NZ Rhizobia

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Rhizobia taxonomy

The current taxonomy of rhizobia [Updated 14th September 2009]

The species listed here are all of the most current validly published names for the rhizobia, which currently consists of 76 species found in 13 genera. Rhizobia are nitrogen-fixing bacteria that form root nodules on legume plants. Most of these bacterial species are in the Rhizobiacae family in the alpha-proteobacteria and are in either the Rhizobium, Mesorhizobium, Ensifer, or Bradyrhizobium genera. However recent research has shown that there are many other rhizobial species in addition to these. In some cases these new species have arisen through lateral gene transfer of symbiotic genes.

Taxonomy is a complicated and ever-changing discipline of science, the list below is not "official" by any means, and it is merely my compilation and interpretation of the literature. An alternative list is maintained by the "ICSP Subcommittee on the taxonomy of Rhizobium and Agrobacterium".

It is important to note that there are other non-rhizobial species present in these genera. For example in the Rhizobium genus, there is Rhizobium radiobacter — formerly known as Agrobacterium tumefaciens. However these species are not listed here, as the 'Agrobacteria' do not form nitrogen fixing symbiotic root nodules (unless they contain a symbiotic plasmid – see Velazquez et. al. 2005). I have another page about these bacteria that could be confused with 'true' rhizobia.

To see all of the currently valid members of a genus, including non-rhizobial species, click on the name of the genus in the text after each title. This will take you to the LPSN website.

This page was compiled from my own research; a paper by J.G. Howieson and J. Brockwell presented at the 14th Australian Nitrogen Fixation Conference, and the NCBI and LPSN websites.

This page is updated regularly. If you know of any additions or corrections please email me. I do try to keep up, but I am working on different projects now.

If you wish you can cite this page as:
Weir, B. S. (2009) The current taxonomy of rhizobia. New Zealand rhizobia website. http://www.rhizobia.co.nz/taxonomy/rhizobia.html. Last updated: 14th September, 2009. (check title for latest update date)

Rhizobium

The genus Rhizobium (Frank 1889) was the first named (from Latin meaning root living), and for many years this was a 'catch all' genus for all rhizobia. Some species were later moved in to new genera based on phylogenetic analyses. It currently consists of 22 species.

Rhizobium cellulosilyticum
New. ( García-Fraile et. al. 2007)
Rhizobium daejeonense
 
Rhizobium etli
 
Rhizobium galegae  
Rhizobium gallicum  
Rhizobium giardinii  
Rhizobium hainanense  
Rhizobium huautlense  
Rhizobium indigoferae
 
Rhizobium leguminosarum
Type species. See note below
Rhizobium loessense
formerly "Rhizobium huanglingense"
Rhizobium lusitanum
 
Rhizobium miluonense
New. Gu et. al. (2008)
Rhizobium mongolense  
Rhizobium multihospitium New. Han et. al. (2008)
Rhizobium oryzae New. Peng et. al. (2008)
Rhizobium phaseoli Confirmed as a species. Ramirez-Bahena et. al. (2008)
Rhizobium pisi New. Ramirez-Bahena et. al. (2008)
Rhizobium sullae
formerly "Rhizobium hedysari"
Rhizobium tropici  
Rhizobium undicola formerly Allorhizobium undicola
Rhizobium yanglingense  

Note that Rhizobium trifolii is a later synonym of R. leguminosarum. R. phaseoli is a valid separate species, and some isolates formerly known as R. leguminosarum are now R. pisi. (Ramirez-Bahena et. al. 2008)

Mesorhizobium

The genus Mesorhizobium was described by Jarvis et al. in 1997. Several species were moved from Rhizobium to this genus.It currently consists of 19 species.

Mesorhizobium albiziae Wang et. al., 2007
Mesorhizobium alhagi New Chen et. al., 2009
Mesorhizobium amorphae  
Mesorhizobium australicum New (Nandasena et. al., 2009)
Mesorhizobium caraganae Wang et. al., 2007
Mesorhizobium chacoense  
Mesorhizobium ciceri formerly Rhizobium ciceri
Mesorhizobium gobiense Han et. al., 2008b
Mesorhizobium huakuii formerly Rhizobium huakuii
Mesorhizobium loti formerly Rhizobium loti, Type species
Mesorhizobium mediterraneum formerly Rhizobium mediterraneum
Mesorhizobium metallidurans Vidal et. al. (2009)
Mesorhizobium opportunistum New Nandasena et. al., 2009
Mesorhizobium plurifarium  
Mesorhizobium shangrilense
New Lu et. al., 2009
Mesorhizobium septentrionale
(ref)
Mesorhizobium tarimense
Han et. al., 2008b
Mesorhizobium temperatum
(ref)
Mesorhizobium tianshanense formerly Rhizobium tianshanense

Ensifer (formerly Sinorhizobium)

The Sinorhizobium genus was described by Chen et al. in 1988. However some recent studies show that Sinorhizobium and the genus Ensifer (Casida, 1982) belong to a single taxon. Ensifer is the earlier heterotypic synonym (it was named first) and thus takes priority (Young, 2003). This means that all Sinorhizobium spp. must be renamed as Ensifer spp. according to the Bacteriological code. The taxonomy of this genus was verified in 2007 by Martens et. al. Read their paper for a more detailed explanation. The genus currently consists of 15 species.

