Editing Agrobacterium (section)

==Nomenclatural history==
Leading up to the 1990s, the genus ''Agrobacterium'' was used as a [[wastebasket taxon]]. With the advent of [[16S ribosomal RNA|16S sequencing]], many ''Agrobacterium'' species (especially the marine species) were reassigned to genera such as ''[[Ahrensia]]'', ''[[Pseudorhodobacter]]'', ''[[Ruegeria]]'', and ''[[Stappia]]''.<ref>{{cite journal | vauthors = Uchino Y, Yokota A, Sugiyama J | title = Phylogenetic position of the marine subdivision of ''Agrobacterium'' species based on 16S rRNA sequence analysis | journal = The Journal of General and Applied Microbiology | volume = 43 | issue = 4 | pages = 243–247 | date = August 1997 | pmid = 12501326 | doi = 10.2323/jgam.43.243 | doi-access = free}}</ref><ref>{{cite journal | vauthors = Uchino Y, Hirata A, Yokota A, Sugiyama J | title = Reclassification of marine ''Agrobacterium'' species: Proposals of ''Stappia stellulata'' gen. nov., comb. nov., ''Stappia aggregata'' sp. nov., nom. rev., ''Ruegeria atlantica'' gen. nov., comb. nov., ''Ruegeria gelatinovora'' comb. nov., ''Ruegeria algicola'' comb. nov., and ''Ahrensia kieliense'' gen. nov., sp. nov., nom. rev. | journal = The Journal of General and Applied Microbiology | volume = 44 | issue = 3 | pages = 201–210 | date = June 1998 | pmid = 12501429 | doi = 10.2323/jgam.44.201 | doi-access = free}}</ref> The remaining ''Agrobacterium'' species were assigned to three biovars: biovar 1 (''[[Agrobacterium tumefaciens]]''), biovar 2 (''Agrobacterium rhizogenes''), and biovar 3 (''Agrobacterium vitis''). In the early 2000s, ''Agrobacterium'' was synonymized with the genus ''[[Rhizobium]]''.<ref>{{cite journal | vauthors = Young JM, Kuykendall LD, Martínez-Romero E, Kerr A, Sawada H | title = A revision of ''Rhizobium'' Frank 1889, with an emended description of the genus, and the inclusion of all species of ''Agrobacterium'' Conn 1942 and ''Allorhizobium undicola'' de Lajudie ''et al''. 1998 as new combinations: ''Rhizobium radiobacter'', ''R. rhizogenes'', ''R. rubi'', ''R. undicola'' and ''R. vitis'' | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 51 | issue = Pt 1 | pages = 89–103 | date = January 2001 | pmid = 11211278 | doi = 10.1099/00207713-51-1-89 | doi-access = free}}</ref> This move proved to be controversial.<ref>{{cite journal | vauthors = Farrand SK, van Berkum PB, Oger P | title = ''Agrobacterium'' is a definable genus of the family Rhizobiaceae | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 53 | issue = Pt 5 | pages = 1681–1687 | date = September 2003 | pmid = 13130068 | doi = 10.1099/ijs.0.02445-0 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Young JM, Kuykendall LD, Martínez-Romero E, Kerr A, Sawada H | title = Classification and nomenclature of ''Agrobacterium'' and ''Rhizobium'' | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 53 | issue = Pt 5 | pages = 1689–1695 | date = September 2003 | pmid = 13130069 | doi = 10.1099/ijs.0.02762-0 | doi-access = free }}</ref> The debate was finally resolved when the genus ''Agrobacterium'' was reinstated<ref>{{cite journal |vauthors = Flores-Félix JD, Menéndez E, Peix A, García-Fraile P, Velázquez E | year = 2020 | title = History and current taxonomic status of genus ''Agrobacterium'' | journal = Syst Appl Microbiol | volume = 43 | issue = 1 | pages = 126046  | pmid = 31818496 | doi = 10.1016/j.syapm.2019.126046| hdl = 10174/28328 | s2cid = 209164436 | hdl-access = free }}</ref> after it was demonstrated that it was [[monophyly|phylogenetically distinct]] from ''Rhizobium''<ref>{{cite journal |vauthors = Mousavi SA, Österman J, Wahlberg N, Nesme X, Lavire C, Vial L, Paulin L, de Lajudie P, Lindström K | title = Phylogeny of the ''Rhizobium''-''Allorhizobium''-''Agrobacterium'' clade supports the delineation of ''Neorhizobium'' gen. nov. | journal = Syst Appl Microbiol | year = 2014 | volume = 37 | issue = 3 | pages = 208–215 | doi = 10.1016/j.syapm.2013.12.007 | pmid = 24581678}}</ref><ref>{{cite journal |vauthors = Mousavi SA, Willems A, Nesme X, de Lajudie P, Lindström K | year = 2015 | title = Revised phylogeny of ''Rhizobiaceae'': Proposal of the delineation of ''Pararhizobium'' gen. nov., and 13 new species combinations | journal = Syst Appl Microbiol | volume = 38 | issue = 2 | pages = 84–90 | pmid = 25595870 | doi = 10.1016/j.syapm.2014.12.003}}</ref> and that ''Agrobacterium'' species were unified by a unique [[synapomorphy]]: the presence of the protelomerase gene, ''telA'', which causes all members of the genus to have a linear [[chromid]].<ref>{{cite journal |vauthors = Ramírez-Bahena MH, Vial L, Lassalle F, Diel B, Chapulliot D, Daubin V, Nesme X, Muller D | year = 2014 | title = Single acquisition of protelomerase gave rise to speciation of a large and diverse clade within the ''Agrobacterium''/''Rhizobium'' supercluster characterized by the presence of a linear chromid | journal = Mol Phylogenet Evol | volume = 73 | pages = 202–207 | pmid = 24440816 | doi = 10.1016/j.ympev.2014.01.005}}</ref> By this time, however, the three ''Agrobacterium'' biovars had become defunct; biovar 1 remained with ''Agrobacterium'', biovar 2 was renamed ''[[Rhizobium rhizogenes]]'', and biovar 3 was renamed ''[[Allorhizobium vitis]]''.