Rhizobiales

Rhizobiales
Agrobacterium (SEM image)
Scientific classification
Domain:	Bacteria
Phylum:	Proteobacteria
Class:	Alphaproteobacteria
Order:	Rhizobiales Kuykendall 2006
Families
See text
Synonyms
Hyphomicrobiales Douglas 1957

The Rhizobiales are an order of Gram-negative Alphaproteobacteria.

The rhizobia, which fix nitrogen and are symbiotic with plant roots, appear in several different families. The four families Bradyrhizobiaceae, Hyphomicrobiaceae, Phyllobacteriaceae, and Rhizobiaceae contain at least six genera of nitrogen-fixing, legume-nodulating, microsymbiotic bacteria. Examples are the genera Bradyrhizobium and Rhizobium . Species of the Methylocystaceae are methanotrophs; they use methanol (CH₃OH) or methane (CH₄) as their sole energy and carbon sources. Other important genera are the human pathogens Bartonella and Brucella , as well as Agrobacterium (useful in genetic engineering).

Taxonomy

Accepted families

• Bartonellaceae Gieszczykiewicz 1939 (Approved Lists 1980) emend. Brenner et al. 1993
• Beijerinckiaceae Garrity et al. 2006
• Bradyrhizobiaceae Garrity et al. 2006
• Brucellaceae Breed et al. 1957
• Cohaesibacteraceae Hwang and Cho 2008 emend. Gallego et al. 2010
• Mabikibacteraceae Choi et al. 2017 ^[1]
• Hyphomicrobiaceae Babudieri 1950
• Methylobacteriaceae Garrity et al. 2006
• Methylocystaceae Bowman 2006
• Phyllobacteriaceae Mergaert and Swings 2006
• Rhizobiaceae Conn 1938
• Rhodobiaceae Garrity et al. 2006
• Roseiarcaceae Kulichevskaya et al. 2014
• Xanthobacteraceae Lee et al. 2005

Provisional families

These families have been proposed but not yet validly published according to the rules of the Bacteriological Code.

• "Aurantimonadaceae" Denner et al. 2003
• "Devosiaceae" Yarza et al. 2014 ^[2]
• "Kaistiaceae" Yarza et al. 2014 ^[2]
• "Labriaceae" Beck et al. 2015 ^[3]
• "Lutibaculaceae" Yarza et al. 2014 ^[2]
• "Methyloligellaceae" Yarza et al. 2014 ^[2]
• "Methylopilaceae" Beck et al. 2015 ^[3]
• "Pleomorphomonadaceae" Yarza et al. 2014 ^[2]
• "Rhodomicrobiaceae" Yarza et al. 2014 ^[2]
• "Stappiaceae" Yarza et al. 2014 ^[2]
• "Thermopetrobacteraceae" Yarza et al. 2014 ^[2]

Genera incertae sedis

The following genera belong to the Rhizobiales but have not been assigned to a family.

• AlsobacterBao et al. 2014 ^[4]
• Amorphus Zeevi Ben Yosef et al. 2008 ^[5]
• BauldiaYee et al. 2010 ^[6]
• MethylobrevisPoroshina et al. 2015 ^[7]
• MethyloceanibacterTakeuchi et al. 2014 ^[8]
• MethyloligellaDoronina et al. 2014 ^[9]
• VasilyevaeaYee et al. 2010 ^[6]

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature ^[10] and National Center for Biotechnology Information ^[11] and the phylogeny is based on whole-genome sequences. ^[12]

Brucellaceae   Brucella Meyer and Shaw 1920     Ochrobactrum Holmes et al. 1988     Bartonellaceae Bartonella Strong et al. 1915 (Approved Lists 1980) emend. Brenner et al. 1993     Phyllobacteriaceae     Mesorhizobium Jarvis et al. 1997     Hoeflea Peix et al. 2005       Chelativorans Doronina et al. 2010       Rhizobiaceae         Rhizobium Frank 1889 (Approved Lists 1980) emend. Young et al. 2001     Agrobacterium Conn 1942 (Approved Lists 1980) emend. Sawada et al. 1993         Sinorhizobium Chen et al. 1988 emend. De Lajudie et al. 1994     Ensifer Casida 1982         Candidatus Liberibacter corrig. Jagoueix et al. 1994       Candidatus Hodgkinia McCutcheon et al. 2009       Aurantimonadaceae   Aurantimonas Denner et al. 2003 emend. Rathsack et al. 2011     Fulvimarina Cho and Giovannoni 2003 emend. Rathsack et al. 2011       "Devosiaceae" [lower-alpha 1]     Cucumibacter Hwang and Cho 2008     Maritalea Hwang et al. 2009       Pelagibacterium Xu et al. 2011       "Pleomorphomonadaceae"   Amorphus Zeevi Ben Yosef et al. 2008     Pleomorphomonas Hwang et al. 2009 [lower-alpha 2]       "Kaistiaceae" Kaistia Im et al. 2005 [lower-alpha 3]         Bradyrhizobiaceae       Bradyrhizobium Jordan 1982     Nitrobacter Winogradsky 1892       Rhodopseudomonas Czurda and Maresch 1937         Oligotropha Meyer et al. 1994     Afipia Brenner et al. 1992       Xanthobacteraceae     Ancylobacter Raj 1983     Starkeya Kelly et al. 2000         Xanthobacter Wiegel et al. 1978     Azorhizobium Dreyfus et al. 1988           Methylobacteriaceae   Methylobacterium Methylobacterium Patt et al. 1976 (Approved Lists 1980) emend. Green and Bousfield 1983     Microvirga Kanso and Patel 2003       Beijerinckiaceae       Methylocapsa Dedysh et al. 2002     Methylocella Dedysh et al. 2000 emend. Dunfield et al. 2003       Beijerinckia Derx 1950       Methyloferula Vorobev et al. 2011     Methylocystaceae   Methylosinus (ex Whittenbury et al. 1970) Bowman et al. 1993     Methylocystis (ex Whittenbury et al. 1970) Bowman et al. 1993 emend. Dedysh et al. 2007               Hyphomicrobiaceae  pro parte Hyphomicrobium Stutzer and Hartleb 1899   "Rhodomicrobiaceae" [lower-alpha 4] Rhodomicrobium Duchow and Douglas 1949 (Approved Lists 1980) emend. Imhoff et al. 1984       Rhodobiaceae Parvibaculum Schleheck et al. 2004       Meganema Thomsen et al. 2006 [lower-alpha 5]       Sphingomonas Yabuuchi et al. 1990 emend. Yabuuchi et al. 1999 (outgroup)     Magnetospirillum Schleifer et al. 1992 (outgroup)

