrucomicrobium hints at roles beyond virulence. We review newly discovered sequence homologies (e.g., YopN/TyeA and SepL). We discuss synapomorphies that might be useful in formulating a taxonomy of type-III secretion. The problem of information overload is likely to be ameliorated by launch of a web site devoted to the comparative biology of type-III secretion (http://3base.bham.ac.uk). © 2005 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved.},
   Keywords = {Bacterial virulence
Bioinformatics
Chaperones
Evolution
Genomics
Homology
Symbiosis
Type-III secretion},
   Year = {2005} }




@article{
Pandey04,
   Author = {Pandey, P. and Sahgal, M. and Maheswari, D. K. and Johri, B. N.},
   Title = {Genetic diversity of rhizobia isolated from medicinal legumes growing in the sub-Himalayan region of Uttaranchal},
   Journal = {Current Science},
   Volume = {86},
   Number = {1},
   Pages = {202-207},
   Abstract = {Diversity of rhizobia recovered from five medicinal legumes, Trigonella foenum graecum, Abrus precatorius, Mucuna pruriens, Melilotus officinalis and Vicia angustifolia was investigated. Nine bacterial strains isolated on yeast extract mannitol agar (YEMA) and showing tolerance to 2% NaCl were analysed along with reference strains, Bradyrhizobium japonicum SB102, Sinorhizobium meliloti 102F 34 and Rhizobium gallicum R602sp(T) using restriction patterns produced by amplified DNA coding for 16S rDNA (ARDRA) with two enzymes HaeIII and MspI and were placed in six genotypes. Four isolates from Trigonella, i.e. PP1, PP2, PP3 and PP4 were placed in two genotypes; one genotype was closely related to S. meliloti 102F 34 and the other to B. japonicum SB 102. Genetic diversity was also assessed by repetitive PCR using BOX primers, wherein all the isolates were placed in five genotypes. Based on repetitive PCR, isolates from nodules of Trigonella were placed in single genotype. Nitrogen-fixing ability of the isolates was confirmed by amplification of 781 bp nifH fragment in five isolates, PP1, PP2, PP3, PP4 and PP9.},
      Year = {2004} }




@article{
Pankhurst87,
   Author = {Pankhurst, C. E. and Hopcroft, D. H. and Jones, W. T.},
   Title = {Comparative morphology and flavolan content of \emph{Rhizobium loti} induced effective and ineffective root nodules on \emph{Lotus} species, \emph{Leuceana leucocephala}, \emph{Carmichaelia flagelliformis}, \emph{Ornithopus sativus}, and \emph{Clianthus puniceus}},
   Journal = {Canadian Journal of Botany},
   Volume = {65},
   Number = {12},
   Pages = {2676-2685},
      Year = {1987} }




@article{
Parker99,
   Author = {Parker, M. A.},
   Title = {Mutualism in metapopulations of legumes and rhizobia},
   Journal = {American Naturalist},
   Volume = {153},
   Number = {Suppl.},
   Abstract = {The evolution of geographic mosaic patterns was analysed for symbioses of legume plants and root-nodule bacteria (rhizobia), where plants were commonly polymorphic for genes affecting mutualism specificity. Typically, some alleles conferred broad compatibility, and others restricted the set of bacterial genotypes accepted by plants as mutualist partners. Metapopulation simulation models with genetic assumptions matching the observed form of symbiotic specificity showed that selection could generate a stable geographic mosaic if certain conditions were satisfied regarding competitive abilities, fitness benefits from mutualism, and migration rates. The structure of geographic variation in natural populations of the annual legume Amphicarpaea bracteata, together with patterns of variation in symbiotic fitness, was consistent with the interpretation that a mosaic pattern of differentiation existed. Experimental and observational studies necessary to test more rigorously for mosaic distributions are outlined.},
      Year = {1999} }




@article{
Parker01,
   Author = {Parker, M. A.},
   Title = {Mutualism as a constraint on invasion success for legumes and rhizobia},
   Journal = {Diversity and Distributions},
   Volume = {7},
   Number = {3},
   Pages = {125-136},
   Abstract = {Because hereditary symbiont transmission is normally absent in the mutualism of legume plants and root-nodule bacteria (rhizobia), dispersing plants may often arrive at new habitats where mutualist partners are too rare to provide full benefits. Factors governing invasion success were explored by analysing a system of two coupled pairwise competition models: a legume invader competing with a resident non-mutualistic plant, and a rhizobial population competing with a resident population of nonsymbiotic bacteria. The non-linear dependence of benefits on partner abundance in this mutualism creates the possibility of two alternative population size equilibria, so that a threshold density can exist for invasion. If legumes and rhizobia exceed a critical population size, both species achieve rapid population growth, while if initial densities of both species are below their respective thresholds, they remain rare and are thus vulnerable to extinction in the presence of competitors. Overall, the results indicate that legumes may often fail at colonization attempts within habitats where mutualist partners are scarce. Data on legume prevalence in island floras and rates of geographical spread by legume weeds are consistent with this inference. Predictive insights about invasiveness may emerge from comparative research on key traits identified by the model, especially the shape of the function determining the number of nodules formed at low rhizobial density.},
      Year = {2001} }




@article{
Parker02a,
   Author = {Parker, Matthew A.},
   Title = {Bradyrhizobia from wild Phaseolus, Desmodium, and Macroptilium species in northern Mexico},
   Journal = {Applied and Environmental Microbiology},
   Volume = {68},
   Number = {4},
   Pages = {2044-2048},
   Abstract = {rRNA genetic markers were analyzed in 97 isolates of nodule bacteria from six legume species in Chihuahua, Mexico. The most common genotypes were widely shared across host species and had 16S rRNA sequences identical to those of strains from an eastern North American legume (Amphicarpaea) that are closely related to Bradyrhizobium elkanii.},
      Year = {2002} }




@article{
Parker04,
   Author = {Parker, M. A. and Doyle, J. L. and Doyle, J. J.},
   Title = {Comparative phylogeography of Amphicarpaea legumes and their root-nodule symbionts in Japan and North America},
   Journal = {Journal of Biogeography},
   Volume = {31},
   Number = {3},
   Pages = {425-434},
   Abstract = {Aim Relationships of eastern Asian and eastern North American populations of legumes in the genus Amphicarpaea Elliot ex. Nuttall (Phaseoleae-Glycininae) and their root nodule bacteria (Bradyrhizobium Jordan) were analysed to test whether both organisms share an identical biogeographic history. Location Japan and eastern North America (New York and Illinois). Methods Sequences of three plant genes (chloroplast trnL region, nuclear ribosomal ITS, and histone H3-D) and a segment of the bacterial ribosomal region (partial 16S rRNA and 23S rRNA genes, and the 16S rRNA-23S rRNA ITS) were used to analyse phylogenetic relationships. Results For plants, Japanese populations formed a sister group to a well-supported clade of all North American genotypes. For nodule bacteria associated with Amphicarpaea, isolates from North America did not form a single clade relative to Asian genotypes. Japanese Bradyrhizobium isolates were closely related to particular sub-groups of North American bacteria (lineages 'B' and 'C'), with other American bacteria branching earlier. Main conclusions Plants and bacteria showed clear deviations from a pattern of parallel cladogenesis. The most basal Amphicarpaea lineage was associated with a recently-diverged bacterial group, while one recently-diverged plant lineage had symbionts that branched in a basal position relative to the other Amphicarpaea bacteria. When analysed with data on symbiotic compatibility from inoculation experiments, the molecular phylogenies suggested that for plants, at least one transition has occurred toward more promiscuous nodulation behaviour. Among bacteria, strains with narrow host range on Amphicarpaea appear to be ancestral to symbiotic generalists.},
      Year = {2004} }




@article{
Parker02b,
   Author = {Parker, M. A. and Lafay, B. and Burdon, J. J. and van Berkum, P.},
   Title = {Conflicting phylogeographic patterns in rRNA and nifD indicate regionally restricted gene transfer in Bradyrhizobium},
   Journal = {Microbiology},
   Volume = {148},
   Pages = {2557-2565},
   Abstract = {Major differences in evolutionary relationships of the 16S rRNA gene and the nitrogenase alpha-subunit gene (nifD) were observed among 38 strains of Bradyrhizobium sp. nodule bacteria from North America, Central America, Asia and Australia. Two lineages were evident in the 16S rRNA phylogeny representing strains related to Bradyrhizobium japonicum (29 isolates) or Bradyrhizobium elkanii (9 isolates). Both clades were distributed across most or all of the geographic regions sampled. By contrast, in the nifD tree almost all isolates were placed into one of three groups each exclusively composed of taxa from a single geographic region (North Temperate, Central America or Australia). Isolates that were closely related or identical in gene sequence at one locus often had divergent sequences at the other locus and a partition homogeneity test indicated that the 16S rRNA and nifD phylogenies were significantly incongruent. No evidence for any gene duplication of nifD was found by Southern hybridization analysis on a subset of the strains, so unrecognized paralogy is not likely to be responsible for the discrepancy between 16S rRNA and nifD tree topologies. These results are consistent with a model whereby geographic areas were initially colonized by several diverse 16S rRNA lineages, with subsequent horizontal gene transfer of nifD leading to increased nifD sequence homogeneity within each regional population.},
      Year = {2002} }




@article{
Parker01b,
   Author = {Parker, M. A. and Peters, N. K.},
   Title = {Rhizobitoxine production and symbiotic compatibility of Bradyrhizobium from Asian and North American lineages of Amphicarpaea},
   Journal = {Canadian Journal of Microbiology},
   Volume = {47},
   Number = {10},
   Pages = {889-894},
   Abstract = {Reciprocal inoculations with Bradyrhizobium sp. isolates from the North American legume Amphicarpaea bracteata (L.) Fern. (Phaseoleae-Glycininae) and from a Japanese population of its close relative Amphicarpaea edgeworthii (Benth.) var. japonica were performed to analyze relative symbiotic compatibility. Amphicarpaea edgeworthii plants formed few or no nodules with any North American bradyrhizobial strains isolated from A. bracteata, but all A. bracteata lineages formed effective nitrogen-fixing nodules with Japanese Bradyrhizobium isolates from A. edgeworthii. However, one group of A. bracteata plants (lineage Ia) when inoculated with Japanese bradyrhizobia developed a striking leaf chlorosis similar to that known to be caused by rhizobitoxine. The ?-cystathionase inhibition assay demonstrated that significant amounts of rhizobitoxine were present in nodules formed by these Japanese bradyrhizobia. No North American bradyrhizobial isolate from A. bracteata induced chlorosis on any plants, and the ?-cystathionase assay failed to detect rhizobitoxine in nodules formed by these isolates. The role of rhizobitoxine in A. edgeworthii nodulation development was tested by inoculating plants with a Bradyrhizobium elkanii rhizobitoxine-producing strain, USDA 61, and two mutant derivatives, RX17E and RX18E, which are unable to synthesize rhizobitoxine. Amphicarpaea edgeworthii inoculated with wild-type USDA 61 developed >150 nodules per plant, while plants inoculated with RX17E and RX18E developed fewer than 10 nodules per plant. Thus, efficient nodule development in A. edgeworthii appears to be highly dependent on rhizobitoxine production by Bradyrhizobium strains.},
   Keywords = {Bradyrhizobium elkanii
Geographic variation
Leguminosae
Mutualism},
   Year = {2001} }




@article{
Parker98,
   Author = {Parker, M. A. and Spoerke, J. M.},
   Title = {Geographic structure of lineage associations in a plant-bacterial mutualism},
   Journal = {Journal of Evolutionary Biology},
   Volume = {11},
   Number = {5},
   Pages = {549-562},
   Abstract = {Two species linked by a mutualistic relationship may evolve correlated population differentiation if there is long-term continuity of interactions between specific partners. This phenomenon was analyzed by multilocus enzyme electrophoresis on the annual legume Amphicarpaea bracteata and its nitrogen-fixing bacterial symbionts (Bradyrhizobium sp.) sampled from >20 sites over a 1000 km area. Three analyses indicated that genetic differentiation was correlated in the two organisms. First, the genetic distance between bacterial populations at each pair of sites was significantly positively related to the genetic distance between their host plant populations, as evaluated by the Mantel test. Second, a cluster analysis revealed that several divergent lineages were present both among plants and among bacteria. Bacterial lineages showed a highly nonrandom distribution across plant lineages that was consistent in each of two regions sampled. Finally, there were numerous cases where populations of the same plant lineage 1000 km apart harbored bacterial isolates with an identical multilocus genotype. Thus, despite recurrent opportunities for partner switching, particular genotypes of these two organisms associate consistently across multiple habitats throughout their geographic range.},
   Keywords = {Bradyrhizobium
Coevolution
Geographic variation
Leguminosae
Mutualism},
   Year = {1998} }




@article{
Parniske00,
   Author = {Parniske, Martin},
   Title = {Intracellular accommodation of microbes by plants: a common developmental program for symbiosis and disease?},
   Journal = {Current Opinion in Plant Biology},
   Volume = {3},
   Number = {4},
   Pages = {320-328},
   Abstract = {Plant cells engage in mutualistic and parasitic endosymbioses with a wide variety of microoganisms, ranging from Gram-negative (Rhizobium, Nostoc) and Gram-positive bacteria (Frankia), to oomycetes (Phytophthora), Chytridiomycetes, Zygomycetes (arbuscular mycorrhizal fungi) and true fungi (Erysiphe, ascomycete; Puccinia, basidiomycete). Endosymbiosis is characterised by the 'symbiosome', a compartment within host cells in which the symbiotic microorganism is either partially or completely enclosed by a host-derived membrane. The analysis of plant mutants indicates that the genetic requirements for the interaction with rhizobia and arbuscular mycorrhiza fungi are partially overlapping. The extent to which plants use similar or identical developmental programs for the intracellular accommodation of different microorganisms is, however, not clear. For example, plant cells actively weaken their cell wall to facilitate bacterial colonisation, whereas penetration by fungal symbionts appears not to be assisted in this manner. Moreover, different transport requirements are imposed on the symbiotic interface of different interactions indicating that additional system-specific components are likely to exist.},
      Year = {2000} }




@book{
NZPlant,
   Author = {Parsons, M. J. and Douglas, P. and McMillain, B. H.},
   Title = {Current names for wild plants in New Zealand},
   Publisher = {Manaaki Whenua Press},
   Address = {Lincoln},
   Keywords = {Plants},
   Year = {1998} }




@article{
Patel84,
   Author = {Patel, J. J. and Craig, A. S.},
   Title = {Isolation and characterisation of bacteriophages active against strains of \emph{R.~trifolii} used in legume inoculants in New Zealand.},
   Journal = {New Zealand Journal of Science},
   Volume = {27},
   Number = {1},
   Pages = {81-86},
   Abstract = {Bacteriophages active against strains of Rhizobium trifolii used in the manufacture of clover inoculants in New Zealand were isolated from all of 5 sampling sites in a well-established clover-ryegrass pasture. -from Authors},
      Year = {1984} }




@article{
Patriarca04,
   Author = {Patriarca, E. J. and Tat\`e, R. and Ferraioli, S. and Iaccarino, M.},
   Title = {Organogenesis of legume root nodules},
   Journal = {International Review of Cytology},
   Volume = {234},
   Pages = {201-262},
   Abstract = {The N2-fixing nodules elicited by rhizobia on legume roots represent a useful model for studying plant development. Nodule formation implies a complex progression of temporally and spatially regulated events of cell differentiation/ dedifferentiation involving several root tissues. In this review we describe the morphogenetic events leading to the development of these histologically well-structured organs. These events include (1) root hair deformation, (2) development and growth of infection threads, (3) induction of the nodule primordium, and (4) induction, activity, and persistence of the nodular meristem and/or of foci of meristematic activities. Particular attention is given to specific aspects of the symbiosis, such as the early stages of intracellular invasion and to differentiation of the intracellular form of rhizobia, called symbiosomes. These developmental aspects were correlated with (1) the regulatory signals exchanged, (2) the plant genes expressed in specific cell types, and (3) the staining procedures that allow the recognition of some cell types. When strictly linked with morphogenesis, the nodulation phenotypes of plant and bacterial mutants such as the developmental consequence of the treatment with metabolic inhibitors, metabolic intermediates, or the variation of physical parameters are described. Finally, some aspects of nodule senescence and of regulation of nodulation are discussed.},
   Keywords = {Bacteroid
Endocytosis
Meristem
N2 fixation
Nodule senescence
Nodule structure
Signals
Symbiosis
Symbiosome},
   Year = {2004} }




@article{
Patrick92,
   Author = {Patrick, H. N. and Lowther, W. L.},
   Title = {Response of \emph{Lotus corniculatus} to inoculation and pelleting on a range of Otago tussock grassland environments},
   Journal = {Proceedings of the New Zealand Grassland Association},
   Volume = {54},
   Pages = {105-109},
      Year = {1992} }




@article{
Patrick95,
   Author = {Patrick, H. N. and Lowther, W. L.},
   Title = {Influence of the number of rhizobia on the nodulation and establishment of \emph{Trifolium ambiguum}},
   Journal = {Soil Biology \& Biochemistry},
   Volume = {27},
   Number = {4-5},
   Pages = {717-720},
   Abstract = {Rhizobium leguminosarum by. trifolii in New Zealand soils is ineffective on Trifolium ambiguum and inoculation with an effective strain of rhizobia is essential for nodulation. We investigated the effect of inoculation on the establishment of oversewn T. ambiguum (cv. Monaro) in different tussock grassland environments. Peat-based inoculant was applied to seed at a range of rates, in a gum arabic-lime pellet, and when sown 1 day after inoculation the number of rhizobia ranged from 0.2 x 10(3) to 260 x 10(3) seed (-1). Over the 9 sites, seedling nodulation progressively increased from 5% up to 66% as the number of rhizobia seed(-1) increased. Seedling establishment at the end of the first year was directly related to nodulation. These results have important practical implications in improving the establishment of this legume, as the number of rhizobia required to maximize nodulation is higher than that obtained by inoculation at the recommended rate.},
      Year = {1995} }




@article{
Pavlova00,
   Author = {Pavlova, Z. B. and Lutova, L. A.},
   Title = {Nodulation as a model for studying differentiation in higher plants},
   Journal = {Russian Journal of Genetics},
   Volume = {36},
   Number = {9},
   Pages = {975-988},
   Abstract = {The stages of the legume-rhizobial symbiosis and nodule structure in various legume plants are briefly reviewed. Modern data on the mechanisms involved in the control of nodule initiation and morphogenesis are considered. © 2000 MAIK "Nauka/Interperiodica".},
      Year = {2000} }




