Rhizobiaceae

The Rhizobiaceae is a family of proteobacteria comprising multiple subgroups that enhance and hinder plant development.[4] Some bacteria found in the family are used for plant nutrition and collectively make up the rhizobia. Other bacteria such as Agrobacterium tumefaciens and A. rhizogenes severely alter the development of plants in their ability to induce crown galls or hairy roots found on the stem.[4] The family has been of an interest to scientists for centuries in their ability to associate with plants and modify plant development.[4] The Rhizobiaceae are, like all Proteobacteria, Gram-negative. They are aerobic, and the cells are usually rod-shaped.[5] Many species of the Rhizobiaceae are diazotrophs which are able to fix nitrogen and are symbiotic with plant roots.

Rhizobiaceae
Agrobacterium tumefaciens as it begins to infect a carrot cell
Scientific classification
Domain:	Bacteria
Phylum:	Proteobacteria
Class:	Alphaproteobacteria
Order:	Rhizobiales
Family:	Rhizobiaceae Conn 1938
Genera[1]
Agrobacterium (Smith and Townsend 1907) Conn 1942 Allorhizobium de Lajudie et al. 1998 Carbophilus Meyer et al. 1994 Ciceribacter Kathiravan et al. 2013 Ensifer Casida 1982 Kaistia Im et al. 2005 Neorhizobium Mousavi et al. 2015[2] Pararhizobium Mousavi et al. 2015[2] Pseudorhizobium Kimes et al. 2015[3] Rhizobium Frank 1889 Shinella An et al. 2006 Sinorhizobium Chen et al. 1988 Candidatus Liberibacter Jagoueix et al. 1994

Relation to Agrobacterium

Agrobacterium has been recognized as being related to the Rhizobium.[6] Evidence supporting the association was conducted by phylogentic inferences based on 16S rDNA sequence analyses showing the genera could not be distinguished as separate monophyletic clades.[6]

The issue of Agrobacterium and other genera subsumed by Rhizobium is not yet settled, as some newer phylogenetic data suggests that subclades can still be created.[7][8]

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[1] and the National Center for Biotechnology Information (NCBI),[9] and the phylogeny is based on 16S rRNA-based LTP release 106 by The All-Species Living Tree Project [10]

Rhizobium lusitanum Valverde et al. 2006     Rhizobium rhizogenes (Riker et al. 1930) Young et al. 2001[11]     Agrobacterium rubi Hildebrand 1940         Rhizobium multihospitium Han et al. 2008     Rhizobium tropici Martínez-Romero et al. 1991       Rhizobium miluonense Gu et al. 2008         Rhizobium leguminosarum (Frank 1879) Frank 1889 (Approved Lists 1980) emend. Ramírez-Bahena et al. 2008[12]           Rhizobium endophyticum López-López et al. 2011     Rhizobium tibeticum Hou et al. 2009       Rhizobium etli Segovia et al. 1993         Rhizobium pisi Ramírez-Bahena et al. 2008       Rhizobium phaseoli Dangeard 1926 (Approved Lists 1980) emend. Ramírez-Bahena et al. 2008     Rhizobium fabae Tian et al. 2008       Rhizobium hainanense Chen et al. 1997         Arthrobacter viscosus Gasdorf et al. 1965[13]     Rhizobium alamii Berge et al. 2009     Rhizobium mesosinicum Lin et al. 2009         Rhizobium sullae Squartini et al. 2002       Rhizobium indigoferae Wei et al. 2002       Rhizobium gallicum Amarger et al. 1997     Rhizobium yanglingense Tan et al. 2001       Rhizobium mongolense Van Berkum et al. 1998     Rhizobium oryzae Peng et al. 2008       Rhizobium loessense Wei et al. 2003       Rhizobium tubonense Zhang et al. 2011             Rhizobium cellulosilyticum García-Fraile et al. 2007     Rhizobium soli Yoon et al. 2010         Neorhizobium galegae Lindström 1989     Neorhizobium vignae Ren et al. 2011         Neorhizobium huautlense Wang et al. 1998     Neorhizobium alkalisoli Lu et al. 2009                       Aureimonas altamirensis (Jurado et al. 2006) Rathsack et al. 2011[12][14][15]     Aureimonas frigidaquae (Kim et al. 2008) Rathsack et al. 2011[14][15]       Aureimonas ureilytica (Weon et al. 2007) Rathsack et al. 2011[14][15]       Aurantimonas coralicida Denner et al. 2003 emend. Rathsack et al. 2011.[12][14]       Fulvimarina pelagi Cho and Giovannoni 2003 emend. Rathsack et al. 2011[12][14]       Martelella mediterranea Rivas et al. 2005[12][14]       Allorhizobium undicola (de Lajudie et al. 1998) Young et al. 2001[11]       Allorhizobium vitis (Ophel and Kerr 1990) Young et al. 2001[11]         Allorhizobium borbori Zhang et al. 2011             Beijerinckia fluminensis Döbereiner and Ruschel 1958[16]     Agrobacterium larrymoorei Bouzar and Jones 2001       Agrobacterium radiobacter Beijerinck and van Delden 1902[17]         Rhizobium selenitireducens corrig. Hunter et al. 2008     Rhizobium rosettiformans Kaur et al. 2011           Rhizobium daejeonense Quan et al. 2005           Rhizobium aggregatum (Hirsch and Müller 1986) Kaur et al. 2011     Pararhizobium capsulatum Hirsch and Müller 1986[18]       Pararhizobium giardinii Amarger et al. 1997                     Ensifer mexicanus Lloret et al. 2011     Ensifer terangae (De Lajudie et al. 1994) Young 2003[19]       Ensifer saheli (De Lajudie et al. 1994) Young 2003[19]       Ensifer kostiensis (Nick et al. 1999) Young 2003[19]       Ensifer kummerowiae (Wei et al. 2002) Young 2003[19]       Ensifer fredii (Scholla and Elkan 1984) Young 2003[19]     Sinorhizobium americanum corrig. Toledo et al. 2004         Ensifer arboris (Nick et al. 1999) Young 2003[19]     Ensifer garamanticus Merabet et al. 2010       Ensifer meliloti (Dangeard 1926) Young 2003[19]     Ensifer numidicus Merabet et al. 2010         Ensifer adhaerens Casida 1982[12]