Ensifer abri
D
Ensifer americanum
 
Ensifer arboris  
Ensifer fredii formerly Rhizobium fredii, Type species
Ensifer indiaense D
Ensifer kostiense
Ensifer kummerowiae
Ensifer medicae
Ensifer meliloti formerly Rhizobium meliloti
Ensifer mexicanus New (Lloret et. al. 2007)
'Sinorhizobium morelense' E
Ensifer adhaerens
A
Ensifer saheli
B
Ensifer terangae
C
Ensifer xinjiangense  


A - This name is a earlier heterotypic synonym of Sinorhizobium morelense (see Young, 2003)
B - This species is also known as Sinorhizobium sahelense (why?)
C - This species is incorrectly known as Sinorhizobium teranga
D - Although these species have been published (Ogasawara, et. al. 2003), they have not yet been included in the "Validation List" of the International Journal of Systematic and Evolutionary Microbiology.
E - This species is distinct from Ensifer adhaerens but cannot yet be named Ensifer. See Martens et. al. 2007 for details.

Bradyrhizobium

The Bradyrhizobium genus was described by Jordan in 1982. It currently consists of 8 species.

Bradyrhizobium canariense
 
Bradyrhizobium elkanii  
Bradyrhizobium iriomotense New (Islam et. al., 2008)
Bradyrhizobium japonicum formerly Rhizobium japonicum, Type species
Bradyrhizobium jicamae New (Ramírez-Bahena et. al., 2009)
Bradyrhizobium liaoningense  
Bradyrhizobium pachyrhizi New (Ramírez-Bahena et. al., 2009)
Bradyrhizobium yuanmingense
 

Azorhizobium

The Azorhizobium genus was described by Dreyfus et al. in 1988. It currently consists of 2 species.

Azorhizobium caulinodans Type species
Azorhizobium doebereinerae formerly Azorhizobium johannae

Methylobacterium

The Methylobacterium genus currently contains only one rhizobial species.

Methylobacterium nodulans
 

Burkholderia

The Burkholderia genus currently contains seven named rhizobial members and others as Burkholderia sp.

Burkholderia caribensis
Burkholderia cepacia * see note below
Burkholderia mimosarum New
Burkholderia nodosa New Chen et al (2007)
Burkholderia phymatum
Burkholderia sabiae New Chen et al (2008)
Burkholderia tuberum

Note that although Burkholderia cepacia is considered to nodulate by Rasolomampianina et al. 2005. Mol. Ecol. 14:4135 and Vandamme et al. 2002. Syst. Appl. Microbiol. 25:507, Vandamme et al. 2007 (chapter 1, page 7) notes that recent experiments revealed that nodA and nif genes are not longer detected on these strains and he suggests that the strains lost the characteristic, or the original observation was based on experimental error. Thank you Paulina Estrada de los Santos for this observation.

Cupriavidus

Cupriavidus formerly Wautersia, formerly Ralstonia, has recently undergone several taxonomic revisions. This genus currently contains a single rhizobial species.

Cupriavidus taiwanensis

Devosia

The Devosia genus currently contains only a single rhizobial species.

Devosia neptuniae

Herbaspirillum

The Herbaspirillum genus currently contains a single rhizobial species.

Herbaspirillum lusitanum

Ochrobactrum

The Ochrobactrum genus currently contains two rhizobial species.

Ochrobactrum cytisi new (Zurdo-Piñeiro et. al. 2007)
Ochrobactrum lupini

Phyllobacterium

The Phyllobacterium genus currently contains three rhizobial species.

Phyllobacterium trifolii
Phyllobacterium ifriqiyense new Mantelin et. al. (2006) F
Phyllobacterium leguminum new Mantelin et. al. (2006) F

F Note: isolated from nodules, but not proven to nodulate

Shinella

The Shinella genus currently contains a single rhizobial species.