@article{
Pena96,
   Author = {Pe\~na, R. C. and Cassels, B. K.},
   Title = {Phylogenetic relationships among Chilean \emph{Sophora species}},
   Journal = {Biochemical Systematics and Ecology},
   Volume = {24},
   Number = {7-8},
   Pages = {725-733},
   Abstract = {Phylogenetic affinities among Chilean Sophora species are not clear. We suggest a new hypothesis for the origin of the section Edwardsia on the basis of parsimony analysis, which allows a South American origin to be established for the species of this section. The seed alkaloid composition did not provide useful information for the filiation of Edwardsia species, and the shortest tree was obtained using morphological characters only. Two branches are clearly distinguishable by the pubescence of the leaflets and the flag/wings length ratio: one of them includes S. chrysophylla, S. tetraptera, S. toromiro, S. howinsula and S. denudata; the other one includes S. macnabiana, S. microphylla, S. masafuerana, S. prostrata and S. fernandeziana. In contrast, S. macrocarpa, an ancient element of the South American flora, is closely related to species belonging to the section Sophora represented in the region by S. tomentosa, S. linearifolia and S. rhynchocarpa. Sections Calia and Styphnolobium are clearly related to each other, both morphologically and chemically. Copyright © 1996 Elsevier Science Ltd.},
   Keywords = {Cladistics
Papilionaceae
Quinolizidine alkaloids
Sophora},
   Year = {1996} }




@article{
Pena00,
   Author = {Pe\~na, R. C. and Iturriaga, L. and Montenegro, G. and Cassels, B. K.},
   Title = {Phylogenetic and biogeographic aspects of \emph{Sophora} sect.~\emph{Edwardsia} (Papilionaceae)},
   Journal = {Pacific Science},
   Volume = {54},
   Number = {2},
   Pages = {159-167},
   Abstract = {Sophora comprises 45-50 species of worldwide distribution, but no general proposal as to the evolution of this group has been put forth. We used cladistic relationships of the quinolizidine alkaloids (matrine, sparteine, methylcytisine, anagyrine, and sophoranol) with morphological and palynological characters to suggest a hypothesis of evolutionary and biogeographic relationships. The mainland Chilean species of Sophora appear to have been derived from ancestors phylogenetically near the extant Argentinean species S. linearifolia and S. rhynchocarpa and the psammophyte S. tomentosa, growing at tropical coastal sites around the world. The Boreotropic hypothesis of Lavin and Luckow is incorporated in our model as the most parsimonious explanation of the evolution of the species of Edwardsia. Sophora is a taxonomic group that meets the following criteria: a center of diversity in North America, an early Tertiary record in North America, and a pantropical distribution. Styphnolobium and Sophora (including Calia) are representatives of Sophora s.l. in the United States, suggesting a migration of the latter from the Northern Hemisphere to South America. Consistent with the Boreotropic hypothesis, a primary diversification center in South America and subsequent migration to the Indian Ocean and New Zealand, the Juan Fernandez Archipelago, Easter Island, and possibly the Hawaiian Islands is the simplest explanation for the evolution of the Edwardsia species.},
      Year = {2000} }




@article{
Peixoto03,
   Author = {Peixoto, L. and Zavala, A. and Romero, H. and Musto, H.},
   Title = {The strength of translational selection for codon usage varies in the three replicons of Sinorhizobium meliloti},
   Journal = {Gene},
   Volume = {320},
   Number = {1-2},
   Pages = {109-116},
   Abstract = {The genome of the nitrogen-fixing bacterium Sinorhizobium meliloti is composed of three replicons of 3.65 (chromosome), 1.35 (pSymA) and 1.68 Mb (pSymB), respectively. While the chromosome encodes for most of the housekeeping functions, the three elements may contribute to symbiosis, though pSymA is absolutely necessary for nodulation and nitrogen fixation, since it harbours all the characterized nodulation and symbiotic fixation genes. On the other hand, the majority of the sequences located in this megaplasmid are probably not expressed during the free-living stage of the organism. Since most of the sequences located in pSymA are transcribed only at the stage of bacteroids when most probably the fate of the bacterium is to die, the mutations occurring at this stage will not be fixed in the population. Therefore, if natural selection contributes to the codon usage pattern in this species, its effect will be much weaker for the genes placed in pSymA. A codon usage analysis of the genes comprising the three replicons is consistent with the conclusion that selection for translational speed shapes the codon usage of the two replicons which are important for competitive cell growth while the codon usage of the third replicon reflects primarily the mutational bias. © 2003 Elsevier B.V. All rights reserved.},
   Keywords = {Genome organization
Rhizobia
Symbiosis
Synonymous codon usage
Synonymous substitutions},
   Year = {2003} }




@article{
Peng02a,
   Author = {Peng, G.X. and Tan, Z.Y. and Wang, E.T. and Reinhold-Hurek, B. and Chen, W.F. and Chen, W.X.},
   Title = {Identification of isolates from soybean nodules in Xinjiang Region as Sinorhizobium xinjiangense and genetic differentiation of S. xinjiangense from Sinorhizobium fredii},
   Journal = {International Journal of Systematic and Evolutionary Microbiology},
   Volume = {52},
   Number = {2},
   Pages = {457-462},
   Abstract = {Eight fast-growing rhizobial isolates from Xinjiang soils were identified as Sinorhizobium xinjiangense by analyses of 16S rRNA gene sequences, SDS-PAGE of proteins, intergenic spacer sequences and DNA-DNA hybridization. Based on all of the results, these isolates and the reference strains for S. xinjiangense were a distinct genomic species, although the 16S rRNA genes were closely related to that of Sinorhizobium fredii.},
   Keywords = {DNA-DNA relatedness
Phylogeny
Sinorhizobium xinjiangense
Soybean
Xinjiang region
genetic variability
Sinorhizobium
Sinorhizobium fredii
Sinorhizobium xinjiangense
Sinorhizobium fredii
Sinorhizobium xinjiangense},
   Year = {2002} }




@article{
Peng02b,
   Author = {Peng, S. and Biswas, J.C. and Ladha, J.K. and Gyaneshwar, P. and Chen, Y.},
   Title = {Influence of rhizobial inoculation on photosynthesis and grain yield of rice},
   Journal = {Agronomy Journal},
   Volume = {94},
   Number = {4},
   Pages = {925-929},
   Abstract = {Rhizobial inoculation increases grain yield in rice (Oryza sativa L.), a nonlegume plant, but little is known about the mechanism(s) involved. This study was conducted to determine whether inoculation with rhizobia could influence leaf photosynthesis of rice plants under greenhouse conditions. Rice seeds and pot soil were inoculated with three rhizobial strains with or without added N fertilizer. Single-leaf net photosynthetic rates were measured with portable photosynthesis systems (LI-6200 and LI-6400) at several growth stages. Stomatal conductance, chlorophyll fluorescence, specific leaf weight, and leaf N content were also measured. Grain yield and yield components were determined at maturity. A significant increase in single-leaf net photosynthetic rate by rhizobial inoculation was observed in all three independent experiments. The effect of rhizobial inoculation on photosynthesis was greater in zero-N than in 90 kg N ha<sup>-1</sup> treatment. The increase in photosynthetic rate by rhizobial inoculation was 12% averaged across all treatments in the three experiments. The effects of rhizobial inoculation on stomatal conductance, specific leaf weight, and leaf N content were relatively small and less consistent than photosynthetic rate. Chlorophyll fluorescence data suggest that the increase in photosynthetic rate following rhizobial inoculation was not associated with conversion efficiency of light energy in photosystem II. Rhizobial inoculation increased grain yield by 16%. The increase in grain yield was due to an increase in total biomass production rather than harvest index. These results suggest that certain strains of rhizobia can promote rice growth and yield through mechanisms that improve single-leaf net photosynthetic rate.},
   Keywords = {Biomass
Chlorophyll
Crops
Grain (agricultural product)
Greenhouses
Nitrogen fertilizers
Photosynthesis
Plants (botany)
Seed
Stomatal conductance
Agronomy
Oryza sativa},
   Year = {2002} }




@article{
Penmetsa97,
   Author = {Penmetsa, R. V. and Cook, D. R.},
   Title = {A legume ethylene-insensitive mutant hyperinfected by its rhizobial symbiont},
   Journal = {Science},
   Volume = {275},
   Number = {5299},
   Pages = {527-530},
   Abstract = {Development of the Rhizobium-legume symbiosis is controlled by the host plant, although the underlying mechanisms have remained obscure. A mutant in the annual legume Medicago truncatula exhibits an increase of more than an order of magnitude in the number of persistent rhizobial infections. Physiological and genetic analyses indicate that this same mutation confers insensitivity to the plant hormone ethylene for multiple aspects of plant development, including nodulation. These data support the hypothesis that ethylene is a component of the signaling pathway controlling rhizobial infection of legumes.},
      Year = {1997} }




@article{
Pennington01,
   Author = {Pennington, R. T. and Lavin, M. and Ireland, H. and Klitgaard, B. and Preston, J. and Hu, J.-M.},
   Title = {Phylogenetic relationships of basal Papilionoid legumes based upon sequences of the chloroplast \emph{trnL} intron},
   Journal = {Systematic Botany},
   Volume = {26},
   Number = {3},
   Pages = {537-556},
   Abstract = {Abstract: The Swartzieae, Sophoreae, Dipterygeae, and Dalbergieae
are considered the most basal tribes of the subfamily Papilionoideae
(Leguminosae). Nucleotide sequences from the chloroplast trnL intron
for the majority of genera of these tribes were analyzed
cladistically together with placeholder representatives of more
derived tribes. Preliminary results indicate radical changes are
necessary for papilionoid classification because Swartzieae,
Sophoreae, and Dalbergieae are polyphyletic. Their constituent
genera are mixed in a series of monophyletic groups, many of which
have never been proposed previously, and the relationships amongst
which are poorly resolved. Some of these groups, such as the
genistoid and dalbergioid clades, are species-rich because they
contain major papilionoid radiations. In other cases, putatively
basal genera form small clades with no derived taxa included. There
is weak evidence that Bobgunnia, Swartzia, Cyathostegia, Bocoa, and
Ateleia (all Swartzieae) may be the sister group to all other
papilionoids, and that a large clade is congruent with a 50kb
inversion in the chloroplast large single copy (LSC) region.},
      Year = {2001} }




@article{
Peoples92,
   Author = {Peoples, M. B. and Craswell, E. T.},
   Title = {Biological nitrogen fixation: investments, expectations and actual contributions to agriculture},
   Journal = {Plant and Soil},
   Volume = {141},
   Number = {1-2},
   Pages = {13-39},
   Abstract = {Inputs of biologically fixed N into agricultural systems may be derived from symbiotic relationships involving legumes and Rhizobium spp., partnerships between plants and Frankia spp. or cyanobacteria, or from non-symbiotic associations between free-living diazotrophs and plant roots. It is assumed that these N2-fixing systems will satisfy a large portion of their own N requirements from atmospheric N2, and that additional fixed N will be contributed to soil reserves for the benefit of other crops or forage species. This paper reviews the actual levels of N2 fixation attained by legume and non-legume associations and assesses their role as a source of N in tropical agriculture. Factors influencing N2 fixation are discussed and possible strategies for improving the amount of N2 fixed are identified. -Authors},
      Year = {1992} }




@article{
Perez98,
   Author = {Perez-Ramirez, N. O. and Rogel, M. A. and Wang, E. and Castellanos, J. Z. and Mart\'inez-Romero, E.},
   Title = {Seeds of \emph{Phaseolus vulgaris} bean carry \emph{Rhizobium etli}},
   Journal = {FEMS Microbiology Ecology},
   Volume = {26},
   Number = {4},
   Pages = {289-296},
   Abstract = {The presence of soil bacteria on seeds could provide an explanation for bacterial geographical spread. We report that Phaseolus vulgaris bean seeds naturally carry rhizobia on their testa. One hundred eighteen Rhizobium isolates from L-3-1-1-1 seeds were characterized by multilocus enzyme electrophoresis and compared to Rhizobium species which form nitrogen fixing nodules on the roots of bean plants. As a result of this and other analyses, seed isolates were classified as R. etli. Seed borne rhizobia are probably moisture limited and are acquired from contaminating soil during the harvesting process as seeds from non-opened pods do not carry them. Rhizobia on seeds are in a presumably desiccated or dormant state as they require a rehydration process during which they are antibiotic sensitive. With an improved procedure to detect rhizobia on seeds, we found that 5 out of 13 Phaseolus vulgaris bean cultivars tested harbor rhizobia on the seeds. (C) 1998 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.},
      Year = {1998} }




@article{
Perret01,
   Author = {Perret, X. and Parsons, J. and Viprey, V. and Reichwald, K. and Broughton, W. J.},
   Title = {Repeated sequences of the genomes of Rhizobium sp. NGR234 and Sinorhizobium meliloti: A comparative analysis by shotgun sequencing
[Séquences re?pe?te?es des ge?nomes de Rhizobium sp. NGR234 et Sinorhizobium meliloti: Une analyse comparative par se?quenc?age ale?atoire]},
   Journal = {Canadian Journal of Microbiology},
   Volume = {47},
   Number = {6},
   Pages = {548-558},
   Abstract = {Amongst prokaryotic genomes, those of nitrogen-fixing members of the Rhizobiaceae family are relatively large (6-9 Mb), often include mega-plasmids of 1.5-2 Mb, and contain numerous families of repeated DNA sequences. Although most essential nodulation and nitrogen fixation genes are well characterized, these represent only a small fraction of the DNA content. Little is known about the detailed structure of rhizobial genomes. With the development of sequencing techniques and new bio-informatic tools such studies become possible, however. Using the 2275 shot-gun sequences of ANU265 (a derivative of NGR234 cured of pNGR234a), we have identified numerous families of repeats. Amongst these, the 58-bp-long NGRREP-4 represents the third most abundant DNA sequence after the RIME1 and RIME2 repeats, all of which are also found in Sinorhizobium meliloti. Surprisingly, studies on the distribution of these elements showed that in proportion to its size, the chromosome of NGR234 carries many more RIME modules than pNGR234a or pNGR234b. Together with the presence in NGR234 and S. meliloti 1021 of an insertion sequence (IS) element more conserved than essential nodulation and nitrogen fixation genes, these results give new insights into the origin and evolution of rhizobial genomes.},
   Keywords = {BIME
Repeats
Shot-gun},
   Year = {2001} }




@article{
Perret00,
   Author = {Perret, Xavier and Staehelin, Christian and Broughton, William J.},
   Title = {Molecular basis of symbiotic promiscuity},
   Journal = {Microbiology and Molecular Biology Reviews},
   Volume = {64},
   Number = {1},
   Pages = {180-201},
   Abstract = {Eukaryotes often form symbioses with microorganisms. Among these, associations between plants and nitrogen-fixing bacteria are responsible for the nitrogen input into various ecological niches. Plants of many different families have evolved the capacity to develop root or stem nodules with diverse genera of soil bacteria. Of these, symbioses between legumes and rhizobia (Azorhizobium, Bradyrhizobium, Mesorhizobium, and Rhizobium) are the most important from an agricultural perspective. Nitrogen-fixing nodules arise when symbiotic rhizobia penetrate their hosts in a strictly controlled and coordinated manner. Molecular codes are exchanged between the symbionts in the rhizosphere to select compatible rhizobia from pathogens. Entry into the plant is restricted to bacteria that have the "keys" to a succession of legume "doors". Some symbionts intimately associate with many different partners (and are thus promiscuous), while others are more selective and have a narrow host range. For historical reasons, narrow host range has been more intensively investigated than promiscuity. In our view, this has given a false impression of specificity in legume-Rhizobium associations. Rather, we suggest that restricted host ranges are limited to specific niches and represent specialization of widespread and more ancestral promiscuous symbioses. Here we analyze the molecular mechanisms governing symbiotic promiscuity in rhizobia and show that it is controlled by a number of molecular keys.},
      Year = {2000} }




@article{
Peters86,
   Author = {Peters, N. K. and Frost, J. W. and Long, S. R.},
   Title = {A plant flavone, luteolin, induces expression of Rhizobium meliloti nodulation genes},
   Journal = {Science},
   Volume = {233},
   Number = {4767},
   Pages = {977-980},
   Abstract = {The symbiotic interaction of Rhizobium meliloti and alfalfa results in the formation of nitrogen-fixing root nodules. Rhizobium meliloti nodABC genes are required for the early host responses of cortical cell divisions and root hair curling. The induction of nodABC expression by alfalfa exudates demonstrates host-symbiont signaling at an early stage in nodule development. The inducer molecule for nodABC expression was isolated from plant exudate by constructing a nodABC-lacZ fusion to monitor the inducing activity. From ultraviolet-visible absorption spectra, proton nuclear magnetic resonance, and mass spectrometry, the inducer was determined to be 3',4',5,7-tetrahydroxyflavone (luteolin). Luteolin is a normal secondary plant metabolite found throughout the plant kingdom that may serve to control nodABC expression during nodule development. This regulatory role for a flavone contrasts with the function of some flavonoids as defense compounds.},
      Year = {1986} }




@article{
Peterson96,
   Author = {Peterson, R. L. and Farquhar, M. L.},
   Title = {Root Hairs: Specialized Tubular Cells Extending Root Surfaces},
   Journal = {Botanical Review},
   Volume = {62},
   Number = {1},
   Pages = {1-40},
   Abstract = {Root hairs are tubular extensions of epidermal cells that have their origin either in any protoderm cell or in specialized protoderm cells called trichoblasts. These latter cells are the result of an asymmetric cytokinesis determined by the positioning of a pre-prophase band of microtubules. The smaller sibling cell is the trichoblast and specializes physiologically and structurally prior to root hair outgrowth. Several genes are involved in the initiation and outgrowth of root hairs. Elongation of root hairs is by tip growth, and, correlated with this, cytoplasmic organelles and cytoskeletal elements show a polarized distribution; the apical dome consists of numerous vesicles, many associated with cell wall synthesis. The relationship between cellulose microfibril deposition and the pattern of cortical microtubules has received considerable attention, as has the role of the cytoskeleton and calcium in controlling cytoplasmic streaming. Root hairs extend the absorbing surface of the root and therefore have been studied in terms both of physiological characteristics of the plasma membrane and uptake of water and of various ions in the soil solution. Many plant species develop soil sheaths (rhizosheaths) which protect the root surface from desiccation and harbour various microorganisms; root hairs are intimately involved in these sheaths. Various growth regulators have been studied in terms of their effect on the structure and function of root hairs. Root hairs play a significant role in the interaction between plants and nitrogen-fixing microorganisms (e.g., Rhizobium, Frankia) and symbiotic mycorrhizal fungi.},
      Year = {1996} }