References

1. J.P. Euzéby. "Proteobacteria (scroll down for Rhizobiaceae)". LPSN. Archived from the original on 2013-01-27. Retrieved 2012-05-02.
2. Mousavi SA, Willems A, Nesme X, de Lajudie P, Lindström K (2015). "Revised phylogeny of Rhizobiaceae: proposal of the delineation of Pararhizobium gen. nov., and 13 new species combinations". Syst Appl Microbiol. 38 (2): 84–90. doi:10.1016/j.syapm.2014.12.003. PMID 25595870.
3. Kimes NE, López-Pérez M, Flores-Félix JD, Ramírez-Bahena MH, Igual JM, Peix A, Rodriguez-Valera F, Velázquez E (2015). "Pseudorhizobium pelagicum gen. nov., sp. nov. isolated from a pelagic Mediterranean zone". Syst Appl Microbiol. 38 (5): 293–299. doi:10.1016/j.syapm.2015.05.003. PMID 26078205.
4. Spaink, Herman P.; Kondorosi, Adam; Hooykaas, Paul (2012-12-06). The Rhizobiaceae: Molecular Biology of Model Plant-Associated Bacteria. Springer Science & Business Media. ISBN 9789401150606.
5. Garrity, George M.; Brenner, Don J.; Krieg, Noel R.; Staley, James T. (eds.) (2005). Bergey's Manual of Systematic Bacteriology, Volume Two: The Proteobacteria, Part C: The Alpha-, Beta-, Delta-, and Epsilonproteobacteria. New York, New York: Springer. ISBN 978-0-387-24145-6.
6. Young, J. M.; Kuykendall, L. D.; Martínez-Romero, E.; Kerr, A.; Sawada, H. (2003-01-01). "Classification and nomenclature of Agrobacterium and Rhizobium – a reply to Farrand et al. (2003)". International Journal of Systematic and Evolutionary Microbiology. 53 (5): 1689–1695. doi:10.1099/ijs.0.02762-0. PMID 13130069.
7. Mousavi SA, Österman J, Wahlberg N, Nesme X, Lavire C, Vial L, Paulin L, de Lajudie P, Lindström K (2014). "Phylogeny of the Rhizobium–Allorhizobium–Agrobacterium clade supports the delineation of Neorhizobium gen. nov". Syst Appl Microbiol. 37 (3): 208–15. doi:10.1016/j.syapm.2013.12.007. PMID 24581678.
8. Mousavi SA, Willems A, Nesme X, de Lajudie P, Lindström K (2015). "Revised phylogeny of Rhizobiaceae: proposal of the delineation of Pararhizobium gen. nov., and 13 new species combinations". Syst Appl Microbiol. 38 (2): 84–90. doi:10.1016/j.syapm.2014.12.003. PMID 25595870.
9. Sayers; et al. "Rhizobiaceae". NCBI taxonomy database. Retrieved 2012-05-02.
10. All-Species Living Tree Project."16S rRNA-based LTP release 106 (full tree)" (PDF). SILVA RDB. Retrieved 2012-05-02.
11. These species were formerly classified in the genus Agrobacterium.
12. This is the type species for the genus.
13. Arthrobacter viscosus is currently classified in the Micrococcaceae. See Arthrobacter.
14. Species found in the genera Aurantimonas, Aureimonas, Fulvimarina, and Martelella are all currently classified in the Aurantimonadaceae.
15. The species in the genus Aureimonas were formerly classified in the genus Aurantimonas.
16. Beijerinckia fluminensis is currently classified in the Beijerinckiaceae.
17. This includes Agrobacterium tumefaciens (Smith and Townsend 1907) Conn 1942.
18. Blastobacter capsulatus is currently classified in the Bradyrhizobiaceae.
19. These species were formerly classified in the genus Sinorhizobium.