@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 s