@article{
Picard92,
   Author = {Picard, C. and Ponsonnet, C. and Paget, E. and Nesme, X. and Simonet, P.},
   Title = {Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction},
   Journal = {Applied and Environmental Microbiology},
   Volume = {58},
   Number = {9},
   Pages = {2717-2722},
   Abstract = {In order to develop a rapid and specific detection test for bacteria in soil, we improved a method based on the polymerase chain reaction (PCR). Each step of the protocol, including direct lysis of cells, DNA purification, and PCR amplification, was optimized. To increase the efficiency of lysis, a step particularly critical for some microorganisms which resist classical techniques, we used small soil samples (100 mg) and various lytic treatments, including sonication, microwave heating, and thermal shocks. Purification of nucleic acids was achieved by passage through up to three Elutip d columns. Finally, PCR amplifications were optimized via biphasic protocols using booster conditions, lower denaturation temperatures, and addition of formamide. Two microorganisms were used as models: Agrobacterium tumefaciens, which is naturally absent from the soil used and was inoculated to calibrate the validity of the protocol, and Frankia spp., an actinomycete indigenous to the soil used. Specific primers were characterized either in the plasmid- borne vir genes for A. tumefaciens or in the variable regions of the 16S ribosomal gene for Frankia spp. Specific detection of the inoculated A. tumefaciens strain was routinely obtained when inocula ranged from 107 to 103 cells. Moreover, the strong correlation we observed between the size of the inocula and the results of the PCR reactions permitted assessment of the validity of the protocol in enumerating the number of microbial cells present in a soil sample. This allowed us to estimate the indigenous population of Frankia spp. at 0.2 x 105 genomes (i.e., amplifiable target sequences) per g of soil.},
      Year = {1992} }




@book{
Pieters27,
   Author = {Pieters, A. J.},
   Title = {Green manuring --- Principles and practice},
   Publisher = {John Wiley},
   Address = {New York},
      Year = {1927} }




@article{
Pinero88,
   Author = {Pinero, D. and Martinez, E. and Selander, R. K.},
   Title = {Genetic diversity and relationships among isolates of Rhizobium leguminosarum biovar phaseoli.},
   Journal = {Applied and Environmental Microbiology},
   Volume = {54},
   Number = {11},
   Pages = {2825-2832},
   Abstract = {Fifty-one isolates of Rhizobium leguminosarum biovar phaseoli from various geographic and ecological sources, largely in Mexico, were characterized by the electrophoretic mobilities of 15 metabolic enzymes, and 46 distinctive multilocus genotypes (electrophoretic types [ETs]) were distinguished on the basis of allele profiles at the enzyme loci. Mean genetic diversity per enzyme locus among the 46 ETs was 0.691, the highest value yet recorded for any species of bacterium. The occurrence of strong nonrandom associations of alleles over loci suggested a basically clonal population structure, reflecting infrequent recombination of chromosomal genes. Multilocus genotypic diversity was unusually high, with the most strongly differentiated pairs of ETs having distinctive alleles at all 15 loci and major clusters of ETs diverging at genetic distances as large as 0.89. This great diversity in the chromosomal genome raises the possibility that R. leguminosarum biovar phaseoli is a polyphyletic assemblage of strains. As other workers have suggested, the inclusion of all strains capable of nodulating beans in a single biovar or species is genetically unrealistic and taxonomically misleading. A biologically meaningful classification of Rhizobium spp. should be based on assessment of variation in the chromosomal genome rather than on phenotypic characters, especially those mediated for the most part or wholly by plasmid-borne genes, such as host relationships.},
   Keywords = {genetic variability
Variation (Genetics)},
   Year = {1988} }




@article{
Planet02,
   Author = {Planet, P. J.},
   Title = {Reexamining microbial evolution through the lens of horizontal transfer},
   Journal = {EXS},
   Volume = {92},
   Pages = {247-303},
   Abstract = {Our ability to understand the evolution of microbial organisms revolves around a central and increasingly unsettled question: what is the nature of the mode of inheritance? The extent to which genetic information is passed vertically from parent to daughter or horizontally between distant relatives must guide reconstructions and inferences of evolutionary history, and has direct bearing on any ideas about the mechanisms of selection and diversification. Recent evidence suggests that we may have previously underestimated the contribution of horizontal gene transfer, and the dynamics and extent of this process are only beginning to be understood. The recent flood of complete genome sequences of microorganisms has already presented us with a vast array of data from which to test our hypotheses about the evolution of the entire tree of life, but what remains unclear is how we can make sense of this unwieldy data set. Analyses of this newly available data set should include explicit examinations of the contributions of both types of inheritance.},
   Keywords = {*Evolution
*Gene Transfer, Horizontal
*Microbiology
Operon
Species Specificity},
   Year = {2002} }




@article{
Pocknall89,
   Author = {Pocknall, D. T.},
   Title = {Late Ecocene to Early Miocene vegetation and climate history of New Zealand},
   Journal = {Journal - Royal Society of New Zealand},
   Volume = {19},
   Number = {1},
   Pages = {1-18},
   Abstract = {In the Middle Eocene (Bortonian) the vegetation was dominated by Casuarina and several species of Proteaceae. This association was replaced in the Late Eocene (Kaiatan) by one dominated by the Nothofagus fusca group. In the latest Eocene (late Kaiatan and Runangan), the Nothofagus fusca group was replaced by the Nothofagus brassii group, which remained dominant until the Early Miocene. Vegetational data do not support the interpretation, based on oxygen isotope studies, that the climate was warm-temperate throughout much of the late Eocene. -from Author},
   Keywords = {Eocene
Miocene
vegetation history
New Zealand
Casuarina
Nothofagus brassii
Nothofagus fusca
Proteaceae},
   Year = {1989} }




@article{
Pocknall84,
   Author = {Pocknall, D. T. and Mildenhall, D. C.},
   Title = {Late Oligocene - early Miocene spores and pollen from Southland, New Zealand.},
   Journal = {New Zealand Geological Survey Paleontological Bulletin},
   Volume = {51},
   Abstract = {Late Oligocene-early Miocene Gore Lignite Measures and associated marine and estuarine deposits cover several thousand square kilometres of eastern and northern Southland. The more common and drillhole and surface sections within these deposits are described in this bulletin. Five new genera are described and 68 species considered. The new genera are Luminidites, Glencopollis, Dicrassipollis, Lateropora and Bluffopollis. Thirty new species are described. These are Dictyophyllidites arcuatus, Foveotriletes verrucosus, Polypodiisporites irregularis, P. radiatus, Podocarpidites rugulatus, 'Assamiapollenites' inanis, 'A'. incognitus, Nupharipollis mortonensis, Tricolpites perlongicolpus, Glenocopollis ornatus, Lymingtonia cenozoica, Anisotricolporites truncatus, Canthiumidites oblatus, Dicrassipollis balteus, Gothanipollis perplexus, Ilexpollenites verrucatus, Margocolporites scabratus, Nuxpollenites varicosus, Rhoipites aralioides, R. retiformis, 'R'. triangulatus, Tetracolporopollenites costatus, Tetracolporites spectabilis, Lateropora glabra, Diporites aspis, Bluffopollis maculatus, Proteacidites nexinus, P. rectus, P. stratosus, and Harrisipollenites kapukaensis. In addition Harrisipollenites Mildenhall \& Crosbie, Monogemmites Krutzsch, Margocolporites Ramanujam and Tetracolporites Couper are emended. Seven species are recombined, and revised descriptions are given for seven others. Four new biostratigraphic zones are recognised},
   Keywords = {Bluffopollis
Chatton Formation
Dicrassipollis
early Miocene
Glencopollis
Gore lignite Measures
late Oligocene
Lateropora
Lower Nothofagidites matauraensis Zone
Luminidites
new combinations
new pollen zones
new taxa
palynology
Proteacidites isopogiformis zone
Rhoipites waimumuensis Zone
Southland
Tricolpites latispinosus Zone
Upper Nothofagidites matauraensis Zone},
   Year = {1984} }




@article{
Pole89b,
   Author = {Pole, M.},
   Title = {Early Miocene floras from central Otago, New Zealand},
   Journal = {Journal - Royal Society of New Zealand},
   Volume = {19},
   Number = {2},
   Pages = {121-125},
   Abstract = {Thirty eight taxa of plant macrofossils are recognised from Early Miocene (Altonian) sediments of the Manuherikia Group, Central Otago. They include 4 ferns, 4 conifers, 1 palm, 24 "broadleaved' angiosperms and 5 fructifications of higher plants. Identification of leaves is speculative, although specimens can be placed in form to Nothofagus and Eucalyptus are present and fructifications can be placed into Myrtaceae, Casuarinaceae, Leguminosae, and Palmae. Most of the angiospermous fossil taxa do not have comparable representatives in the extant New Zealand flora, and conversely, common elements of the extant flora are not found in the fossil assemblage. This suggests a significant turnover in the New Zealand flora, at least at the species level, since the Early Miocene. -from Author},
   Keywords = {Eucalyptus
Manuherikia Group
Miocene
Nothofagus
palaeoclimate
palaeoflora
Tertiary
New Zealand, South Island, Otago},
   Year = {1989} }




@article{
Pole94,
   Author = {Pole, M.},
   Title = {The New Zealand flora - Entirely long-distance dispersal?},
   Journal = {Journal of Biogeography},
   Volume = {21},
   Number = {6},
   Pages = {625-635},
   Keywords = {Cretaceous
dispersal
flora
Pleistocene
Tertiary
Fiji
New Zealand
Pacific, Kermadec Islands
Pacific, Lord Howe Island
Pacific, Norfolk Island},
   Year = {1994} }




@article{
Pole99,
   Author = {Pole, M. and Douglas, B.},
   Title = {Plant macrofossils of the Upper Cretaceous Kaitangata Coalfield, New Zealand},
   Journal = {Australian Systematic Botany},
   Volume = {12},
   Number = {3},
   Pages = {331-364},
   Abstract = {Uppermost Cretaceous sediments from the Cretaceous Kaitangata Coal Mine and the Wangaloa coast (south of Dunedin, New Zealand) were investigated for dispersed plant macrofossils. The gymnosperms include two cycads (Macrozamia sp. and Pterostoma sp.), Ginkgo sp., three further possible ginkgophyte taxa, and ten conifer taxa. The conifers include two new conifer genera and species, Maikuku stephaniae and Waro riderensis, which are placed in the Taxodiaceae s.l., five forms which can be placed into pre-existing genera (Araucaria sp., Otakauia lanceolata, Kaia minuta, Kakahuia sp. 'Kai Point', and Paahake cf. P papillatus), and three others which are not identified to genus (Araucariaceae gen. indet., cf. Dacrycarpus, and 'Wangaloa conifer'). There are also 13 types of angiosperm cuticle, including one in the Lauraceae, and one with affinities to Chloranthaceae and Monimiaceae. Sample heterogeneity as regards taxa present and their abundance suggests taxonomic heterogeneity in the original vegetation.},
   Keywords = {Cretaceous
fossil
macrophyte
New Zealand
Araucaria
Dacrycarpus
Ginkgo
Kaia minuta
Kakahuia
Macrozamia
Maikuku stephaniae
Otakauia lanceolata
Paahake
Pterostoma
Wangaloa
Waro riderensis},
   Year = {1999} }




@article{
Pole92,
   Author = {Pole, M.S.},
   Title = {Fossils of Leguminosae from the Miocene Manuherikia Group of New Zealand},
   Journal = {Advances in Legume Systematics: Part 4. The Fossil Record},
   Pages = {251-258},
      Year = {1992} }




@article{
Pole01,
   Author = {Pole, M. S.},
   Title = {Can long-distance dispersal be inferred from the New Zealand plant fossil record?},
   Journal = {Australian Journal of Botany},
   Volume = {49},
   Number = {3},
   Pages = {357-366},
   Abstract = {New Zealand is generally thought to have been physically isolated from the rest of the world for over 60 million years. But physical isolation may not mean biotic isolation, at least on the time scale of millions of years. Are New Zealand's present complement of plants the direct descendants of what originally rafted from Gondwana? Or has there been total extinction of this initial flora with replacement through long-distance dispersal (a complete biotic turnover)? These are two possible extremes which have come under recent discussion. Can the fossil record be used to decide the relative importance of the two endpoints, or is it simply too incomplete and too dependent on factors of chance? This paper suggests two approaches to the problem - The use of statistics to apply levels of confidence to first appearances in the fossil record and the analysis of trends based on the entire palynorecord. Statistics can suggest that the first appearance of a taxon was after New Zealand broke away from Gondwana-as long as the first appearance in the record was not due to an increase in biomass from an initially rare state. Two observations can be drawn from the overall palynorecord that are independent of changes in biomass: (1) The first appearance of palynotaxa common to both Australia and New Zealand is decidedly non-random. Most taxa occur first in Australia. This suggests a bias in air or water transport from west to east. (2) The percentage of endemic palynospecies in New Zealand shows no simple correlation with the time New Zealand drifted into isolation. The conifer macrorecord also hints at complete turnover since the Cretaceous.},
   Keywords = {dispersal
fossil
plant
New Zealand},
   Year = {2001} }




@article{
Pole89a,
   Author = {Pole, M. S. and Holden, A. M. and Campbell, J. D.},
   Title = {Fossil legumes from the Manuherikia Group (Miocene), Central Otago, New Zealand},
   Journal = {Journal - Royal Society of New Zealand},
   Volume = {19},
   Number = {3},
   Pages = {225-228},
   Abstract = {Leguminosae fossils are prominent in the Nevis Oil Shale Member of the Manuherikia Group in Central Otako, New Zealand. Valves from legumes up to 74 mm long are found as compressions in laminated mudstone along with other plant microfossils and freshwater mussels. -Authors},
   Keywords = {leguminosae
Manuherikia Group
Miocene
Nevis Oil Shale Member
Tertiary
New Zealand, Central Otago},
   Year = {1989} }




@incollection{
Pohill81-Carm,
   Author = {Polhill, R. M.},
   Title = {Tribe 17. Carmichaeliae Hutch. (1964)},
   BookTitle = {Advances in Legume Systematics, Part I},
   Editor = {Polhill, R. M. and Raven, P. H.},
   Publisher = {Royal Botanic Gardens},
   Address = {Kew, England},
   Pages = {364-366},
      Year = {1981} }




@book{
Polhill81,
   Author = {Polhill, R. M. and Raven, P. H. and Stirton, C. H.},
   Title = {Evolution and systematics of the Leguminosae},
   Publisher = {Royal Botanic Gardens},
   Address = {Kew, England.},
   Series = {Advances in legume systematics, part I},
      Year = {1981} }




@article{
Pongsilp02,
   Author = {Pongsilp, N. and Teaumroong, N. and Nuntagij, A. and Boonkerd, N. and Sadowsky, M. J.},
   Title = {Genetic structure of indigenous non-nodulating and nodulating populations of Bradyrhizobium in soils from Thailand},
   Journal = {Symbiosis},
   Volume = {33},
   Number = {1},
   Pages = {39-58},
   Abstract = {One hundred and thirty symbiotic and non-symbiotic strains of Bradyrhizobium were directly isolated from inoculated soybean and uninoculated legume-free virgin field soils in Thailand using a direct selection medium. About 47% and 58% of the isolates obtained from inoculated and uninoculated fields, respectively, were characterized as being non-symbiotic bradyrhizobia. Partial and nearly full-length sequence analyses of regions encoding 16S rRNA indicated that the non-symbionts were closely related to Bradyrhizobium elkanii (79-99% identity) and Bradyrhizobium japonicum (96-100% identity). Southern hybridization analyses showed that DNA from the non-symbiotic bradyrhizobia failed to hybridize to nif and nod gene probes. rep-PCR DNA fingerprint analyses, done using the BOXA1R primer, indicated the symbionts and non-symbionts could be separated into two distinct clusters. There was no relationship between the geographical origin of isolates and groups made based on serological reaction or their ability to nodulate soybean, cowpea, mungbean, or siratro. These results indicate that a relatively large percentage of non-nodulating bradyrhizobia are present in Thai soils.},
   Keywords = {16S rDNA
Bradyrhizobium
Non-nodulating
Soil bacteria
Soil populations
Soybean},
   Year = {2002} }




@article{
Poole02,
   Author = {Poole, A. M. and Logan, D.T. and Sjöberg, B.-M.},
   Title = {The evolution of the ribonucleotide reductases: Much ado about oxygen},
   Journal = {Journal of Molecular Evolution},
   Volume = {55},
   Number = {2},
   Pages = {180-196},
   Abstract = {Ribonucleotide reduction is the only known biological means for de novo production of deoxyribo-nucleotides, the building blocks of DNA. These are produced from ribonucleotides, the building blocks of RNA, and the direction of this reaction has been taken to support the idea that, in evolution, RNA preceded DNA as genetic material. However, an understanding of the evolutionary relationships among the three modern-day classes of ribonucleotide reductase and how the first reductase arose early in evolution is still far off. We propose that the diversification of this class of enzymes is inherently tied to microbial colonization of aerobic and anaerobic niches. The work is of broader interest, as it also sheds light on the process of adaptation to oxygenic environments consequent to the evolution of atmospheric oxygen.},
   Keywords = {Aerobic
Anaerobic
DNA origins
Oxygen evolution
Ribonucleotide reductase},
   Year = {2002} }




@incollection{
Posada03,
   Author = {Posada, D.},
   Title = {Selecting models of evolution},
   BookTitle = {The Phylogentic Handbook: A practical approach to DNA and protein phylogeny},
   Editor = {Salemi, Marco and Vandamme, Anne-Mieke},
   Publisher = {Cambridge University Press},
   Address = {Cambridge},
   Pages = {256-282},
      Year = {2003} }




@article{
Posada04,
   Author = {Posada, D. and Buckley, T. R.},
   Title = {Model selection and model averaging in phylogenetics: Advantages of akaike information criterion and bayesian approaches over likelihood ratio tests},
   Journal = {Systematic Biology},
   Volume = {53},
   Number = {5},
   Pages = {793-808},
   Abstract = {Model selection is a topic of special relevance in molecular phylogenetics that affects many, if not all, stages of phylogenetic inference. Here we discuss some fundamental concepts and techniques of model selection in the context of phylogenetics. We start by reviewing different aspects of the selection of substitution models in phylogenetics from a theoretical, philosophical and practical point of view, and summarize this comparison in table format. We argue that the most commonly implemented model selection approach, the hierarchical likelihood ratio test, is not the optimal strategy for model selection in phylogenetics, and that approaches like the Akaike Information Criterion (AIC) and Bayesian methods offer important advantages. In particular, the latter two methods are able to simultaneously compare multiple nested or nonnested models, assess model selection uncertainty, and allow for the estimation of phylogenies and model parameters using all available models (model-averaged inference or multimodel inference). We also describe how the relative importance of the different parameters included in substitution models can be depicted. To illustrate some of these points, we have applied AIC-based model averaging to 37 mitochondrial DNA sequences from the subgenus Ohomopterus (genus Carabus) ground beetles described by Sota and Vogler (2001).},
   Keywords = {AIC
Bayes factors
BIC
Likelihood ratio tests
Model averaging
Model selection
Model uncertainty
Multimodel inference},
   Year = {2004} }




