Agrobacteria-Rhizobia Complex

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====== Taxonomy ======

===== Disclaimer =====
  * The taxonomy of agrobacteria and rhizobia is complicated by a long history of frequent revisions, which often cause confusions. The information provided here reflects the consensus among the major contributors of this site.
  * For authoritative information, please refer to the [[https://www.the-icsp.org/taxonomic-subcommittees|Subcommittee on Taxonomy of Rhizobia and Agrobacteria]] of the [[https://www.the-icsp.org/|International Committee on Systematics of Prokaryotes (ICSP)]].
    * Minimal standards for the description of new genera and species of rhizobia and agrobacteria. [[https://doi.org/10.1099/ijsem.0.003426]]


===== Phylogeny =====
  * A simplified illustration: see Figure 1 of [[https://doi.org/10.1146/annurev-phyto-021622-125009]]
  * Strains with genome sequences available as of 2022: see Figure S2 of [[https://doi.org/10.1146/10.1098/rstb.2020.0466]]


===== Genus Names =====
  * //Agrobacterium//: 1 circular chromosome (~2.9 Mb) +  1 linear chromid (~2.2 Mb); BV1 & BV1-like. The linear chromid is a specific trait.
  * //Allorhizobium//: 1 circular chromosome (~3.7 Mb) +  1 circular chromid (~1.3 Mb); BV3.
  * //Rhizobium//: 1 circular chromosome (~3.8-4.8 Mb) +  1 or more circular chromids; BV2, BV2-like, and diverse rhizobia.



===== Biovars (BV) of Agrobacteria =====

==== BV1 ====
  * BV1: the //Agrobacterium tumefaciens// species complex, divided into multiple genomospecies (G?), some have Latin names:

^Genomospecies  ^Species Name  ^Representative Strains  ^Note  ^
|G1  |//Agrobacterium fabacearum//  |CNPSo 675<sup>T</sup> (= UMR 1457<sup>T</sup> = LMG 31642<sup>T</sup>), Ach5, 1D1108  |[[https://lpsn.dsmz.de/species/agrobacterium-fabacearum]]; [[https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1183401&lvl=3&lin=f&keep=1&srchmode=1&unlock|NCBI]]; [[https://doi.org/10.1099/ijsem.0.004278|10.1099/ijsem.0.004278]]  |
|G2  |//Agrobacterium pusense//  |DSM 22668<sup>T</sup>, H41, CFBP 5875  |[[https://lpsn.dsmz.de/species/agrobacterium-pusense]]  |
|G3  |//Agrobacterium tomkonis//  |IIF1SW-B1<sup>T</sup> (= LMG 32164<sup>T</sup> = NRRL B-65602<sup>T</sup>), SUL3, CFBP 6623  |[[https://lpsn.dsmz.de/species/agrobacterium-tomkonis]]  |
|G4  |//Agrobacterium radiobacter//  |B6, 1D1460  |  |
|G5  |NA  |CFBP 6625, CFBP 6626  |  |
|G6  |NA  |NCPPB 925, CFBP 5499, CFBP 5877  |  |
|G7  |//Agrobacterium deltaense//  |YIC4121<sup>T</sup>, 1D1609  |[[https://lpsn.dsmz.de/species/agrobacterium-deltaense]]; Nomenclatural status: not validly published; Taxonomic status: preferred name (not correct name)  |
|G8  |//Agrobacterium fabrum//  |<color #ff0000>C58</color>  |[[https://lpsn.dsmz.de/species/agrobacterium-fabrum]]; Nomenclatural status: not validly published; Taxonomic status: preferred name (not correct name)   |
|G9  |//Agrobacterium salinitolerans//  |[[https://lpsn.dsmz.de/species/agrobacterium-salinitolerans]]; YIC 5082<sup>T</sup>, CFBP 5506, CFBP 5507  |  |
|G12  |NA  |  |  |
|G13  |NA  |CFBP 6927  |  |
|G14  |//Agrobacterium nepotum//  |39/7  |  |
|G15  |//Agrobacterium viscosum//  |ATCC 31113  |  |
|G16  |NA  |  |  |
|G17  |NA  |  |  |
|G18  |NA  |  |  |
|G19  |//Agrobacterium burrii//  |Rnr<sup>T</sup> (= CFBP 8705<sup>T</sup> = DSM 112541<sup>T</sup>)  |[[https://doi.org/10.1094/PHYTO-11-21-0463-SC]]  |
|G20  |//Agrobacterium shirazense//  |OT33<sup>T</sup> (= CFBP 8901<sup>T</sup> = DSM 112540<sup>T</sup>)  |[[https://doi.org/10.1094/PHYTO-11-21-0463-SC]]  |
|G21  |NA  |K599, MAFF210266  |  |
|G22  |NA  |KCJK1736  |  |
|NA  |//Agrobacterium arsenijevicii//  |KFB 330<sup>T</sup> (= CFBP 8308<sup>T</sup> = LMG 28674<sup>T</sup>)  |sister of //Agrobacterium nepotum//; [[https://doi.org/10.1016/j.syapm.2015.06.001]]; [[https://lpsn.dsmz.de/species/agrobacterium-arsenijevicii|LPSN]]  |
|NA  |//Agrobacterium leguminum//  |MOPV5<sup>T</sup> (= CECT 30096<sup>T</sup> = LMG 31779<sup>T</sup>)  |sister of //Agrobacterium deltaense//; [[https://doi.org/10.1099/ijsem.0.005120]]  |

==== BV1-like ====
  * BV1-like: sister group of BV1; similar to BV1 in having a linear chromid; All species classified to the genus //Agrobacterium//
    * //Agrobacterium bohemicum//
    * //Agrobacterium cavarae//; sister to //Agrobacterium larrymoorei// [[https://doi.org/10.1099/ijsem.0.004441]]
    * //Agrobacterium larrymoorei//
    * //Agrobacterium rosae//
    * //Agrobacterium rubi// = Genomospecies 11 (G11)
    * //Agrobacterium skierniewicense//
    * //Agrobacterium vaccinii//

==== BV2 ====
  * BV2: Genomospecies 10 (G10), current name = //Rhizobium rhizogenes//


==== BV2-like ====
  * Two different clades
    * Clade 1: //Rhizobium leucaenae//
    * Clade 2: //Rhizobium freirei//, //Rhizobium tropici//
==== BV3 ====
  * BV3: previously //Agrobacterium vitis//, now //Allorhizobium// spp. Narrow host range, limited to grapevine.