Shinella kummerowiae New. Lin et. al. (2008)


References

A general excellent resource is:
List of Bacterial names with Standing in Nomenclature (LBSN). (2004) Available http://www.bacterio.cict.fr/

For the full list of references for each strain, please check my PhD thesis, Table 1.1, page 3. New References added since the publication of my thesis will be listed below:

Chun Tao Gu, En Tao Wang, Chang Fu Tian, Tian Xu Han, Wen Feng Chen, Xin Hua Sui and Wen Xin Chen (2008). Rhizobium miluonense sp. nov., a symbiotic bacterium isolated from Lespedeza root nodules. Int J Syst Evol Microbiol 58: 1364-1368. Abstract

Valverde, Angel, Igual, Jose M., Peix, Alvaro, Cervantes, Emilio, Velazquez, Encarna. Rhizobium lusitanum sp. nov. a bacterium that nodulates Phaseolus vulgaris. Int J Syst Evol Microbiol 2006 56: 2631-2637. Abstract

Sophie Mantelin, Marion Fischer-Le Saux, Frederic Zakhia, Gilles Bena, Sophie Bonneau, Habib Jeder, Philippe de Lajudie and Jean-Claude Cleyet-Marel (2006) Emended description of the genus Phyllobacterium and description of four novel species associated with plant roots: Phyllobacterium bourgognense sp. nov., Phyllobacterium ifriqiyense sp. nov., Phyllobacterium leguminum sp. nov. and Phyllobacterium brassicacearum sp. nov. Int J Syst Evol Microbiol 56 (4): 827

Chen, Wen-Ming, James, Euan K., Coenye, Tom, Chou, Jui-Hsing, Barrios, Edmundo, de Faria, Sergio M., Elliott, Geoffrey N., Sheu, Shih-Yi, Sprent, Janet I., Vandamme, Peter. (2006) Burkholderia mimosarum sp. nov., isolated from root nodules of Mimosa spp. from Taiwan and South America. Int J Syst Evol Microbiol 56: 1847-1851. Abstract

Lloret L, Ormeno-Orrillo E, Rincon R, Martinez-Romero J, Rogel-Hernandez MA, Martinez-Romero E. (2007) Ensifer mexicanus sp. nov. a new species nodulating Acacia angustissima (Mill.) Kuntze in Mexico. Syst Appl Microbiol. Abstract

Martens, Miet, Delaere, Manuel, Coopman, Renata, De Vos, Paul, Gillis, Monique, Willems, Anne. (2007) Multilocus sequence analysis of Ensifer and related taxa Int J Syst Evol Microbiol 57: 489-503. Abstract

Garcia-Fraile, Paula, Rivas, Raul, Willems, Anne, Peix, Alvaro, Martens, Miet, Martinez-Molina, Eustoquio, Mateos, Pedro F., Velazquez, Encarna. (2007) Rhizobium cellulosilyticum sp. nov., isolated from sawdust of Populus alba Int J Syst Evol Microbiol 57: 844-848. Abstract

Zurdo-Pineiro, Jose Luis, Rivas, Raul, Trujillo, Martha E., Vizcaino, Nieves, Carrasco, Jose Antonio, Chamber, Manuel, Palomares, Antonio, Mateos, Pedro F., Martinez-Molina, Eustoquio, Velazquez, Encarna. (2007) Ochrobactrum cytisi sp. nov., isolated from nodules of Cytisus scoparius in Spain Int J Syst Evol Microbiol 57: 784-788. Abstract

Wang, Feng Qin, Wang, En Tao, Liu, Jie, Chen, Qiang, Sui, Xin Hua, Chen, Wen Feng, Chen, Wen Xin. (2007) Mesorhizobium albiziae sp. nov., a novel bacterium that nodulates Albizia kalkora in a subtropical region of China. Int J Syst Evol Microbiol 57: 1192-1199 Abstract

Wang, Feng Qin, WChen, Wen-Ming, de Faria, Sergio M., James, Euan K., Elliott, Geoffrey N., Lin, Kuan-Yin, Chou, Jui-Hsing, Sheu, Shih-Yi, Cnockaert, M., Sprent, Janet I., Vandamme, Peter (2007) Burkholderia nodosa sp. nov., isolated from root nodules of the woody Brazilian legumes Mimosa bimucronata and Mimosa scabrella Int J Syst Evol Microbiol, May 2007; 57: 1055 - 1059. Abstract

Han, Tian Xu, Wang, En Tao, Wu, Li Juan, Chen, Wen Feng, Gu, Jin Gang, Gu, Chun Tao, Tian, Chang Fu, Chen, Wen Xin. (2007) Rhizobium multihospitium sp. nov., isolated from multiple legume species native of Xinjiang, China Int J Syst Evol Microbiol 58: 1693-1699 Abstract

Chen WM, de Faria SM, Chou JH, James EK, Elliott GN, Sprent JI, Bontemps C, Young JP, Vandamme P. (2008) Burkholderia sabiae sp. nov., isolated from root nodules of Mimosa caesalpiniifolia. Int J Syst Evol Microbiol. 58(9):2174-9. Abstract