@article{
Posada01,
   Author = {Posada, David and Crandall, Keith A.},
   Title = {Evaluation of methods for detecting recombination from DNA sequences: Computer simulations},
   Journal = {Proceedings of the National Academy of Sciences of the United States of America},
   Volume = {98},
   Number = {24},
   Pages = {13757-13762},
   Abstract = {Recombination is a key evolutionary process that shapes the architecture of genomes and the genetic structure of populations. Although many statistical methods are available for the detection of recombination from DNA sequences, their absolute and relative performance is still unknown. Here we evaluated the performance of 14 different recombination detection algorithms. We used the coalescent with recombination to simulate DNA sequences with different levels of recombination, genetic diversity, and rate variation among sites. Recombination detection methods were applied to these data sets, and whether they detected or not recombination was recorded. Different recombination methods showed distinct performance depending on the amount of recombination, genetic diversity, and rate variation among sites. The model of nucleotide substitution under which the data were generated did not seem to have a significant effect. Most methods increase power with more sequence divergence. In general, recombination detection methods seem to capture the presence of recombination, but they are not very powerful. Methods that use substitution patterns or incompatibility among sites were more powerful than methods based on phylogenetic incongruence. Most methods do not seem to infer more false positives than expected by chance. Especially depending on the amount of diversity in the data, different methods could be used to attain maximum power while minimizing false positives. Results shown here will provide some guidance in the selection of the most appropriate method/s for the analysis of the particular data at hand.},
      Year = {2001} }




@article{
Posada98,
   Author = {Posada, David and Crondall, Keith A.},
   Title = {Modeltest: testing the model of DNA substitution},
   Journal = {Bioinformatics},
   Volume = {14},
   Number = {9},
   Pages = {817-818},
   Keywords = {DNA},
   Year = {1998} }




@article{
Potter55,
   Author = {Potter, L. F.},
   Title = {Isolation of rhizobia from preserved nodules},
   Journal = {Applied Microbiology},
   Volume = {3},
   Number = {3},
   Pages = {160-1},
      Year = {1955} }




@article{
Prakash81,
   Author = {Prakash, R. K. and Schilperoort, R. A. and Nuti, M. P.},
   Title = {Large plasmids of fast-growing rhizobia: homology studies and location of structural nitrogen fixation (\emph{nif}) genes},
   Journal = {Journal of Bacteriology},
   Volume = {145},
   Number = {3},
   Pages = {1129-1136},
   Abstract = {A single large plasmid was isolated from multiplasmid-harboring strains Rhizobium leguminosarum 1001 and R. trifolii 5. These single plasmids, as well as the largest plasmid detectable in R. phaseoli 3622, hybridized with part of the nif structural genes of Klebsiella pneumoniae. In contrast, the plasmids of R. meliloti strains V7 and L5-30 did not show hybridization with the nif genes of K. pneumoniae, indicating that these genes might be located either on the chromosome or on a much larger plasmid which as yet has not been isolated. Studies of the homology between plasmids of fast-growing Rhizobium species showed that a specific deoxyribonucleic acid sequence, which carries the structural genes for nitrogenase, is highly conserved on a plasmid in R. leguminosarum, R. trifolii, and R. phaseoli. Furthermore, it was found that this type of plasmid in the different species shares extensive deoxyribonucleic acid homology, suggesting that strains in the R. leguminosarum cluster have preserved a nif plasmid.},
   Keywords = {Base Sequence
*Genes, Structural
Klebsiella pneumoniae/genetics
*Nitrogen Fixation
Nitrogenase/*genetics
Nucleic Acid Hybridization
*Plasmids
Rhizobium/*genetics/metabolism
Support, Non-U.S. Gov't},
   Year = {1981} }




@article{
Prebble02,
   Author = {Prebble, M. and Shulmeister, J.},
   Title = {An analysis of phytolith assemblages for the quantitative reconstruction of late Quaternary environments of the Lower Taieri Plain, Otago, South Island, New Zealand II. Paleoenvironmental reconstruction},
   Journal = {Journal of Paleolimnology},
   Volume = {27},
   Number = {4},
   Pages = {415-427},
   Abstract = {Fossil phytolith assemblages from a 154.5 m longdrill core from the Lower Taieri Plain, Otago, New Zealand are presented. Transfer functions, based on modern phytolith assemblages from sites within the same region, were applied to the fossil phytolith data set, and validated using Modern Analogue Technique (MAT) assemblage matching. Analogues for much of the Holocene and some of the Last Interglacial (provisionally Oxygen Isotope Stage 5c) were obtained. Late Glacial/Holocene precipitation and pH estimates are consistent with other paleoclimate records from the Otago region. The phytolith-based precipitation and pH estimates may act as a combined proxy for soil weathering. The precipitation estimates may also act as a useful index of Effective Precipitation (EP). Temperature estimates derived have limited use for paleoclimate interpretation. Estimates produced for the mid-Holocene indicate a wetter environment than the present (50-100 mm greater EP) with increased soil weathering (high precipitation/low pH). Soil conductivity estimates were below estuarine levels during a diatom inferred marine transgression. This lack of phytolith response to conductivity changes is put down to a probable delayed development of suitable habitats for saltmarsh plant species during the rapid transgression. The Last Interglacial estimates indicate conditions somewhat drier (200 mm less EP) than the Holocene. Consistently low log conductivity (below 0.7 ?S cm) estimates from the Last Interglacial contrast with the estuarine environments of the Holocene, indicating freshwater conditions in the Plain during at least part of the Last Interglaciation.},
   Keywords = {Calibration
Climate reconstruction
Late Quaternary
Modern Analogue Technique
New Zealand
Otaga
Phytoliths
Transfer functions
fossil assemblage
paleoclimate
paleoenvironment
phytolith
Quaternary
sediment core
transfer function
New Zealand},
   Year = {2002} }




@article{
Prevost03,
   Author = {Prevost, D. and Drouin, P. and Laberge, S. and Bertrand, A. and Cloutier, J. and Levesque, G.},
   Title = {Cold-adapted rhizobia for nitrogen fixation in temperate regions},
   Journal = {Canadian Journal of Botany},
   Volume = {81},
   Number = {12},
   Pages = {1153-1161},
   Abstract = {Rhizobia from Canadian soils were selected for cold adaptation with the aim of improving productivity of legumes that are subjected to cool temperatures during the growing season. One approach was to use rhizobia associated with legume species indigenous to arctic and subarctic regions: (i) Mesorhizobium sp. isolated from Astragalus and Oxytropis spp. and (H) Rhizobium leguminosarum from Lathryrus spp. The majority of these rhizobia are considered psychrotrophs because they can grow at 0 degreesC. The advantages of cold adaptation of arctic Mesorhizobium to improve legume symbiosis were demonstrated with the temperate forage legume sainfoin (Onobrychis viciifolia). In laboratory and field studies, arctic rhizobia were more efficient than temperate (commercial) rhizobia in improving growth of sainfoin and were more competitive in forming nodules. Biochemical studies on cold adaptation showed higher synthesis of cold shock proteins in cold-adapted than in nonadapted arctic rhizobia. Since arctic Mesorhizobium cannot nodulate agronomically important legumes, the nodulation genes and the bacterial signals (Nod factors) were characterized as a first step to modifying the host specificity of nodulation. Another valuable approach was to screen for cold adaptation, that is, rhizobia naturally associated with agronomic legumes cultivated in temperate areas. A superior strain of Sinorhizobium meliloti adapted for nodulation of alfalfa at low temperatures was selected and was the most efficient for improving growth of alfalfa in laboratory and field studies. This strain also performed well in improving regrowth of alfalfa after overwintering under cold and anaerobic (ice encasement) stresses, indicating a possible cross-adaptation of selected rhizobia for various abiotic stresses inherent to temperate climates.},
      Year = {2003} }




@article{
Prithiviraj03,
   Author = {Prithiviraj, B. and Zhou, X. and Souleimanov, A. and Khan, W. M. and Smith, D. L.},
   Title = {A host-specific bacteria-to-plant signal molecule (Nod factor) enhances germination and early growth of diverse crop plants},
   Journal = {Planta},
   Volume = {216},
   Number = {3},
   Pages = {437-45},
   Abstract = {Lipo-chitooligosaccharides (LCOs), or Nod factors, are host-specific bacteria-to-plant signal molecules essential for the establishment of a successful N(2)-fixing legume-rhizobia symbiosis. At submicromolar concentrations Nod factors induce physiological changes in host and non-host plants. Here we show that the Nod factor Nod Bj V(C18:1,MeFuc) of Bradyrhizobium japonicum 532C enhances germination of a variety of economically important plants belonging to diverse botanical families: Zea mays, Oryza sativa (Poaceae), Beta vulgaris (Chenopodaceae), Glycine max, Phaseolus vulgaris (Fabaceae), and Gossypium hirsutum (Malvaceae), under laboratory, greenhouse and field conditions. Similar increases in germination were observed for filtrates of genistein-induced cultures of B. japonicum 532C, while non-induced B. japonicum, induced Bj 168 (a nodC mutant of B. japonicum deficient in Nod factor synthesis) or the pentamer of chitin did not invoke such responses, demonstrating the role of Nod factor in the observed effects. In addition, three out of four synthetic LCOs evaluated also promoted germination of corn, soybean and Arabidopsis thaliana seeds. LCO also enhanced the early growth of corn seedlings under greenhouse conditions. These findings suggest the possible use of LCOs for improved crop production.},
   Keywords = {Bacteria/*growth \& development
Beta vulgaris/drug effects/growth \& development
Germination/*drug effects/physiology
Gossypium/drug effects/growth \& development
Lipopolysaccharides/metabolism/*pharmacology
Nitrogen Fixation/drug effects/physiology
Oryza sativa/drug effects/growth \& development
Plants/growth \& development/*microbiology
Seeds/*drug effects/growth \& development
Signal Transduction/*drug effects/physiology
Soybeans/drug effects/growth \& development
Support, Non-U.S. Gov't
Support, U.S. Gov't, Non-P.H.S.
Symbiosis/drug effects/physiology
Zea mays/drug effects/growth \& development},
   Year = {2003} }




@article{
Provorov96a,
   Author = {Provorov, N. A.},
   Title = {Coevolution of legumes and root nodule bacteria: Taxonomical and genetical aspects},
   Journal = {Zhurnal Obshchei Biologii},
   Volume = {57},
   Number = {2},
   Pages = {52-78},
   Abstract = {The origin and evolution mechanisms of legume-rhizobian simbiosis in comparison with other mutualistic and antagonistic system interactions have been examined. In was shown that the legume nodulation was more ancient feature than nitrogen-fixing symbiosis formation while their microsymbionts rhizobia developed a nitrogen-fixing ability earlier than the ability to induce the nodulation. The plant host's primary role in symbiosis evolution is confirmed by the fact that: a) legumes form a separate taxonomic group thus differing in this respect from rhizobia: b) macroevolution of symbiosis resulted in increase specificity of interaction between the partners, increased complexity of ultrastructural organisation, and higher nitrogen-fixing activity of nodules. Symbiosis microevolution is provided by: a) an increase in density and genetic heterogeneity of rhizobian populations during their interaction With their hosts; b) <<symbiotic>> rhizobia genes recombinational instability and their transmission among different lines; c) the maintenance of polymorfism in accordance with their ability to autotrophic and symbiotrophic nutrition in legum population. The persistence of nitrogen-fixing genes in rhizobian populations and the increase in their nitrogen-fixing activity is provided by mechanism of group selection, i.e. preferential multiplication of nitrogen-fixing clones in nodules. This form of selection is due to the <<altruism>> of bacteria cells that have undergone irreversible differentiation into bacteroids while the rest of the nodule clone returns to the soil population after the plant death. The legume rhizobian simbiosis is not connected by a direct evolutionary relationship with such bacteria-plant systems as <<soil bacteria-dicotyledons>> or <<micorhiza-actinorhiza>>.},
      Year = {1996} }




@article{
Provorov96b,
   Author = {Provorov, N. A.},
   Title = {Evolution of symbiotic genetic systems in rhizobia},
   Journal = {Genetika},
   Volume = {32},
   Number = {8},
   Pages = {1029-1040},
   Abstract = {Probable molecular and population-genetic mechanisms of microevolution of the genetic systems controlling interactions of root nodule bacteria with legumes, as well as the main pathways of their macroevolution, are reviewed. It is suggested that synchronization of the rates of bacterial and plant genome evolution was the condition necessary for coevolution of root nodule bacteria and legumes. This could have been achieved via an increase in recombination activity of the bacterial genome during the formation of the virulence gene system. The latter process was associated with changes in the pattern of certain genes controlling different metabolic functions in nonsymbiotic nitrogen-fixing organisms (origin of Bradyrhizobium and Azorhizobium, the ''primary'' root nodule bacteria capable of nitrogen fixation ex planta). Increased genetic instability could have been to the transfer of main symbiotic genes into plasmids. This, in turn, resulted in the development of a complex genetic population structure (origin of ''nonsymbiotic'' subpopulations providing for a high frequency of horizontal transfer of symbiotic genes) and made possible the development of new rhizobia forms via symbiotic gene transfer to different soil bacteria (origin of Rhizobium, the ''secondary'' root nodule bacteria incapable of nitrogen fixation ex planta). Comparing the patterns of genes controlling interactions with plants in Rhizobium and Agrobacterium showed that symbiotic and parasitic traits of these related microorganisms developed independently, although similar mechanisms could be responsible for evolution of nodulation in the rhizobia-legume system and for evolution of phytoparasitic systems. It is suggested that both Rhizobium and Agrobacterium originated from saprophytic soil microorganisms capable of synthesizing certain cell wall molecules (polysaccharides, glucans, etc.) allowing them to persist in tissues of higher plants.},
      Year = {1996} }




@article{
Provorov98b,
   Author = {Provorov, N. A.},
   Title = {Coevolution of rhizobia with legumes: Facts and hypotheses},
   Journal = {Symbiosis},
   Volume = {24},
   Number = {3},
   Pages = {337-367},
   Abstract = {The ability to form N-2-fixing symbioses has a monophyletic (paraphyletic) origin in legumes and a polyphyletic origin in rhizobia. Analysis of taxonomic data suggests that in legumes nodulation is a more ancient property than symbiotrophic nitrogen nutrition while in rhizobia the ability to nodulate their hosts is of a more recent origin than the ability to fix N-2. The ancestors of both partners are supposed to have possessed the preadaptations which ensured a subsequent evolution of the symbiotic system. The plant preadaptations might have been: spontaneous formation of the nodule-like structures and an ability to permit a persistence of potential symbionts in them. The bacterial preadaptations might have been: the ability to fix N-2 and to resist (escape) the plant defense reactions. In rhizobia the nodulation ability is supposed to evolve mainly via the individual selection, while the ability for symbiotic N-2 fixation - via the kin selection of the clones. Evolution of nod genes in rhizobia is supposed to elicit formation of the mechanisms for restriction (regulation) of nodulation in hosts. Although the legume-rhizobia coevolution for nodulation might have the marked similarities with the gene-for-gene coevolution, the direct evolutionary relationships between legume-rhizobia symbioses and the phytopathogenic systems are not probable. The plant-bacteria coevolution is suggested to be based on:(i) intensive intergenomic recombination and horizontal transfer of genes in rhizobia populations; (ii) increasing the genetic heterogeneity of these populations via interaction with the hosts.},
      Year = {1998} }




@article{
Provorov00b,
   Author = {Provorov, N. A.},
   Title = {Population genetics of nodule bacteria},
   Journal = {Zhurnal Obshchei Biologii},
   Volume = {61},
   Number = {3},
   Pages = {229-257},
   Abstract = {The data are reviewed on the population structure and evolutionary dynamics of the nodule bacteria (rhizobia) which are among the most intensively studied microorganisms. High level of the population polymorphism was demonstrated for the rhizobia populations using the enzyme electrophoresis (MLEE profiles). The average value of Nei's coefficient of heterogeneity (H = 1 - Sigma (2)(Pi) [n /(n - 1)]) were: 0,590 for rhizobia (Rhizobium, Bradyrhizobium), 0,368 for enterobacteria (Escherichia, Salmonella, Shigella) and 0,452 for pathogenic bacteria (Bordetella, Borrelia, Eryispelotrix, Haemophilus, Heliobacter, Listeria, Mycobacterium, Neisseria, Staphylococcus) populations. In spite of being devoid of the effective systems for the gene conjugative transfer, many rhizobia populations possess an essentially panmictic structure. However, the enterobacteria populations in which the gene transfer may be facilitated due to the conjugative F- and R-factors, usually display the clonal population structure. The legume host plant is proved to be a key factor that determines the high levels of polymorphism and of panmixia as well as high evolutionary rates of the symbiotic bacteria populations. The host may ensure: a) an increase in mutation and gene transfer frequencies; b) stimulation of the competitive (selective) processes in both symbiotic and free-living rhizobia populations. A "cyclic" model of the rhyzobia microevolution is presented which allows to assess the inputs the interstrain competition for the saprophytic growth and for the host nodulation into evolution of a plant-associated rhizobia population. The nodulation competitiveness in the rhizobia populations is responsible for the frequency-dependent selection of the rare genotypes which may arise in the soil bacterial communities as a result of the transfer of symbiotic (sym) genes from virulent rhizobia strains to either avirulent rhizobia or to the other (saprophytic, phytopathogenic) bacteria. Therefore, the nodulation competitiveness may ensure: a) panmictic structure of the natural rhizobia populations; b) high taxonomic diversity of rhizobia which was apparently caused by a broad sym gene expansion in the soil bacterial communities. The kin selection models are presented which explain evolution of the "altruistic" (essential for the host plant, but not for the bacteria themselves) symbiotic traits (e.g., the ability for symbiotic nitrogen fixation and for differentiation into non-viable bacteroids) in the rhizobia populations. These models are based on preferential multiplication of the nitrogen-fixing clones either in planta (due to an elevated supply of the nitrogen-fixing nodules with photosynthates) or ex planta (due to a release of the rhizopines from the nitrogen-fixing nodules). Speaking generally, interactions with the host plants provide a range of mechanisms increasing a genetic heterogeneity and an evolutionary potential in the associated rhizobia populations.},
      Year = {2000} }




@article{
Provorov02b,
   Author = {Provorov, N. A. and Borisov, A. Y. and Tikhonovich, I. A.},
   Title = {Comparative genetics and evolutionary morphology of symbioses formed by plants with nitrogen-fixing microbes and endomycorrhizal fungi},
   Journal = {Zhurnal Obshchei Biologii},
   Volume = {63},
   Number = {6},
   Pages = {451-472},
   Abstract = {Results of comparative morphological and genetic analyses are described for two major plant-microbe endosymbioses: N-2-fixing nodules (with rhizobia or actinomycetes Frankia) and arbuscular mycorrhiza (with Glomales fungi). Development from the primordia formed de novo in root tissues is common for all known types of N-2-fixing nodules. However, their structure varies greatly with respect to: (i) tissue topology (location of vascular bundles is peripheral in legumes but central in non-legumes); (ii) position of nodule primordium (inner or outer cortex in legumes, whereas pericycle in non-legumes); (iii) stability of apical meristem (persistent in the indeterminate nodules, transient in the determinate ones). In addition, legumes vary in ability to form compartments harboring endosymbiotic rhizobia that can be located intercellularly (infection threads) and intracellularly (symbiosomes). Using pea (Pisum sativum) symbiotic mutants, the nodule developmental program is dissected into a range of spatially and temporarily differentiated steps composing four sub-programs (development of endosymbiotic compartments; nodule histogenesis; autoregulation of nodulation; bacteroid differentiation). The developmental mutations are suggested in some cases to reverse the endosymbiotic system into the morphologically simpler forms some of which may correspond to the ancestral stages of nodule evolution. Origination of legume-rhizobial and actinorhizal symbioses is suggested to be based on a set of preadaptations many of which had been evolved in angiosperms during coevolution with arbuscular mycorrhizal fungi (e.g. inter- and intracellular maintenance of symbionts, their control via defence-like reactions and recognition of chitin-like molecules). Analysis of parallel morphological variation in symbiotic mutants and wild-growing legume species enables us to reconstruct the major stages of evolution for N-2-fixing symbioses. This evolution proceeded to a sufficient degree independently from the basic physiological function of nodules (symbiotic N-2-fixation) and possibly a recruiting of plant genes that initially fulfilled various "non-symbiotic" functions into the genetic networks monitoring plant-microbe interactions.},
      Year = {2002} }




