The current taxonomy of rhizobia

Update in progress: Jan 2016

This page lists all of the current validly-published binomial names for the rhizobia, which currently consists of 98 species 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. 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".

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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 in each section. This will take you to the LPSN taxonomy 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 finding new rhizobial genera in particular is difficult. To compare the differences between updates check the change log. This page can be cited as:

Weir, B.S. (2016) The current taxonomy of rhizobia. NZ Rhizobia website. Last updated: X Jan, 2016



class: Alphaproteobacteria order: Rhizobiales family: Rhizobiaceae

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 49 rhizobial species (and 11 non rhizobial species). Rhizobium in New Zealand.

Rhizobium alamii Berge et al. (2009)
Rhizobium alkalisoli Lu et al. (2009b), See note B
Rhizobium azibense  
Rhizobium calliandrae  
Rhizobium cauense  
Rhizobium cellulosilyticum García-Fraile et al. (2007)
Rhizobium daejeonense  
Rhizobium endophyticum López-López et al. (2011)
Rhizobium etli  
Rhizobium fabae  
Rhizobium freirei  
Rhizobium galegae See note B
Rhizobium gallicum  
Rhizobium giardinii  
Rhizobium grahamii  
Rhizobium hainanense  
Rhizobium halophytocola  
Rhizobium herbae Ren et al. (2011b)
Rhizobium huautlense See note B
Rhizobium indigoferae  
Rhizobium jaguaris  
Rhizobium laguerreae  
Rhizobium leguminosarum Type species. See note A
Rhizobium leucaenae formerly Rhizobium tropici type A strains
Rhizobium loessense formerly Rhizobium huanglingense
Rhizobium lusitanum  
Rhizobium mayense  
Rhizobium mesoamericanum  
Rhizobium mesosinicum Lin et al. (2009)
Rhizobium miluonense Gu et al. (2008)
Rhizobium mongolense  
Rhizobium multihospitium Han et al. (2008)
Rhizobium oryzae Peng et al. (2008)
Rhizobium paranaense  
Rhizobium petrolearium  
Rhizobium phaseoli Confirmed as a species. Ramirez-Bahena et al. (2008)
Rhizobium pisi Ramirez-Bahena et al. (2008)
Rhizobium tibeticum Hou et al. (2009)
Rhizobium sophorae  
Rhizobium sophoriradicis  
Rhizobium sphaerophysae  
Rhizobium sullae formerly Rhizobium hedysari
Rhizobium taibaishanense  
Rhizobium tropici  
Rhizobium tubonense Zhang et al. (2011)
Rhizobium undicola formerly Allorhizobium undicola
Rhizobium vallis  
Rhizobium vignae Ren et al. (2011)
Rhizobium yanglingense  

ARhizobium 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).
BThe genus Neorhizobium was created by Mousavi et al. 2013 including R. alkalisoli, R. galegae, and R. huautlense. I choose not to follow this taxonomy as I feel it is incomplete, and not useful without a wider analysis.
NB: for non rhizobia Rhizobium such as R. soli and R. radiobacter see the not rhizobia page.



class: Alphaproteobacteria order: Rhizobiales family: Phyllobacteriaceae

The genus Mesorhizobium was described by Jarvis et al. in 1997. Several Rhizobium species were transferred to this genus. It currently consists of 21 rhizobia species (and 1 non-rhizobial species). Mesorhizobium in New Zealand.

Mesorhizobium abyssinicae  
Mesorhizobium albiziae Wang et al. (2007)
Mesorhizobium alhagi Chen et al. (2010)
Mesorhizobium amorphae  
Mesorhizobium australicum Nandasena et al. (2009)
Mesorhizobium camelthorni Chen et al. (2011)
Mesorhizobium caraganae Wang et al. (2007)
Mesorhizobium chacoense  
Mesorhizobium ciceri formerly Rhizobium ciceri
Mesorhizobium erdmanii  
Mesorhizobium gobiense Han et al. (2008b)
Mesorhizobium hawassense  
Mesorhizobium huakuii formerly Rhizobium huakuii
Mesorhizobium jarvisii  
Mesorhizobium loti formerly Rhizobium loti, Type species
Mesorhizobium mediterraneum formerly Rhizobium mediterraneum
Mesorhizobium metallidurans Vidal et al. (2009)
Mesorhizobium muleiense  
Mesorhizobium opportunistum Nandasena et al. (2009)
Mesorhizobium plurifarium  
Mesorhizobium qingshengii  
Mesorhizobium robiniae Zhou et al. (2010)
Mesorhizobium sangaii  
Mesorhizobium shangrilense Lu et al. (2009)
Mesorhizobium shonense  
Mesorhizobium silamurunense  
Mesorhizobium septentrionale  
Mesorhizobium tamadayense  
Mesorhizobium tarimense Han et al. (2008b)
Mesorhizobium temperatum  
Mesorhizobium tianshanense formerly Rhizobium tianshanense