Tian Xu Han, Li Li Han, Li Juan Wu, Wen Feng Chen, Xin Hua Sui, Jin Gang Gu, En Tao Wang and Wen Xin Chen (2008) Mesorhizobium gobiense sp. nov. and Mesorhizobium tarimense sp. nov., isolated from wild legumes growing in desert soils of Xinjiang, China. Int J Syst Evol Microbiol. 58(11):2610-2618. Abstract

Guan, Su Hua, Chen, Wen Feng, Wang, En Tao, Lu, Yang Li, Yan, Xue Rui, Zhang, Xiao Xia, Chen, Wen Xin. (2008) Mesorhizobium caraganae sp. nov., a novel rhizobial species nodulated with Caragana spp. in China Int J Syst Evol Microbiol 2008 58: 2646-2653. Abstract

Ramirez-Bahena, Martha Helena, Garcia-Fraile, Paula, Peix, Alvaro, Valverde, Angel, Rivas, Raul, Igual, Jose M., Mateos, Pedro F., Martinez-Molina, Eustoquio, Velazquez, Encarna (2008) Revision of the taxonomic status of the species Rhizobium leguminosarum (Frank 1879) Frank 1889AL, Rhizobium phaseoli Dangeard 1926AL and Rhizobium trifolii Dangeard 1926AL. R. trifolii is a later synonym of R. leguminosarum. Reclassification of the strain R. leguminosarum DSM 30132 (=NCIMB 11478) as Rhizobium pisi sp. nov. Int J Syst Evol Microbiol 2008 58: 2484-2490. Abstract

Lin, Dong Xu, Wang, En Tao, Tang, Hui, Han, Tian Xu, He, Yu Rong, Guan, Su Hua, Chen, Wen Xin (2008) Shinella kummerowiae sp. nov., a symbiotic bacterium isolated from root nodules of the herbal legume Kummerowia stipulacea. Int J Syst Evol Microbiol 2008 58: 1409-1413 Abstract

Peng, Guixiang, Yuan, Qinghua, Li, Huaxing, Zhang, Wu, Tan, Zhiyuan (2008) Rhizobium oryzae sp. nov., isolated from the wild rice Oryza alta. Int J Syst Evol Microbiol 2008 58: 2158-2163 Abstract

Vidal, Celine, Chantreuil, Clemence, Berge, Odile, Maure, Lucette, Escarre, Jose, Bena, Gilles, Brunel, Brigitte, Cleyet-Marel, Jean-Claude. (2009) Mesorhizobium metallidurans sp. nov., a metal-resistant symbiont of Anthyllis vulneraria growing on metallicolous soil in Languedoc, France. Int J Syst Evol Microbiol 2009 59: 850-855 Abstract

Nandasena, Kemanthi G., O'Hara, Graham W., Tiwari, Ravi P., Willems, Anne, Howieson, John G. (2009). Mesorhizobium australicum sp. nov. and Mesorhizobium opportunistum sp. nov., isolated from Biserrula pelecinus L. in Australia Int J Syst Evol Microbiol 2009 59: 2140-2147 Abstract

Chen, Weimin, Zhu, Wenfei, Bontemps, Cyril, Young, J. Peter W., Wei, Gehong. Mesorhizobium alhagi sp. nov., isolated from root nodules of the wild legume Alhagi sparsifolia Int J Syst Evol Microbiol 2009 0: ijs.0.014043-0 Abstract

Lu, Yang Li, Chen, Wen Feng, Han, Li Li, Wang, En Tao, Zhang, Xiao Xia, Chen, Wen Xin, Han, Su Zhen. Mesorhizobium shangrilense sp. nov., isolated from root nodules of Caragana spp. Int J Syst Evol Microbiol 2009 0: ijs.0.007393-0 Abstract

Ramirez-Bahena, Martha Helena, Peix, Alvaro, Rivas, Raul, Camacho, Maria, Rodriguez-Navarro, Dulce N., Mateos, Pedro F., Martinez-Molina, Eustoquio, Willems, Anne, Velazquez, Encarna Bradyrhizobium pachyrhizi sp. nov. and Bradyrhizobium jicamae sp. nov., isolated from effective nodules of Pachyrhizus erosus Int J Syst Evol Microbiol 2009 59: 1929-1934 Abstract

Islam, M.S., Kawasaki, H., Muramatsu, Y., Nakagawa, Y., and Seki, T. "Bradyrhizobium iriomotense sp. nov., isolated from a tumor-like root of the legume Entada koshunensis from Iriomote Island in Japan." Biosci. Biotechnol. Biochem. (2008)72:1416-1429. Abstract doi:10.1271/bbb.70739

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