@article{
Provorov02a,
   Author = {Provorov, N. A. and Borisov, A. Y. and Tikhonovich, I. A.},
   Title = {Developmental genetics and evolution of symbiotic structures in nitrogen-fixing nodules and arbuscular mycorrhiza},
   Journal = {Journal of Theoretical Biology},
   Volume = {214},
   Number = {2},
   Pages = {215-232},
   Abstract = {Genetic and molecular mechanisms of development are compared for two major plant-microbe endosymbioses: N-2-fixing nodules (with rhizobia or actinomycetes Frankia) and arbuscular mycorrhiza (with Glomales fungi). Development from the primordia formed de novo in root tissues is common for all known types of N-2-fixing nodules. However, their structure varies greatly with respect to: (i) tissue topology (location of vascular bundles is peripherical in legumes or central in non-legumes); (ii) position of nodule primordium (inner or outer cortex in legumes, pericycle in non-legumes); (iii) stability of apical meristem (persistent in the indeterminate nodules, transient in the determinate ones). In addition, legumes vary in ability to form compartments harboring endosymbiotic rhizobia and located intercellularly (infection threads) and intracellularly (symbiosomes). Using pea (Pisum sativum) symbiotic mutants, the nodule developmental program is dissected into a range of spatially and temporarily differentiated steps comprising four sub-programs (development of endosymbiotic compartments; nodule histogenesis; autoregulation of nodulation; bacteroid differentiation). The developmental mutations are suggested in some cases to reverse the endosymbiotic system into the morphologically simpler forms some of which may correspond to the ancestral stages of nodule evolution. The origin of legume-rhizobial and actinorhizal symbioses is suggested to be based on a set of preadaptations many of which had been evolved in angiosperms during coevolution with arbuscular mycorrhizal fungi (e.g., inter- and intracellular maintenance of symbionts, their control via defence-like reactions and recognition of chitin-like molecules). An analysis of parallel morphological variation in symbiotic mutants and wild-growing legume species enables us to reconstruct the major stages of evolution for N-2-fixing symbioses. (C) 2002 Academic Press.},
      Year = {2002} }




@article{
Provorov98a,
   Author = {Provorov, N. A. and Vorob'ev, N. I.},
   Title = {Population Genetics of Nodule Bacteria: Simulation of Cyclic Processes in Bacterial-Plant Systems},
   Journal = {Russian Journal of Genetics},
   Volume = {34},
   Number = {12},
   Pages = {1455-1461},
   Abstract = {A model allowing the analysis of the role of reproduction in legume nodules and transfer of the symbiotic sym genes in the evolution of legume facultative symbionts, nodule bacteria (rhizobia), was elaborated. The model describes the formation of new symbiont populations as a result of the sym gene transfer from initial symbionts to avirulent soil bacteria and reproduction of the formed virulent recombinants in nodules. The microevolution of a closed bacterial-plant system was analyzed. The system was assumed to have several constant parameters: the numbers of initial symbionts and local avirulent bacteria, the frequency of the formation of new symbionts as a result of the sym gene transfer, the total number of nodules formed by initial and new symbionts, and the number of bacteria released into the soil after the degradation of a nodule. According to the model, the microevolution of the system consists of a number of cycles, each involving (1) transfer of the sym genes from nodule strains to local bacteria, which produces new virulent symbionts; (2) competition of virulent strains (initial and new symbionts) for nodulation; (3) in planta reproduction and release of virulent clones into the soil; and (4) competition of virulent and avirulent local strains for ex planta saprophytic living. A recurrent equation, which allows the estimation of the numbers of new symbionts at all evolutionary cycles, was obtained. The microevolution rate of the system was shown to depend mostly on the number of nodules formed by bacteria on plant roots and, to the least extent, on the numbers of initial symbionts.},
      Year = {1998} }




@article{
Provorov00c,
   Author = {Provorov, N. A. and Vorob'ev, N. I.},
   Title = {Evolutionary genetics of nodule bacteria: Molecular and population aspects},
   Journal = {Russian Journal of Genetics},
   Volume = {36},
   Number = {12},
   Pages = {1323-1335},
   Abstract = {The molecular analysis of the genetic systems controlling the main stages of nodule bacteria (rhizobia) interaction with a legume host (signaling at early stages and symbiotic nitrogen fixation) has shown that the widespread recombination of genetic material in free-living ancestors of rhizobia was an important factor in the evolution of these systems. These recombinations could be conditioned by a high content of repeated DNA sequences and the IS elements in the rhizobial genome. A high recombination activity of rhizobia is manifested in the panmictic structure of their populations, which is associated with frequency-dependent selection favoring rare recombinants. This selection is realized through the competition of virulent strains for the nodule formation and can be controlled by the genes whose expression depends on population density (via the quorum sensing mechanism). A high degree of panmixia in rhizobial populations is associated with their ecotypic polymerphism, manifested as the coexistence of symbiotic and nonsymbiotic strains. This type of polymorphism is caused by individual selection during the periodic changes of ecological niches (soil-plant host) in the rhizobia life cycle. The rhizobia-plant interaction stimulates selection in bacterial populations, which results in the increased levels of their heterogeneity and panmixia. The combination of individual and frequency-dependent selection types resulted in the high rates of symbiosis evolution and polyphyletic origin of diverse rhizobial species.},
      Year = {2000} }




@article{
Provorov00a,
   Author = {Provorov, N. A. and Vorobyov, N. I.},
   Title = {Population genetics of rhizobia: construction and analysis of an "Infection and Release" model},
   Journal = {J Theor Biol},
   Volume = {205},
   Number = {1},
   Pages = {105-19},
   Abstract = {A mathematical model is created to assess the inputs of sym gene transfer of in planta multiplication and of interstrain competition into dynamics of the rhizobia populations. Their microevolution is presented as a series of the "infection and release" cycles; each cycle includes transfer of sym genes from virulent initial symbionts to avirulent local bacteria yielding the virulent novel symbionts; competition between initial symbionts and novel symbionts for the host nodulation; multiplication of initial symbionts and novel symbionts in planta and their release into soil; competition between the released novel symbionts and resident local bacteria for ex planta survival. A recurrent equation is created to determine the number of novel symbionts at each cycle of evolution of the closed bacteria-plant system. Its analysis demonstrates that under certain, really allowable values of the introduced parameters two major effects may occur: (a) rapid multiplication of novel symbionts arisen from sym gene transfer; and (b) increase of frequency of rare local bacteria genotypes after acquisition of virulence. Multiplication of very rare strains (p<10(-19)) in the plant-associated bacteria population is possible at certain parameters of the system. Variation of the sizes of bacteria populations and of the parameters for interstrain competition may influence the evolutionary rate of the bacteria population. The "infection and release" model represents a selective mechanism which may be responsible for a high taxonomic diversity of rhizobia and for a panmictic structure of their populations.},
   Keywords = {*Genetics, Population
*Models, Genetic
Population Dynamics
Rhizobium/*genetics
Support, Non-U.S. Gov't
*Symbiosis},
   Year = {2000} }




@article{
Provorov03,
   Author = {Provorov, N. A. and Vorobyov, N. I.},
   Title = {Microevolution of nodule bacteria upon generation of mutants with altered survival in the plant-soil system},
   Journal = {Russian Journal of Genetics},
   Volume = {39},
   Number = {12},
   Pages = {1349-1359},
   Abstract = {Simulation of cyclic processes in the plant-soil system was used to analyze the effects of factors responsible for the population dynamics of rhizobia on generation of mutants with changed ex planta viability. Rhizobial evolution in a system of ecological niches (soil, rhizosphere, nodules) was described with recurrent equations. Computer experiments were carried out with parameters determining the mutation pressure, selection, and amplitude of the population wave arising in soil on the release of bacteria from nodules and the rhizosphere. Analysis of the model showed that (1) mutants with enhanced ex planta viability do not completely replace the parental strain and (2) mutants with impaired ex planta viability may be fixed in the population. The maintenance of genotypes subject to elimination from the soil and rhizosphere by Darwinian selection was associated with frequency-dependent selection (FDS), which is effective in competition for nodulation. The FDS index was proposed to characterize FDS pressure and was shown to determine the population polymorphism for adaptive traits. An increase in population wave amplitude proved to increase the fixation level (the proportion in the limiting state of the system) of mutants with enhanced viability and to decrease it in mutants with low viability. The results obtained with the model agreed with the data that, in edaphic stress, rhizobial populations remain highly polymorphic, which is associated with the maintenance of sensitive strains. The simulation procedure may be employed in estimating the genetic consequences of introduction of modified rhizobial strains in the environment.},
      Year = {2003} }




@article{
Pryor04,
   Author = {Pryor, H. N. and Lowther, W. L. and Elliot, R. M. and Ronson, C. W.},
   Title = {Effect of rhizobia from caucasian clover (Trifolium ambiguum) on nodulation and nitrogen fixation of white clover (Trifolium repens)},
   Journal = {New Zealand Journal of Agricultural Research},
   Volume = {47},
   Number = {1},
   Pages = {75-83},
   Abstract = {Three glasshouse trials investigated N2 fixation in white clover following inoculation with rhizobia from caucasian clover. We grew white clover in agar, vermiculite/perlite and soils low in available-N and with no detectable rhizobia. Media were subsequently treated with inoculum containing rhizobia effective on either (i) caucasian clover, (ii) white clover, or (iii) mixtures of the two. The percentage of ineffective nodules on white clover increased as the proportion of rhizobia from caucasian clover in the inoculant mix increased. However, the percentages of ineffective nodules on white clover were less than the proportion of ineffective rhizobia in the inoculant, indicating that the ineffective rhizobia were less competitive in nodule formation. Foliage yield and symbiotic N2 fixation in white clover were not significantly affected when ineffective rhizobia from caucasian clover made up 67% or less of the inoculant. However, when ineffective rhizobia made up a high proportion of the inoculant mix (>92%), both foliage yield and N 2 fixation were significantly reduced compared with plants inoculated with only white clover rhizobia. Extrapolation of the present glasshouse results to the field is difficult and further field trials are required to determine if rhizobia from caucasian clover have any effect on symbiotic N 2 fixation of white clover in pastoral situations.},
   Keywords = {Caucasian clover
Competition
Nitrogen fixation
Nodulation
Rhizobia
Trifolium ambiguum
Trifolium repens
White clover},
   Year = {2004} }




@article{
Pryor98,
   Author = {Pryor, H. N. and Lowther, W. L. and McIntyre, H. J. and Ronson, C. W.},
   Title = {An inoculant Rhizobium strain for improved establishment and growth of hexaploid Caucasian clover (Trifolium ambiguum)},
   Journal = {New Zealand Journal of Agricultural Research},
   Volume = {41},
   Number = {2},
   Pages = {179-189},
   Abstract = {Strains of Rhizobium leguminosarum bv. trifolii present in New Zealand soils are ineffective on Caucasian clover (Trifolium ambiguum) and inoculation with an effective strain of rhizobia is essential for nodulation. However, problems have been encountered with nodulation of oversewn Caucasian clover and this study was conducted to determine whether nodulation could be improved by the use of an improved strain of rhizobia. Five strains of rhizobia were compared with a re-isolate (ICC105) of the recommended New Zealand commercial inoculant strain (ICMP4073b) for their effect on the establishment of oversewn hexaploid Caucasian clover in Canterbury and Otago, South Island, New Zealand. When strains were incorporated in peat inoculant and used to inoculate seed in a commercial pelleting process, one strain (ICC148) increased the percentage of seedlings nodulated over that obtained with ICC105, from 23% to 49%. In a further evaluation of these two strains, seed was inoculated and lime-coated in the laboratory and stored for either 1 or 20 days before oversewing on 7 tussock grassland sites. Inoculation with ICC148 resulted in a 1.3-fold increase in the percentage of seedlings nodulated over that obtained with ICC105. In addition, dry matter (DM) weights of individual seedlings were increased with strain ICC148. The dry weights of individual Caucasian clover plants after 6 and 13 months increased 1.5 and 3.0-fold, respectively, when inoculated with strain ICC148. Inter-tussock Caucasian clover DM after 17 months was 1870 kg ha(-1) for plants inoculated with ICC105 and 3480 kg ha(-1) for plants inoculated with ICC148. Foliage N contents in spring were increased from 2.6% to 3.1%, when seed was inoculated with ICC148. These results strongly support a change in the Rhizobium strain recommended in New Zealand for hexaploid Caucasian clover to strain ICC148.},
   Keywords = {Caucasian clover; inoculation; nodulation; rhizobia; Rhizobium
leguminosarum bv. trifolii; Trifolium ambiguum},
   Year = {1998} }




@article{
Pueppke96,
   Author = {Pueppke, S. G.},
   Title = {The genetic and biochemical basis for nodulation of legumes by rhizobia},
   Journal = {Critical Reviews in Biotechnology},
   Volume = {16},
   Number = {1},
   Pages = {1-51},
   Abstract = {Soil bacteria of the genera Azorhizobium, Bradyrhizobium, and Rhizobium are collectively termed rhizobia. They share the ability to penetrate legume roots and elicit morphological responses that lead to the appearance of nodules. Bacteria within these symbiotic structures fix atmosphere nitrogen and thus are of immense ecological and agricultural significance. Although modern genetic analysis of rhizobia began less than 20 years ago, dozens of nodulation genes have now been identified, some in multiple species of rhizobia. These genetic advances have led to the discovery of a host surveillance system encoded by nodD and to the identification of Nod factor signals. These derivatives of oligochitin are synthesized by the protein products of nodABC, nodFE, NodPQ, and other nodulation genes; they provoke symbiotic responses on the part of the host and have generated immense interest in recent years. The symbiotic functions of other nodulation genes are nonetheless uncertain, and there remain significant gaps in our knowledge of several large groups of rhizobia with interesting biological properties. This review focuses on the nodulation genes of rhizobia, with particular emphasis on the concept of biological specificity of symbiosis with legume host plants.},
      Year = {1996} }




@article{
Pueppke99,
   Author = {Pueppke, S. G. and Broughton, W. J.},
   Title = {\emph{Rhizobium} sp. strain NGR234 and \emph{R. fredii} USDA257 share exceptionally broad, nested host ranges},
   Journal = {Molecular Plant-Microbe Interactions},
   Volume = {12},
   Number = {4},
   Pages = {293-318},
   Abstract = {Genetically, Rhizobium sp. strain NGR234 and R. fredii USDA257 are closely related. Small differences in their nodulation genes result in NGR234 secreting larger amounts of more diverse lipo-oligosaccharidic Nod factors than USDA257. What effects these differences have on nodulation were analyzed by inoculating 452 species of legumes, representing all three subfamilies of the Leguminosae, as well as the nonlegume Parasponia andersonii, with both strains. The two bacteria nodulated P. andersonii, induced ineffective outgrowths on Delonix regia, and nodulated Chamaecrista fasciculata, a member of the only nodulating genus of the Caesalpinieae tested. Both strains nodulated a range of mimosoid legumes, especially the Australian species of Acacia, and the tribe Ingeae. Highest compatibilities were found with the papilionoid tribes Phaseoleae and Desmodieae. On Vigna spp. (Phaseoleae), both bacteria formed more effective symbioses than rhizobia of the 'cowpea' (V. unguiculata) miscellany. USDA257 nodulated an exact subset (79 genera) of the NGR234 hosts (112 genera). If only one of the bacteria formed effective, nitrogen-fixing nodules it was usually NGR234. The only exceptions were with Apios americana, Glycine max, and G. soja. Few correlations can be drawn between Nod-factor substituents and the ability to nodulate specific legumes. Relationships between the ability to nodulate and the origin of the host were not apparent. As both P. andersonii and NGR234 originate from Indonesia/Malaysia/Papua New Guinea, and NGR234's preferred hosts (Desmodiinae/Phaseoleae) are largely Asian, we suggest that broad host range originated in Southeast Asia and spread outward.},
   Keywords = {genetic difference
plant pathogen interaction
Acacia
Apios americana
Chamaecrista fasciculata
Delonix regia
Glycine max
Glycine soja
Parasponia andersonii
Rhizobium fredii},
   Year = {1999} }




@article{
Puhler04,
   Author = {Puhler, A. and Arlat, M. and Becker, A. and Gottfert, M. and Morrissey, J. P. and O'Gara, F.},
   Title = {What can bacterial genome research teach us about bacteria-plant interactions?},
   Journal = {Current Opinion in Plant Biology},
   Volume = {7},
   Number = {2},
   Pages = {137-147},
   Abstract = {Biological research is changing dramatically. Genomic and post-genomic research is responsible for the accumulation of enormous datasets, which allow the formation of holistic views of the organisms under investigation. In the field of microbiology, bacteria represent ideal candidates for this new development. It is relatively easy to sequence the genomes of bacteria, to analyse their transcriptomes and to collect information at the proteomic level. Genome research on symbiotic, pathogenic and associative bacteria is providing important information on bacteria-plant interactions, especially on type-III secretion systems (TTSS) and their role in the interaction of bacteria with plants.},
      Year = {2004} }