Ensifer (formerly Sinorhizobium)

class: Alphaproteobacteria order: Rhizobiales family: Rhizobiaceae

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. There has been some discussion in the literature if Ensifer or Sinorhizobium is correct Young (2010), this website follows the opinion of the Judicial Commission, and will use Ensifer. The genus currently consists of 17 species. Ensifer in New Zealand.

Ensifer abri D
Sinorhizobium americanum F
Ensifer arboris  
Ensifer fredii formerly Rhizobium fredii, former Type of Sinorhizobium G
Ensifer garamanticus Merabet et al. (2010)
Ensifer indiaense D
Ensifer kostiensis  
Ensifer kummerowiae  
Ensifer medicae  
Ensifer meliloti formerly Rhizobium meliloti
Ensifer mexicanus Lloret et al. (2007)
'Sinorhizobium morelense' E
Ensifer adhaerens A
Ensifer numidicus Merabet et al. (2010)
Ensifer saheli B
Ensifer sojae Li et al. (in press)
Ensifer terangae C

A — This name is a earlier heterotypic synonym of Sinorhizobium morelense (see Young, 2003)
B — This species should be called “Sinorhizobium sahelense” in technically correct Latin (referring to Sahel), but according to a note on Rule 61 of the Code, since S. saheli appears on a IJSEM list it cannot be corrected.
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, and no type strains exist in international culture collections.
E — This name may be a later heterotypic synonym of Ensifer adhaerens Young (2003), or a distict species Martens et al. (2007).
F — Not yet formally renamed as Ensifer.
GEnsifer xinjiangense is later heterotypic synonym of Ensifer fredii.



class: Alphaproteobacteria order: Rhizobiales family: Bradyrhizobiaceae

The Bradyrhizobium genus was described by Jordan in 1982. It currently consists of 9 rhizobia species (and 1 non rhizobial species). Bradyrhizobium in New Zealand .

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



class: Betaproteobacteria order: Burkholderiales family: Burkholderiaceae

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

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

X — Note that although Burkholderia cepacia is considered to nodulate by Rasolomampianina et al. (2005) and Vandamme et al. (2002), 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.



class: Alphaproteobacteria order: Rhizobiales family: Phyllobacteriaceae

The Phyllobacterium genus currently contains three rhizobial species. Phyllobacterium in New Zealand.

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

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



class: Alphaproteobacteria order: Rhizobiales family: Methylobacteriaceae

The Microvirga genus currently contains three rhizobial species. Microvirga in New Zealand.

Microvirga lupini Ardley et al. (in press)
Microvirga lotononidis Ardley et al. (in press)
Microvirga zambiensis Ardley et al. (in press)



class: Alphaproteobacteria order: Rhizobiales family: Hyphomicrobiaceae

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



class: Alphaproteobacteria order: Rhizobiales family: Brucellaceae

The Ochrobactrum genus currently contains two rhizobial species. Ochrobactrum in New Zealand.

Ochrobactrum cytisi Zurdo-Piñeiro et al. 2007
Ochrobactrum lupini  



class: Alphaproteobacteria order: Rhizobiales family: Methylobacteriaceae

The Methylobacterium genus contains only a single rhizobial species. Methylobacterium in New Zealand.

Methylobacterium nodulans  



class: Betaproteobacteria order: Burkholderiales family: Burkholderiaceae

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

Cupriavidus taiwanensis  



class: Alphaproteobacteria order: Rhizobiales family: Hyphomicrobiaceae

The Devosia genus currently contains only a single rhizobial species (and 1 potentially non rhizobial species).

Devosia neptuniae  



class: Alphaproteobacteria order: Rhizobiales family: Rhizobiaceae

The Shinella genus currently contains a single rhizobial species.

Shinella kummerowiae Lin et al. (2008)



A general excellent resource is:
List of Prokaryotic names with Standing in Nomenclature (LPSN). Available

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 are listed below:

As of 2016 References will be added to the original publication in the column after the species name and doi: link to the paper. Note that this is NOT the authority, just the original publication.