@article{
Pupo97,
   Author = {Pupo, G. M. and Karaolis, D. K. R. and Lan, R. and Reeves, P. R.},
   Title = {Evolutionary relationships among pathogenic and nonpathogenic \emph{Escherichia coli} strains inferred from multilocus enzyme electrophoresis and \emph{mdh} sequence studies},
   Journal = {Infection and Immunity},
   Volume = {65},
   Number = {7},
   Pages = {2685-2692},
   Abstract = {Within the species Escherichia coli, there are commensal strains and a variety of pathogenic strains, including enteropathogenic E. coli (EPEC), enterohemorrhagic E. coli (EHEC), enterotoxigenic E. coli (ETEC), enteroinvasive E. coli (EIEC), and urinary tract infection (UTI) strains. The pathogenic strains are identified by serotype and by possession of specific virulence determinants (toxins and adhesions, etc.) encoded by either monocistronic genes, plasmids, or pathogenicity islands. Although there are studies on the relationships between selected pathogenic strains, the relatedness among the majority of the pathogenic forms to each other, to commensal E. coli, and to the genus Shigella (which has often been suggested to be part of E. coli) has not been determined. We used multilocus enzyme electrophoresis (MLEE) at 10 enzyme loci and the sequence of the mdh housekeeping gene to study the genetic relationships of pathogenic E. coli strains (including Shigella clones), namely, 5 EPEC strains (serotypes O111 and O55), 3 EHEC strains (serotype O157), 6 ETEC strains (serotypes P78, O159, and O148), 5 EIEC strains (serotypes O124, O28, and O112), and 13 Shigella strains representing clones Flexneri, Dysenteriae, Boydii, and Sonnei, to commensal E. coli strains. Both the MLEE and mdh sequence trees reveal that EPEC, EHEC, ETEC, EIEC, and UTI strains are distributed among the ECOR set groups, with no overall clustering of EPEC, ETEC, EJEC, or UTI strains. The genus Shigella is shown to comprise a group of closely related pathogenic E. coli strains. Six pathogenic strains, i.e., M502 (EIEC; O112ac:NM), M503 (EPEC; O111:H12), M526 (ETEC; O159:H4), M522 (EPEC; O111ac:H12) M524 (ETEC; O78:H11), and M506 (ETEC; O78:H11), were found to have mdh sequences identical to those of five ECOR group A strains (ECOR5, ECOR10, ECOR14, ECOR6, and K-121). All 11 strains are closely related by MLEE. The results indicate that pathogenic strains of E. coli do not have a single evolutionary origin within E. coli but have arisen many times. The results also suggest the possibility that any E. coli strain acquiring the appropriate virulence factors may give rise to a pathogenic form.},
      Year = {1997} }




@article{
Qian02,
   Author = {Qian, J. and Parker, M. A.},
   Title = {Contrasting \emph{nifD} and ribosomal gene relationships among \emph{Mesorhizobium} from \emph{Lotus oroboides} in Northern Mexico},
   Journal = {Systematic and Applied Microbiology},
   Volume = {25},
   Number = {1},
   Pages = {68-73},
   Abstract = {PCR screens for length variation in a 5? portion of 23S ribosomal RNA and in the 3? end of the 16S rRNA-23S rRNA internal transcribed spacer (ITS) region indicated that nodule bacteria from a Mexican population of Lotus oroboides were diverse on a local scale. Three 23S rRNA length variants and five ITS length variants were detected among the 22 isolates. Sequencing of nearly full-length 16S rRNA genes in three isolates indicated that they fell into the genus Mesorhizobium, but comprised two distinct groups. Two isolates were closely related to M. loti LMG 6125T, while the other isolate clustered with an assemblage of Mesorhizobium taxa that included M. amorphae, M. plurifarium and M. huakuii. However, a phylogenetic tree based on 715 bp of the nitrogenase ?-subunit (nifD) gene was significantly discordant with the relationships inferred from rRNA sequences. Two isolates that were nearly identical for 16S rRNA had nifD genes that varied at 2% of sites, and one of these nifD sequences was identical to that of another isolate with a strongly divergent 16S rRNA gene. A plasmid screen followed by Southern hybridization indicated that only one of these strains harbored a plasmid-borne nifD gene. These results imply that gene transfer events have altered the distribution of nifD sequences among lineages within this natural population of Mesorhizobium strains.},
   Keywords = {16S ribosomal RNA
23S ribosomal RNA
Nitrogenase
Recombination
Symbiotic plasmid},
   Year = {2002} }




@article{
Quan05,
   Author = {Quan, Z.-X. and Bae, H.-S. and Baek, J.-H. and Im, W.-T. and Lee, S.-T. and Chen, W.-F.},
   Title = {\emph{Rhizobium daejeonense} sp. nov. isolated from a cyanide treatment bioreactor},
   Journal = {International Journal of Systematic and Evolutionary Microbiology},
   Volume = {55},
   Number = {6},
   Pages = {2543-2549},
   Abstract = {A polyphasic study was carried out to determine the taxonomic position of two aerobic, cyanide-degrading bacterial strains, designated L61T and L22, which had been isolated from a bioreactor for the treatment of nickel-complexed cyanide. The two isolates exhibited almost identical taxonomic characteristics. Phylogenetic analysis inferred from comparative 16S rRNA gene sequences indicated that the isolates fall in a sublineage of the genus Rhizobium comprising the type strains of Rhizobium giardinii, Rhizobium radiobacter, Rhizobium rubi, Rhizobium larrymoorei, Rhizobium vitis, Rhizobium undicola, Rhizobium loessense, Rhizobium galegae and Rhizobium huautlense. Cells of the two isolates are Gram-negative, aerobic, motile and non-spore-forming rods (0.6-0.7 × 1.1-1.3 ?m), with peritrichous flagella. The DNA G+C content is 60.1-60.9 mol%. Cellular fatty acids are C16:0 (2.2-3.3 %), C18:0 (2.1-3.2 %), C19:0 cyclo ?8c(9.9-16.8%), C20:3?6,9,12c(2.7-3.3 %), summed feature 3(7.2-7.7 %) and summed feature 7 (67.8-73.7 %). The strains formed nodules on a legume plant, Medicago sativa. A nifH gene encoding denitrogenase reductase, the key component of the nitrogenase enzyme complex, was detected in L61T by PCR amplification by using a nifH-specific primer system. Strains L61T and L22 were distinguished from the type strains of recognized Rhizobium species in the same sublineage based on low DNA-DNA hybridization values (2-4 %) and/or a 16S rRNA gene sequence similarity value of less than 96 %. Moreover, some phenotypic properties with respect to substrate utilization as a carbon or nitrogen source, antibiotic resistance and growth conditions could be used to discriminate L61T and L22 from Rhizobium species in the same sublineage. Based on the results obtained in this study, L61T and L22 are considered to be representatives of a novel species of Rhizobium, for which the name Rhizobium daejeonense sp. nov. is proposed. The type strain is L61T (=KCTC 12121T=IAM 15042T=CCBAU 10050T). © 2005 IUMS.},
      Year = {2005} }




@article{
Quatrini02,
   Author = {Quatrini, P. and Scaglione, G. and Cardinale, M. and Caradonna, F. and Puglia, A. M.},
   Title = {Bradyrhizobium sp. nodulating the Mediterranean shrub Spanish broom (Spartium junceum L.)},
   Journal = {Journal of Applied Microbiology},
   Volume = {92},
   Number = {1},
   Pages = {13-21},
   Abstract = {Aims: The molecular diversity of 25 strains of rhizobia, isolated in Sicily from root nodules of the Mediterranean shrubby legume Spanish broom (Spartium junceum L.), is presented in relation to the known rhizobial reference strains. Methods and Results: Our approach to the study of the S. junceum rhizobial diversity combined the information given by the 16S and the intergenic spacer (IGS) 16S-23S rDNA polymorphic region by obtaining them in a single polymerase chain reaction (PCR) step. The PCR fragment size of the S. junceum isolates was 2400-2500 bp and that of the reference strains varied from 2400 in Bradyrhizobium strains to 2800 in Sinorhizobium strains. Inter- and intrageneric length variability was found among the reference strains. Restriction fragment length polymorphisms (RFLP) analysis allowed us to identify eight genotypes among the S. junceum rhizobia that were clustered into two groups, both related to the Bradyrhizobium lineage. Sequencing of representative strains of the two clusters confirmed these data. The 16S-IGS PCR-RFLP approach, when applied to rhizobial reference strains, allowed very close species (i.e. Rhizobium leguminosarum/R. tropici) to be separated with any of the three enzymes used; however, cluster analysis revealed inconsistencies with the 16S-based phylogenesis of rhizobia. Conclusions: Rhizobia nodulating S. junceum in the Mediterranean region belong to the Bradyrhizobium lineage. Our results confirm the resolution power of the 16S-23S rDNA in distinguishing among rhizobia genera and species, as well as the usefulness of the PCR-RFLP method applied to the entire 16S-IGS region for a rapid tracking of the known relatives of new isolates. Significance and Impact of the Study: The present paper is, to our knowledge, the first report on rhizobia nodulating a Mediterranean wild woody legume.},
      Year = {2002} }




@article{
Rasanen99,
   Author = {R\"as\"anen, L. A. and Lindstr\"om, K.},
   Title = {The effect of heat stress on the symbiotic interaction between Sinorhizobium sp. and Acacia senegal},
   Journal = {FEMS Microbiology Ecology},
   Volume = {28},
   Number = {1},
   Pages = {63-74},
   Abstract = {Sinorhizobium sp. strain HAMBI 2180, marked with the ?-glucuronidase (GUS) encoding gusA gene, was used for studying the effect of heat stress on the symbiotic interaction between Acacia senegal seedlings and Sinorhizobium sp. in growth cabinet conditions. The infection process, observed during 18 days after inoculation, was delayed at a root temperature of 40°C compared to a root temperature of ?38°C, but nodulation was retarded already at 38°C. At 42°C no nodules were formed. At this root temperature the development of lateral roots and root hairs was one week delayed. Although the roots had normally deformed root hairs in addition to abnormally deformed ones, only disintegrated infection threads were present. However, the ability to form symbiosis was reversible. Nitrogen-fixing nodules developed on those parts of the roots which were formed after completion of the thermal stress at 42°C. A root temperature of 42°C did not affect the numbers of culturable rhizobia in the A. senegal rhizosphere. Copyright (C) 1999 Federation of European Microbiological Societies.},
   Keywords = {?-Glucuronidase
Acacia senegal
Heat stress
Infection process
Nodulation
Sinorhizobium
environmental stress
interspecific interaction
rhizobacterium
symbiosis
temperature effect
heat stress
mycorrhiza
plant root
rhizobium
sinorhizobium
symbiosis
Acacia senegal
Sinorhizobium},
   Year = {1999} }




@article{
Rasanen03,
   Author = {R\"as\"anen, L. A. and Lindstr\"om, K.},
   Title = {Effects of biotic and abiotic constraints on the symbiosis between rhizobia and the tropical leguminous trees Acacia and Prosopis},
   Journal = {Indian Journal of Experimental Biology},
   Volume = {41},
   Number = {10},
   Pages = {1142-1159},
   Abstract = {N2-fixing, drought tolerant and multipurpose Acacia and Prosopis species are appropriate trees for reforestation of degraded areas in arid and semiarid regions of the tropics and subtropics. Acacia and Prosopis trees form N2-fixing nodules with a wide range of rhizobia, for example African acacias mainly with Sinorhizobium sp. and Mesorhizobium sp., and Australian acacias with Bradyrhizobium sp. Although dry and hot seasons restrict formation of N2-fixing nodules on Acacia and Prosopis spp., fully grown trees and their symbiotic partners are well adapted to survive in harsh growth conditions. This review on one hand deals with major constraints of arid and semiarid soils, i.e. drought, salinity and high soil temperature, which affect growth of trees and rhizobia, and on the other hand with adaptation mechanisms by which both organisms survive through unfavourable periods. In addition, defects in infection and nodulation processes due to various abiotic and biotic constraints are reviewed. This knowledge is important when Acacia and Prosopis seedlings are used for forestation of degraded areas in arid and semiarid tropics.},
   Keywords = {Abiotic stress
Acacia
Heat stress
Prosopis
Salt stress},
   Year = {2003} }




@article{
Rasanen01,
   Author = {R\"as\"anen, L. A. and Sprent, J. I. and Lindstr\"om, K.},
   Title = {Symbiotic properties of sinorhizobia isolated from Acacia and Prosopis nodules in Sudan and Senegal},
   Journal = {Plant and Soil},
   Volume = {235},
   Number = {2},
   Pages = {193-210},
   Abstract = {The host specificity, infection process and effectiveness of nodules produced by several African sinorhizobial strains on different Acacia and Prosopis species (Leguminosae, Mimosoideae) were studied. Sinorhizobium arboris strain HAMBI 1552T, S. kostiense strains HAMBI 1489T and HAMBI 1493, S. saheli strain HAMBI 1496 and S. terangae bv. acaciae strain ORS 1058 induced nitrogen fixing nodules on seedlings of the following African or Latin American species (marked with *): A. angustissima*, A. mellifera, A. nilotica, A. oerfota (synonym A. nubica), A. senegal, A. seyal, A. sieberiana, A. tortilis subsp. raddiana, P. chilensis*, P. cineraria, P. juliflora and R pallida*. All strains increased plant yield significantly compared with uninoculated seedlings watered with nitrogen-free medium, but none appeared to be superior. The sinorhizobial strains were unable to effectively nodulate Sesbania rostrata (Papilionoideae). All roots had hairs, but particularly in the case of Acacia spp. they were often sparse. After inoculation root hairs were deformed and, in general, infection in Acacia spp. occurred through short root hairs and in Prosopis spp. through longer ones. After entry, the rhizobia filled infection pockets in the root hair, which later expanded into sac-like structures. When infection threads occurred, they usually started from sac-like structures. Elongation and ramification of the nodules indicated that Acacia spp. and Prosopis spp. have indeterminate nodules. A persistent apical meristem, which is the characteristic feature of the indeterminate nodule type, was much clearer in Prosopis spp. than in Acacia spp. Sinorhizobial strains formed tumour-like structures with undifferentiated cell tissue on the Australian acacia A. holosericea and ineffective, nodule-like structures on the African P. africana.},
   Keywords = {Acacia
Indeterminate nodule
Infection process
Prosopis
Rhizobia
Symbiosis},
   Year = {2001} }




@article{
Radeva01,
   Author = {Radeva, G. and Jurgens, G. and Niemi, M. and Nick, G. and Suominen, L. and Lindstr\"om, K.},
   Title = {Description of two biovars in the \emph{Rhizobium galegae} species: Biovar orientalis and Biovar officinalis},
   Journal = {Systematic and Applied Microbiology},
   Volume = {24},
   Number = {2},
   Pages = {192-205},
   Abstract = {Twenty-six Rhizobium galegae strains, representing the center of origin of the host plants Galega orientalis and G. officinalis as well as other geographic regions, were used in a polyphasic analysis of the relationships of R. galegae strains. Phage typing, lipopolysaccharide (LPS) profiling, pulsed field gel electrophoresis (PFGE) profiling and rep-PCR (use of repetitive sequences as PCR primers for genomic fingerprinting) with REP and ERIC primers investigated nonsymbiotic properties, whereas plasmid profiling and hybridisation with a nif gene probe, and with nodB, nodD, nod box and an IS sequence from the symbiotic region as probes, were used to reveal the relationships of symbiotic genes. The results were used in pairwise calculations of distances between the strains, and the distances were visualised as a dendrogram. Indexes of association were compared for all tests pooled, and for chromosomal tests and symbiotic markers separately, to display the input of the different categories of tests on the grouping of the strains. Our study shows that symbiosis related genetic traits in R. galegae divide strains belonging to the species into two groups, which correspond to strains forming an effective symbioses with G. orientalis and G. officinalis respectively. We therefore propose that Rhizobium galegae strains forming an effective symbiosis with Galega orientalis are called R. galegae bv. orientalis and strains forming an effective symbiosis with Galega officinalis are called R. galegae bv. officinalis.},
   Keywords = {Biovars
G. officinalis
Galegae orientalis
Polyphasic taxonomy
Rhizobium galegae
nucleotide sequence
Rhizobium
Rhizobium galegae
Bacterial Typing Techniques
Symbiosis
Galega officinalis
Galega orientalis
Rhizobium galegae},
   Year = {2001} }




@book{
Raine05,
   Author = {Raine, J. I. and Mildenhall, D. C. and Kennedy, E. M.},
   Title = {New Zealand fossil spores and pollen: an illustrated catalogue},
   Publisher = {Institute of Geological and Nuclear Sciences Information Series 68, version 1},
      Year = {2005} }




@article{
Rajapakse92,
   Author = {Rajapakse, S. and Macgregor, A. N.},
   Title = {Serological Analysis of Rhizobium-Meliloti Strains Used in Commercial Alfalfa Inoculants in New-Zealand},
   Journal = {New Zealand Journal of Agricultural Research},
   Volume = {35},
   Number = {3},
   Pages = {355-358},
   Abstract = {Agglutination and fluorescent antibody techniques were used to study the possibility of distinguishing two Rhizobium meliloti inoculant strains PDD 2751 and PDD 2752, from each other and from R. meliloti strains NZP 4027 and NZP 201 1, and two field isolates. Cross-agglutination tests conducted with unabsorbed antiserum of PDD 2752 or absorbed antiserum of PDD 2751 could distinguish PDD 2751 from PDD 2752. PDD 2751 could also be distinguished from all other strains and isolates by cross-agglutination using unabsorbed antiserum of PDD 2752. However, PDD 2752 could not be distinguished from the rest by cross-agglutination. In the fluorescent antibody test, antiserum produced was not specific to the strain. Therefore this method does not allow for strain recognition in R. meliloti.},
   Keywords = {medicago-sativa; alfalfa; rhizobium-meliloti; strain recognition;
serology; agglutination; indirect fluorescent antibody test},
   Year = {1992} }




@article{
Ramey04,
   Author = {Ramey, B. E. and Fuqua, C. and Koutsoudis, M. and Bodman, S. B. V.},
   Title = {Biofilm formation in plant-microbe associations},
   Journal = {Current Opinion in Microbiology},
   Volume = {7},
   Number = {6},
   Pages = {602-609},
   Abstract = {Bacteria adhere to environmental surfaces in multicellular assemblies described as biofilms. Plant-associated bacteria interact with host tissue surfaces during pathogenesis and symbiosis, and in commensal relationships. Observations of bacteria associated with plants increasingly reveal biofilm-type structures that vary from small clusters of cells to extensive biofilms. The surface properties of the plant tissue, nutrient and water availability, and the proclivities of the colonizing bacteria strongly influence the resulting biofilm structure. Recent studies highlight the importance of these structures in initiating and maintaining contact with the host by examining the extent to which biofilm formation is an intrinsic component of plant-microbe interactions.},
   Keywords = {SEEDS},
   Year = {2004} }




@article{
Randhawa03,
   Author = {Randhawa, G. S. and Kumar, A.},
   Title = {Milestones in the genetical research on rhizobia},
   Journal = {Indian Journal of Experimental Biology},
   Volume = {41},
   Number = {10},
   Pages = {1095-1100},
   Abstract = {The first isolation of the rhizobial bacteria from the legume roots was done in 1888. Since then a large number of scientists have made efforts to understand the molecular basis of Rhizobium-legume symbiosis. The important developments of 115 years of genetical research on rhizobia have been listed in this article.},
   Keywords = {Legume
Nitrogen fixation
Rhizobium
Symbiosis},
   Year = {2003} }




@article{
Rao76,
   Author = {Rao, A. V.},
   Title = {Root exudation in relation to innoculation with rhizobia},
   Journal = {Zentralbl Bakteriol Parasitenkd Infektionskr Hyg},
   Volume = {131},
   Number = {1},
   Pages = {79-82},
   Keywords = {Carbohydrates/analysis
Carboxylic Ester Hydrolases/analysis
Comparative Study
Glycoside Hydrolases/analysis
Nitrogen/analysis
Phenols/analysis
Plants/*metabolism/microbiology
Rhizobium/*growth \& development
*Soil Microbiology},
   Year = {1976} }




@article{
Rao94,
   Author = {Rao, J. R. and Fenton, M. and Jarvis, B. D. W.},
   Title = {Symbiotic plasmid transfer in \emph{Rhizobium leguminosarum} biovar \emph{trifolii} and competition between the inoculant strain ICMP2163 and transconjugant soil bacteria},
   Journal = {Soil Biology and Biochemistry},
   Pages = {339-351},
      Year = {1994} }




@article{
Rasolomampianina05,
   Author = {Rasolomampianina, R. and Bailly, X. and Fetiarison, R. and Rabevohitra, R. and Bena, G. and Ramaroson, L. and Raherimandimby, M. and Moulin, L. and De Lajudie, P. and Dreyfus, B. and Avarre, J.-C.},
   Title = {Nitrogen-fixing nodules from rose wood legume trees (\emph{Dalbergia} spp.) endemic to Madagascar host seven different genera belonging to $\alpha$- and $\beta$-Proteobacteria},
   Journal = {Molecular Ecology},
   Volume = {14},
   Number = {13},
   Pages = {4135-4146},
   Abstract = {Abstract Although legume biodiversity is concentrated in tropical regions, the majority of studies on legume nodulating bacteria (LNB) are focused on cultivated leguminous plants from temperate regions. However, recent works on tropical regions tend to indicate that the actual diversity of LNB is largely underestimated. In this study, we report the isolation and characterization of 68 nitrogen-fixing root nodule bacteria collected from eight endemic tree species of Dalbergia in Madagascar. The isolates were characterized by (i) restriction fragment length polymorphism (RFLP) analysis of 16S-IGS rDNA, (ii) 16S rDNA gene sequencing and (iii) nodulation tests. Results revealed a wide diversity of bacteria present in the nodules of Dalbergia. Among the 68 isolated bacteria, 65 belonged to Bradyrhizobium, Mesorhizobium, Rhizobium, Azorhizobium and Phyllobacterium from the alpha-class of Proteobacteria, and three isolates belonged to Burkholderia and Ralstonia from the beta-class of Proteobacteria. Our results also show for the first time that a strain belonging to the Burkholderia cepacia complex is able to induce efficient nodules on a legume plant.},
      Year = {2005} }




@article{
Raven73,
   Author = {Raven, P. H.},
   Title = {Evolution of subalpine and alpine plant groups in New Zealand},
   Journal = {New Zealand Journal of Botany},
   Volume = {11},
   Pages = {177-200},
      Year = {1973} }




@article{
Recourt91,
   Author = {Recourt, K. and Schripsema, J. and Kijne, J. W. and van Brussel, A. A. and Lugtenberg, B. J.},
   Title = {Inoculation of Vicia sativa subsp. nigra roots with Rhizobium leguminosarum biovar viciae results in release of nod gene activating flavanones and chalcones.},
   Journal = {Plant molecular biology},
   Volume = {16},
   Number = {5},
   Pages = {841-852},
   Abstract = {Flavonoids released by roots of Vicia sativa subsp. nigra (V. sativa) activate nodulation genes of the homologous bacterium Rhizobium leguminosarum biovar viciae (R. l. viciae). Inoculation of V. sativa roots with infective R. l. viciae bacteria largely increases the nod gene-inducing ability of V. sativa root exudate (A.A.N. van Brussel et al., J Bact 172: 5394-5401). The present study showed that, in contrast to sterile roots and roots inoculated with R. l. viciae cured of its Sym plasmid, roots inoculated with R. l. viciae harboring its Sym plasmid released additional nod gene-inducing flavonoids. Using 1H-NMR, the structures of the major inducers released by inoculated roots, 6 flavanones and 2 chalcones, were elucidated. Roots extracts of (un)inoculated V. sativa contain 4 major non-inducing, most likely glycosylated, flavonoids. Therefore, the released flavonoids may either derive from the root flavonoids or inoculation with R. l. viciae activates de novo flavonoid biosynthesis.},
      Year = {1991} }




@article{
Reeve99,
   Author = {Reeve, W. G. and Tiwari, R. P. and Worsley, P. S. and Dilworth, M. J. and Glenn, A. R. and Howieson, J. G.},
   Title = {Constructs for insertional mutagenesis, transcriptional signal localization and gene regulation studies in root nodule and other bacteria},
   Journal = {Microbiology},
   Volume = {145},
   Number = {6},
   Pages = {1307-1316},
      Year = {1999} }




@article{
Reuber93,
   Author = {Reuber, T. L. and Walker, G. C.},
   Title = {Biosynthesis of succinoglycan, a symbiotically important exopolysaccharide of Rhizobium meliloti},
   Journal = {Cell},
   Volume = {74},
   Number = {2},
   Pages = {269-280},
   Abstract = {The exo genes of Rhizobium meliloti are needed for the synthesis of an acidic exopolysaccharide, succinoglycan. We have assigned biosynthetic roles to the products of the exo genes by characterizing succinoglycan biosynthetic intermediates from exo mutant strains. We propose a model of succinoglycan biosynthesis in which the products of the exoY and exoF genes function in the addition of the first sugar, galactose, to the lipid carrier; the products of the exoA, exoL, exoM, exoO, exoU, and exoW genes function in subsequent sugar additions; and the product of the exoV gene functions in the addition of pyruvate. The products of the exoP, exoQ, and exoT genes are required for polymerization of the octasaccharide subunits or transport of the completed polymer.},
      Year = {1993} }




@article{
Rezzonico05,
   Author = {Rezzonico, F. and Binder, C. and Défago, G. and Moënne-Loccoz, Y.},
   Title = {The type III secretion system of biocontrol Pseudomonas fluorescens KD targets the phytopathogenic chromista Pythium ultimum and promotes cucumber protection},
   Journal = {Molecular Plant-Microbe Interactions},
   Volume = {18},
   Number = {9},
   Pages = {991-1001},
   Abstract = {The type III secretion system (TTSS) is used by Proteobacteria for pathogenic or symbiotic interaction with plant and animal hosts. Recently, TTSS genes thought to originate from the phytopathogen Pseudomonas syringae were evidenced in Pseudomonas fluorescens KD, which protects cucumber from the oomycete Pythium ultimum (kingdom Chromista/Stramenopila). However, it is not known whether the TTSS contributes to plant protection by the bacterium and, if so, whether it targets the plant or the phytopathogen. Inactivation of TTSS gene hrc V following the insertion of an omega cassette strongly reduced the biocontrol activity of the pseudomonad against P. ultimum on cucumber when compared with the wild type, but had no effect on its root-colonization ability. Analysis of a plasmid-based transcriptional hrpJ?-inaZ reporter fusion revealed that expression in strain KD of the operon containing hrcV was strongly stimulated in vitro and in situ by the oomycete and not by the plant. In vitro, both strain KD and its hrc V mutant reduced the activity level of the pectinase polygalacturonase (a key pathogenicity factor) from P. ultimum, but the reduction was much stronger with the wild type. Together, these results show that the target range of bacterial TTSS is not restricted to plants and animals but also can include members of Chromista/Stramenopila, and suggest that virulence genes acquired horizontally from phytopathogenic bacteria were functionally recycled in biocontrol saprophytic Pseudomonas spp., resulting in enhanced plant protection by the latter. © 2005 The American Phytopathological Society.},
      Year = {2005} }




@article{
Rice94,
   Author = {Rice, D. J. and Somasegaran, P. and MacGlashan, K. and Bohlool, B. B.},
   Title = {Isolation of insertion sequence ISRLdTAL1145-1 from a Rhizobium sp. (Leucaena diversifolia) and distribution of homologous sequences identifying cross-inoculation group relationships},
   Journal = {Applied and Environmental Microbiology},
   Volume = {60},
   Number = {12},
   Pages = {4394-4403},
   Abstract = {Insertion sequence (IS) element ISRLdTAL1145-1 from Rhizobium sp. (Leucaena diversifolia) strain TAL 1145 was entrapped in the sacB gene of the positive selection vector pUCD800 by insertional inactivation. A hybridization probe prepared from the whole 2.5-kb element was used to determine the distribution of homologous sequences in a diverse collection of 135 Rhizobium and Bradyrhizobium strains. The IS probe hybridized strongly to Southern blots of genomic DNAs from 10 rhizobial strains that nodulate both Phaseolus vulgaris (beans) and Leucaena leucocephala (leguminous trees), 1 Rhizobium sp. that nodulates Leucaena spp., 9 R. meliloti (alfalfa) strains, 4 Rhizobium spp. that nodulate Sophora chrysophylla (leguminous trees), and 1 nonnodulating bacterium associated with the nodules of Pithecellobium dulce from the Leucaena cross-inoculation group, producing distinguishing IS patterns for each strain. Hybridization analysis revealed that ISRLdTAL1145- 1 was strongly homologous with and closely related to a previously isolated element, ISRm USDA1024-1 from R. meliloti, while restriction enzyme analysis found structural similarities and differences between the two IS homologs. Two internal segments of these IS elements were used to construct hybridization probes of 1.2 kb and 380 bp that delineate a structural similarity and a difference, respectively, of the two IS homologs. The internal segment probes were used to analyze the structures of homologous IS elements in other strains. Five types of structural variation in homolog IS elements were found. The predominate IS structural type naturally occurring in a strain can reasonably identify the strain's cross-inoculation group relationships. Three IS structural types were found in Rhizobium species that nodulate beans and Leucaena species, one of which included the designated type IIB strain of R. tropici (CIAT 899). Weak homology to the whole IS probe, but not with the internal segments, was found with two Bradyrhizobium japonicum strains. The taxonomic and ecological implications of the distribution of ISRLdTAL1145-1 are discussed.},
   Keywords = {bacterium isolation
gene insertion sequence},
   Year = {1994} }




@article{
Richardson00,
   Author = {Richardson, D. M. and Allsopp, N. and D'Antonio, C. M. and Milton, S. J. and Rejmanek, M.},
   Title = {Plant invasions -- The role of mutualisms},
   Journal = {Biological Reviews of the Cambridge Philosophical Society},
   Volume = {75},
   Number = {1},
   Pages = {65-93},
   Abstract = {Many introduced plant species rely on mutualisms in their new habitats to overcome barriers to establishment and to become naturalized and, in some cases, invasive. Mutualisms involving animal-mediated pollination and seed dispersal, and symbioses between plant roots and microbiota often facilitate invasions. The spread of many alien plants, particularly woody ones, depends on pollinator mutualisms. Most alien plants are well served by generalist pollinators (insects and birds), and pollinator limitation does not appear to be a major barrier for the spread of introduced plants (special conditions relating to Ficus and orchids are described). Seeds of many of the most notorious plant invaders are dispersed by animals, mainly birds and mammals. Our review supports the view that tightly coevolved, plant-vertebrate seed dispersal systems are extremely rare. Vertebrate-dispersed plants are generally not limited reproductively by the lack of dispersers. Most mycorrhizal plants form associations with arbuscular mycorrhizal fungi which, because of their low specificity, do not seem to play a major role in facilitating or hindering plant invasions (except possibly on remote islands such as the Galapagos which are poor in arbuscular mycorrhizal fungi). The lack of symbionts has, however, been a major barrier for many ectomycorrhizal plants, notably for Pinus spp. in parts of the southern hemisphere. The roles of nitrogen-fixing associations between legumes and rhizobia and between actinorhizal plants and Frankia spp. in promoting or hindering invasions have been virtually ignored in the invasions literature. Symbionts required to induce nitrogen fixation in many plants are extremely widespread, but intentional introductions of symbionts have altered the invasibility of many, if not most, systems. Some of the world's worst invasive alien species only invaded after the introduction of symbionts. Mutualisms in the new environment sometimes re-unite the same species that form partnerships in the native range of the plant. Very often, however, different species are involved, emphasizing the diffuse nature of many (most) mutualisms. Mutualisms in new habitats usually duplicate functions or strategies that exist in the natural range of the plant. Occasionally, mutualisms forge totally novel combinations, with profound implications for the behaviour of the introduced plant in the new environment (examples are seed dispersal mutualisms involving wind-dispersed pines and cockatoos in Australia; and mycorrhizal associations involving plant roots and fungi). Many ecosystems are becoming more susceptible to invasion by introduced plants because: (a) they contain an increasing array of potential mutualistic partners (e.g. generalist frugivores and pollinators, mycorrhizal fungi with wide host ranges, rhizobia strains with infectivity across general; and (b) conditions conducive for the establishment of various alien/alien synergisms are becoming more abundant. Incorporating perspectives on mutualisms in screening protocols will improve (but not perfect) our ability to predict whether a given plant species could invade a particular habitat.},
   Keywords = {Biological invasions
Global change
Invasibility
Mycorrhiza
Nitrogen fixation
Pollination
Prediction
Risk assessment
Seed dispersal},
   Year = {2000} }




@book{
Richardson98,
   Author = {Richardson, R. G. and Hill, R. L.},
   Title = {Ulex europaeus \emph{L}.},
   Publisher = {RG and FJ Richardson},
   Address = {Melbourne Australia},
   Volume = {2},
   Series = {Biology of Australian Weeds},
      Year = {1998} }




@article{
Riely04,
   Author = {Riely, B. K. and Ane, J. M. and Penmetsa, R. V. and Cook, D. R.},
   Title = {Genetic and genomic analysis in model legumes bring Nod-factor signaling to center stage},
   Journal = {Current Opinion in Plant Biology},
   Volume = {7},
   Number = {4},
   Pages = {408-413},
   Abstract = {The control of host-specificity in the Rhizobium-legume symbiosis has been a topic of long-standing interest to plant biologists. By the early 1990s, biologists had deciphered the chemical signals that trigger early symbiotic responses. Flavonoids from the plant root trigger bacterial gene expression and the production of lipo-chitooligosaccharide signals (called Nod factors) that are recognized by the plant host. Genetic differences between bacterial strains modify the oligosaccharide backbone, for example by the addition of sulfate, acetate or fucose, and simultaneously alter the host-specificity of the purified Nod factor and the bacterium. Recent studies have begun to reveal the genetic and molecular basis of Nod-factor perception in legumes, a signaling system that also controls plant interactions with mycorrhizal fungi.},
      Year = {2004} }




@article{
Ritsema96,
   Author = {Ritsema, T. and Wijfjes, A. H. M. and Lugtenberg, B. J. J. and Spaink, H. P.},
   Title = {\emph{Rhizobium} nodulation protein NodA is a host-specific determinant of the transfer of fatty acids in Nod factor biosynthesis},
   Journal = {Molecular and General Genetics},
   Volume = {251},
   Number = {1},
   Pages = {44-51},
   Abstract = {In the biosynthesis of lipochitin oligosaccharides (LCOs) the Rhizobium nodulation protein NodA plays an essential role in the transfer of an acyl chain to the chitin oligosaccharide acceptor molecule. The presence of nodA in the nodABCIJ operon makes genetic studies difficult to interpret. In order to be able to investigate the biological and biochemical functions of NodA, we have constructed a test system in which the nodA, nodB and nodC genes are separately present on different plasmids. Efficient nodulation was only obtained if nodC was present on a low-copy-number vector. Our results confirm the notion that nodA of Rhizobium leguminosarum biovar viciae is essential for nodulation on Vicia. Surprisingly, replacement of R. I. bv. viciae nodA by that of Bradyrhizobium sp. ANU289 results in a nodulation-minus phenotype on Vicia. Further analysis revealed that the Bradyrhizobium sp. ANU289 NodA is active in the biosynthesis of LCOs, but is unable to direct the transfer of the R. I. bv. viciae nodFE-dependent multi-unsaturated fatty acid to the chitin oligosaccharide acceptor. These results lead to the conclusion that the original notion that nodA is a common nod gene should be revised.},
   Keywords = {Acyl transfer
Nod factors
nodA
Nodulation
Rhizobium
bacterial protein
fatty acid
oligosaccharide
carbohydrate synthesis
fatty acid transport
nodulation
rhizobium leguminosarum
Genes, Bacterial
Operon},
   Year = {1996} }




@article{
Rivas02,
   Author = {Rivas, R. and Vel\'azquez, E. and Willems, A. and Vizcaino, N. and Subba-Rao, N. S. and Mateos, P. F. and Gillis, M. and Dazzo, F. B. and Mart\'inez-Molina, E.},
   Title = {A new species of \emph{Devosia} that forms a unique nitrogen-fixing root-nodule symbiosis with the aquatic legume \emph{Neptunia natans} (L.f.) Druce},
   Journal = {Applied and Environmental Microbiology},
   Volume = {68},
   Number = {11},
   Pages = {5217-5222},
   Abstract = {Rhizobia are the common bacterial symbionts that form nitrogen-fixing root nodules in legumes. However, recently other bacteria have been shown to nodulate and fix nitrogen symbiotically with these plants. Neptunia natans is an aquatic legume indigenous to tropical and subtropical regions and in African soils is nodulated by Allorhizobium undicola. This legume develops an unusual root-nodule symbiosis on floating stems in aquatic environments through a unique infection process. Here, we analyzed the low-molecular-weight RNA and 16S ribosomal DNA (rDNA) sequence of the same fast-growing isolates from India that were previously used to define the developmental morphology of the unique infection process in this symbiosis with N. natans and found that they are phylogenetically located in the genus Devosia, not Allorhizobium or Rhizobium. The 16S rDNA sequences of these two Neptunia-nodulating Devosia strains differ from the only species currently described in that genus, Devosia riboflavina. From the same isolated colonies, we also located their nodD and nifH genes involved in nodulation and nitrogen fixation on a plasmid of approximately 170 kb. Sequence analysis showed that their nodD and nifH genes are most closely related to nodD and nifH of Rhizobium tropici, suggesting that this newly described Neptunia-nodulating Devosia species may have acquired these symbiotic genes by horizontal transfer.},
      Year = {2002} }




@article{
Rivas04b,
   Author = {Rivas, R. and Vel\'azquez, Encarna and Zurdo-Pi\~neiro, Jos\'e Luis and Mateos, Pedro F. and Molina, Eustoquio Mart\'inez},
   Title = {Identification of microorganisms by PCR amplification and sequencing of a universal amplified ribosomal region present in both prokaryotes and eukaryotes},
   Journal = {Journal of Microbiological Methods},
   Volume = {56},
   Number = {3},
   Pages = {413-426},
   Abstract = {The small ribosomal subunit contains 16S rRNA in prokaryotes and 18S rRNA in eukaryotes. Even though it has been known that some small ribosomal sequences are conserved in 16S rRNA and 18S rRNA molecules, they have been used separately for taxonomic and phylogenetic studies. Here, we report the existence of two highly conserved ribosomal sequences in all organisms that allow the amplification of a zone containing approximately 495 bp in prokaryotes and 508 bp in eukaryotes which we have named the "Universal Amplified Ribosomal Region" (UARR). Amplification and sequencing of this zone is possible using the same two universal primers (U1F and U1R) designed on the basis of two highly conserved ribosomal sequences. The UARR encompasses the V6, V7 and V8 domains from SSU rRNA in both prokaryotes and eukaryotes. The internal sequence of this zone in prokaryotes and eukaryotes is variable and the differences become less marked on descent from phyla to species. Nevertheless, UARR sequence allows species from the same genus to be differentiated. Thus, by UARR sequence analysis the construction of universal phylogenetic trees is possible, including species of prokaryotic and eukaryotic microorganisms together. Single isolates of prokaryotic and eukaryotic microorganisms from different sources can be identified by amplification and sequencing of UARR using the same pair of primers and the same PCR and sequencing conditions.},
      Year = {2004} }




@article{
Rivas04a,
   Author = {Rivas, R. and Willems, A. and Palomo, J. L. and Garcia-Benavides, P. and Mateos, P. F. and Mart\'inez-Molina, E. and Gillis, M. and Vel\'azquez, E.},
   Title = { \emph{Bradyrhizobium betae} sp. nov., isolated from roots of  \emph{Beta vulgaris} affected by tumour-like deformations},
   Journal = {International Journal of Systematic and Evolutionary Microbiology},
   Volume = {54},
   Number = {4},
   Pages = {1271-1275},
   Abstract = {Some varieties of sugar beet, Beta vulgaris, cultivated in northern Spain have large deformations that resemble the tumours produced by Agrobacterium species. In an attempt to isolate the agent responsible for these deformations, several endophytic slow-growing bacterial strains were isolated, the macroscopic morphology of which resembled that of Bradyrhizobium species. These strains were not able to produce tumours in Nicotiana tabacum plants and, based on phylogenetic analysis of their 16S rRNA, they are closely related to the genus Bradyrhizobium. Phenotypic and molecular characteristics of these strains revealed that they represent a species different from all Bradyrhizobium species previously described. Sequence analysis of the 16S-23S rDNA intergenic spacer region indicated that these novel strains form a homogeneous group, related to Bradyrhizobium japonicum, Bradyrhizobium liaoningense and Bradyrhizobium yuanmingense. DNA-DNA hybridization confirmed that these strains represent a novel species of the genus Bradyrhizobium, for which the name Bradyrhizobium betae sp. nov. is proposed. The type strain is PL7HG 1 (T) (=LMG 21987 (T) = CECT 5829(T)).},
      Year = {2004} }




@article{
Rivas03,
   Author = {Rivas, R. and Willems, A. and Subba-Rao, N. S. and Mateos, P. F. and Dazzo, F. B. and Kroppenstedt, R. M. and Mart\'inez-Molina, E. and Gillis, M. and Vel\'azquez, E.},
   Title = {Description of \emph{Devosia neptuniae} sp. nov. that nodulates and fixes nitrogen in symbiosis with \emph{Neptunia natans}, an aquatic legume from India},
   Journal = {Systematic and Applied Microbiology},
   Volume = {26},
   Number = {1},
   Pages = {47-53},
   Abstract = {Neptunia natans is a unique aquatic legume indigenous to tropical and sub-tropical regions and is nodulated symbiotically by rhizobia using an unusual infection process unlike any previously described. Previously, isolates of neptunia-nodulating rhizobia from Senegal were characterized as Allorhizobium undicola. Here we report on a different group of neptunia-nodulating rhizobia isolated from India. Sequencing of the 16S rDNA gene from two of these Indian isolates (strains J1(T) and J2) show that they belong in the genus Devosia rather than Allorhizobium. Currently, the only described Devosia species is D. riboflavina (family Hyphomicrobiaceae, order Rhizobiales). The complete 16S rDNA sequences of strains J1(T) and J2 are 95.9% homologous to the type strain, D. riboflavina LMG 2277(T), suggesting that these neptunia-nodulating strains from India belong to a new Devosia species. This hypothesis was confirmed by further studies of polyphasic taxonomy (DNA-DNA hybridisation, TP-RAPD patterns, SDS-PAGE of Cellular proteins, 16S rDNA RFLP patterns, carbon source Utilisation, cellular fatty acid analysis and other phenotypic characterisations), all of which support the proposal that these neptunia-nodulating strains constitute a new Devosia species, which we name Devosia neptuniae sp. nov. These Gram negative, strictly aerobic short rods are motile by a subpolar flagellum, positive for catalase, oxidase, urease and beta-galactosidase, can utilise several carbohydrates (but not organic acids) as carbon sources and contain C18:0 3-OH, cis-7 C18:1 11-methyl and cis-7 C18:1 as their major cellular fatty acids. Unlike D. riboflavina, the longer-chain C24:1 3-OH and C26:1 3-OH hydroxy fatty acids are not detected. The type strain of D. neptuniae is LMG 21357(T) (CECT 5650(T)). Assignment of this new taxon represents the fourth example in the literature of a non-rhizobial genus of bacteria capable of forming a bonafide dinitrogen-fixing root-nodule symbiosis with legume plants.},
      Year = {2003} }




@article{
Robertson78,
   Author = {Robertson, J. G. and Lyttleton, P. and Bullivant, S. and Grayston, G. F.},
   Title = {Membranes in lupin root nodules. I. The role of Golgi bodies in the biogenesis of infection threads and peribacteroid membranes},
   Journal = {J Cell Sci},
   Volume = {30},
   Pages = {129-49},
   Abstract = {The process of infection of lupin nodule cells by rhizobia was examined using thin-section and freeze-fracture electron-microscopic techniques to characterize the properties of different membranes and to establish relationships between them. The membranes of the Golgi bodies and the endoplasmic reticulum stained with zinc iodide-osmium tetroxide but not with phosphotungstic acid or silver. By contrast the infection thread membranes, peribacteroid membranes, plasma membranes and membranes of cytoplasmic vesicles did not stain with zinc iodide-osmium tetroxide but stained with phosphotungstic acid and silver. The peribacteroid membranes and plasma membranes are, however, different from each other since the particle density on the E face of freeze-fracture replicas of plasma membranes was twice that on the E face of the peribacteroid membranes. An examination of the tips of the infection threads in the cytoplasm of the plant cells, showed that the rhizobia bud off from the infection threads enclosed in the infection thread membranes. The rhizobia continue to divide still surrounded by membranes of plant origin, namely the peribacteroid membranes. Cytoplasmic vesicles are observed in both thin-section and freeze-fracture preparations of nodule tissue closely associated with, and apparently produced by, Golgi bodies. Formation of the walls and membranes of the infection threads and of the peribacteroid membranes involves fusion of the cytoplasmic vesicles with these membranes. It is proposed that the process of infection of plant cells in lupin nodules involves a change in the function of the Golgi body system for the biogenesis of plant cell walls and plasma membranes to include the synthesis of the walls and membranes of the infection threads and also the peribacteroid membranes.},
   Keywords = {Biogenesis
Cell Membrane/ultrastructure
Cytoplasm/ultrastructure
Endoplasmic Reticulum/ultrastructure
Fabaceae/*ultrastructure
Freeze Fracturing
Golgi Apparatus/*ultrastructure
Microscopy, Electron
*Plants, Medicinal
Rhizobium},
   Year = {1978} }




@article{
Robertson85,
   Author = {Robertson, J. G. and Wells, B. and Brewin, N. J. and Wood, E. and Knight, C. D. and Downie, J. A.},
   Title = {The legume-Rhizobium symbiosis: a cell surface interaction},
   Journal = {J Cell Sci Suppl},
   Volume = {2},
   Pages = {317-31},
   Abstract = {This review will examine the early stages of infection of legume roots by strains of Rhizobium that induce nitrogen-fixing nodules. The object is to show that, at least in terms of ultrastructure, the interactions between the plant and the rhizobia occur at the cell surface interface between these organisms. This situation exists at all stages, from the time the bacteria attach to the surface of the root hairs to the time they occur as the nitrogen-fixing form in the cytoplasm of the nodule cells, enclosed by peribacteroid membranes.},
   Keywords = {Cell Adhesion
Cell Wall/*physiology/ultrastructure
Fabaceae/*physiology/ultrastructure
*Plants, Medicinal
Rhizobium/*physiology/ultrastructure
Support, Non-U.S. Gov't
*Symbiosis},
   Year = {1985} }




@book{
HighPure,
   Author = {Roche},
   Title = {High Pure PCR Product Purification Kit, Instruction Manual},
   Publisher = {Roche Applied Science},
   Edition = {2nd},
      Year = {2002} }




@article{
Roche91,
   Author = {Roche, P. and Lerouge, P. and Promé, J.-C. and Debellé, F. and Maillet, F. and Faucher, C. and Truchet, G. and Dénarie?, J.},
   Title = {Molecular basis of symbiotic host specificity in rhizobium meliloti: nodH and nodPQ genes encode the sulfation of lipo-oligosaccharide signals},
   Journal = {Cell},
   Volume = {67},
   Number = {6},
   Pages = {1131-1143},
   Abstract = {The symbiosis between Rhizobium and legumes is highly specific. For example, R. meliloti elicits the formation of root nodules on alfalfa and not on vetch. We recently reported that R. meliloti nodulation (nod) genes determine the production of acylated and sulfated glucosamine oligosaccharide signals. We now show that the biochemical function of the major host-range genes, nodH and nodPQ, is to specify the 6-O-sulfation of the reducing terminal glucosamine. Purified Nod factors (sulfated or not) from nodH+ or nodH- strains exhibited the same plant specificity in a variety of bioassays (root hair deformations, nodulation, changes in root morphology) as the bacterial cells from which they were purified. These results provide strong evidence that the molecular mechanism by which the nodH and nodPQ genes mediate host specificity is by determining the sulfation of the extracellular Nod signals.},
      Year = {1991} }




@article{
Roche96,
   Author = {Roche, Philippe and Maillet, Fabienne and Plazanet, Claire and Debell\'e, Frederic and Ferro, Myriam and Truchet, Georges and Prome, Jean-Claude and D\'enarie, Jean},
   Title = {The common  \emph{nodABC} genes of  \emph{Rhizobium meliloti} are host-range determinants},
   Journal = {Proceedings of the National Academy of Sciences of the United States of America},
   Volume = {93},
   Number = {26},
   Pages = {15305-15310},
   Abstract = {Symbiotic bacteria of the genus Rhizobium synthesize lipo-chitooligosaccharides, called Nod factors (NFs), which act as morphogenic signal molecules on legume hosts. The common nodABC genes, present in all Rhizobium species, are required for the synthesis of the core structure of NFs. NodC is an N-acetylglucosaminyltransferase, and NodB is a chitooligosaccharide deacetylase; NodA is involved in N-acylation of the aminosugar backbone. Specific nod genes are involved in diverse NF substitutions that confer plant specificity. We transferred to R. tropici, a broad host-range tropical symbiont, the ability to nodulate alfalfa, by introducing nod genes of R. meliloti. In addition to the specific nodL and nodFE genes, the common nodABC genes of R. meliloti were required for infection and nodulation of alfalfa. Purified NFs of the R. tropici hybrid strain, which contained chitin tetramers and were partly N-acylated with unsaturated C16 fatty acids, were able to elicit nodule formation on alfalfa. Inactivation of the R. meliloti nodABC genes suppressed the ability of the NFs to nodulate alfalfa. Studies of NFs from nodA, nodB, nodC, and nodI mutants indicate that (i) NodA of R. meliloti, in contrast to NodA of R. tropici, is able to transfer unsaturated C16 fatty acids onto the chitin backbone and (ii) NodC of R. meliloti specifies the synthesis of chitin tetramers. These results show that allelic variation of the common nodABC genes is a genetic mechanism that plays an important role in signaling variation and in the control of host range.},
      Year = {1996} }




@article{
Rodriguez-Echeverria03,
   Author = {Rodr\'iguez-Echeverr\'ia, S. and P\'erez-Fern\'andez, M. A. and Vlaar, S. and Finnan, T. M.},
   Title = {Analysis of the legume--rhizobia symbiosis in shrubs from central western Spain},
   Journal = {Journal of Applied Microbiology},
   Volume = {95},
   Number = {6},
   Pages = {1367-1374},
   Abstract = {Aims: This work analyses the diversity of rhizobia associated with some of the predominant shrubby legumes in central-western Spain. Symbiotic promiscuity and effectiveness were studied using cross-inoculation experiments with shrubby species. Material and Results: Six new bradyrhizobia strains were isolated from nodules collected from wild plants of six leguminous species, Cytisus balansae, C. multiflorus, C. scoparius, C. striatus, Genista hystrix and Retama sphaerocarpa. These isolates were genetically characterized by 16S rDNA partial sequencing and random amplification of polymorphic DNA-PCR fingerprinting. The phylogenetic analysis revealed that these isolates could represent three new Bradyrhizobium species. Shrubby legumes and bradyrhizobia displayed a high symbiotic promiscuity both for infectivity and effectiveness. Symbioses were effective in more than 70% of the associations established by four of the six plant species. Conclusions: Native woody legumes in western Spain are nodulated by Bradyrhizobium strains. The high degree of symbiotic promiscuity and effectiveness highlights the complex dynamics of these communities in wild ecosystems under a Mediterranean-type climate. Furthermore, the results from this study suggest a potential importance of inoculation for these legume species in soil-restoration projects. Significance and Impact of the Study: This is the first study, to our knowledge, that combines both molecular analysis and pot trials to study the rhizobia-legume symbiosis for wild legumes.},
      Year = {2003} }




@article{
Rodriguez-Navarro04,
   Author = {Rodr\'iguez-Navarro, D. N. and Camacho, M. and Leidi, E. O. and Rivas, R. and Vel\'azquez, E.},
   Title = {Phenotypic and genotypic characterization of rhizobia from diverse geographical origin that nodulate Pachyrhizus species},
   Journal = {Systematic and Applied Microbiology},
   Volume = {27},
   Number = {6},
   Pages = {737-745},
   Abstract = {Legumes from the genus Pachyrhizus, commonly known as yam bean, are cultivated in several countries from the American continent and constitute an alternative source for sustainable starch, oil and protein production. The endosymbionts of these legumes have been poorly studied although it is known that this legume is nodulated by fast and slow growing rhizobia. In this study we have analyzed a collection of strains isolated in several countries using different phenotypic and molecular methods. The results obtained by SDS-PAGE analysis, LPS profiling and TP-RAPD fingerprinting showed the high diversity of the strains analyzed, although all of them presented slow growth in yeast mannitol agar (YMA) medium. These results were confirmed using 16S-23S internal transcribed spacer (ITS) region and complete sequencing of the 16S rRNA gene, showing that most strains analyzed belong to different species of genus Bradyrhizobium. Three strains were closely related to B. elkanii and the rest of the strains were related to the phylogenetic group constituted by B. japonicum, B. liaoningense, B. yuanmingense and B. betae. These results support that the study of rhizobia nodulating unexplored legumes in different geographical locations will allow the discovery of new species able to establish legume symbioses.},
   Keywords = {Bradyrhizobia-biodiversity
LPS profiles
Pachyrhizus ahipa
SDS-PAGE analysis
TP-RAPD fingerprinting-ITS sequencing},
   Year = {2004} }




@article{
Rodriguez03,
   Author = {Rodriguez, A. and Frioni, L.},
   Title = {Characterization of rhizobia from native Uruguayan legume trees by the rep-PCR technique},
   Journal = {Revista Argentina de Microbiologia},
   Volume = {35},
   Number = {4},
   Pages = {193-197},
   Abstract = {Methods for identifying and following microorganisms in the environment such as soils, water and plant association have been highly developed in recent years. In this study, we used rep-PCR for the characterization of Rhizobium bacteria isolated from legume trees native of Uruguay which permitted to follow them in plant inoculation assays. Among the primers used, ERIC and BOX1AR, the latter allowed the differentiation of isolates from different legumes and the finding of a high level of homology among rhizobia that nodulate the same legume species. Besides, it demonstrated that the profiles of the isolates recovered from nodules of Acacia caven, were identical to the ones used as inoculants; this confirmed the efficiency of these methods to follow these diazotrophs in the environment.},
      Year = {2003} }




@incollection{
Rodriguez83,
   Author = {Rodriguez, R. L. and Tait, R. C.},
   Title = {Spectrophotometric assay of DNA concentration and purity},
   BookTitle = {Recombinant DNA techniques: An introduction},
   Publisher = {Addison-Wesley publishing company},
   Address = {Reading, Massachusetts},
   Pages = {42-44},
      Year = {1983} }




@article{
Rodriguez04,
   Author = {Rodriguez-Llorente, I. D. and Perez-Hormaeche, J. and Mounadi, K. E. and Dary, M. and Caviedes, M. A. and Cosson, V. and Kondorosi, A. and Ratet, P. and Palomares, A. J.},
   Title = {From pollen tubes to infection threads: recruitment of Medicago floral pectic genes for symbiosis},
   Journal = {Plant J},
   Volume = {39},
   Number = {4},
   Pages = {587-98},
   Abstract = {Summary While the biology of nitrogen-fixing root nodules has been extensively studied, little is known about the evolutionary events that predisposed legume plants to form symbiosis with rhizobia. We have studied the presence and the expression of two pectic gene families in Medicago, polygalacturonases (PGs) and pectin methyl esterases (PMEs) during the early steps of the Sinorhizobium meliloti-Medicago interaction and compared them with related pollen-specific genes. First, we have compared the expression of MsPG3, a PG gene specifically expressed during the symbiotic interaction, with the expression of MsPG11, a highly homologous pollen-specific gene, using promoter-gus fusions in transgenic M. truncatula and tobacco plants. These results demonstrated that the symbiotic promoter functions as a pollen-specific promoter in the non-legume host. Second, we have identified the presence of a gene family of at least eight differentially expressed PMEs in Medicago. One subfamily is represented by one symbiotic gene (MtPER) and two pollen-expressed genes (MtPEF1 and MtPEF2) that are clustered in the M. truncatula genome. The promoter-gus studies presented in this work and the homology between plant PGs, together with the analysis of the PME locus structure and MtPER expression studies, suggest that the symbiotic MsPG3 and MtPER could have as ancestors pollen-expressed genes involved in polar tip growth processes during pollen tube elongation. Moreover, they could have been recruited after gene duplication in the symbiotic interaction to facilitate polar tip growth during infection thread formation.},
      Year = {2004} }




@article{
Rogel01,
   Author = {Rogel, M. A. and Hern\'andez-Lucas, I. and Kuykendall, L. D. and Balkwill, D. L. and Mart\'inez-Romero, E.},
   Title = {Nitrogen-fixing nodules with \emph{Ensifer adhaerens} harboring \emph{Rhizobium tropici} symbiotic plasmids},
   Journal = {Applied and Environmental Microbiology},
   Volume = {67},
   Number = {7},
   Pages = {3264-3268},
   Abstract = {Ensifer adhaerens is a soil bacterium that attaches to other bacteria and may cause l