Natural genetic transformation

Natural genetic transformation has been reported in at least three Rhizobiales species: Agrobacterium tumefaciens , ^[13] Methylobacterium organophilum , ^[14] and Bradyrhizobium japonicum . ^[15] Natural genetic transformation is a sexual process involving DNA transfer from one bacterial cell to another through the intervening medium, and the integration of the donor sequence into the recipient genome by homologous recombination.

See also

• Lar1

Notes

1. Cucumibacter , Maritalea , and Pelagibacterium are currently included in Hyphomicrobiaceae.
2. Pleomorphomonas is currently included in Methylocystaceae.
3. Kaistia is currently included in Rhizobiaceae.
4. Rhodomicrobium is currently included in Hyphomicrobiaceae.
5. Meganema is currently included in Methylobacteriaceae.

References

1. Parker, Charles Thomas; Garrity, George M (1 January 2003). Parker, Charles Thomas; Garrity, George M (eds.). "Taxonomic Abstract for the families". The NamesforLife Abstracts. doi:10.1601/tx.30673.
2. The SILVA database, release 132. Accessed on 5/18/2018. See
   • Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO. (2013). "The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools". Nucleic Acids Res. 41 (Database): D590–D596. doi:10.1093/nar/gks1219. PMC   3531112 . PMID   23193283.
   • Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W, Schleifer KH, Whitman WB, Euzéby J, Amann R, Rosselló-Móra R. (2014). "Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences". Nat Rev Microbiol. 12 (9): 635–45. doi:10.1038/nrmicro3330. hdl:10261/123763. PMID   25118885. S2CID   21895693.
3. Beck, D. A. C.; McTaggart, T. L.; Setboonsarng, U.; Vorobev, A.; Goodwin, L.; Shapiro, N.; Woyke, T.; Kalyuzhnaya, M. G.; Lidstrom, M. E.; Chistoserdova, L. (2015). "Multiphyletic origins of methylotrophy in Alphaproteobacteria, exemplified by comparative genomics of Lake Washington isolates". Environmental Microbiology. 17 (3): 547–54. doi: 10.1111/1462-2920.12736 . PMID   25683159.
4. Bao Z, Sato Y, Fujimura R, Ohta H. (2014). "Alsobacter metallidurans gen. nov., sp. nov., a thallium-tolerant soil bacterium in the order Rhizobiales". Int. J. Syst. Evol. Microbiol. 64 (Pt 3): 775–780. doi:10.1099/ijs.0.054783-0. PMID   24221990.
5. Zeevi ben Yosef D, ben-Dov E, Kushmaro A. (2008). "Amorphus coralli gen. nov., sp. nov., a marine bacterium isolated from coral mucus, belonging to the order Rhizobiales". Int. J. Syst. Evol. Microbiol. 58 (12): 2704–2709. doi: 10.1099/ijs.0.65462-0 . PMID   19060044.
6. Yee B, Oertli GE, Fuerst JA, Staley JT. (2010). "Reclassification of the polyphyletic genus Prosthecomicrobium to form two novel genera, Vasilyevaea gen. nov. and Bauldia gen. nov. with four new combinations: Vasilyevaea enhydra comb. nov., Vasilyevaea mishustinii comb. nov., Bauldia consociata comb. nov. and Bauldia litoralis comb. nov". Int. J. Syst. Evol. Microbiol. 60 (Pt 12): 2960–2966. doi:10.1099/ijs.0.018234-0. PMC   3052453 . PMID   20118292.
7. Poroshina MN, Trotsenko YA, Doronina NV. (2015). "Methylobrevis pamukkalensis gen. nov., sp. nov., a halotolerant restricted facultative methylotroph isolated from saline water". Int. J. Syst. Evol. Microbiol. 65 (4): 1321–1327. doi: 10.1099/ijs.0.000105 . PMID   25667389.
8. Takeuchi M, Katayama T, Yamagishi T, Hanada S, Tamaki H, Kamagata Y, Oshima K, Hattori M, Marumo K, Nedachi M, Maeda H, Suwa Y, Sakata S. (2014). "Methyloceanibacter caenitepidi gen. nov., sp. nov., a facultatively methylotrophic bacterium isolated from marine sediments near a hydrothermal vent". Int. J. Syst. Evol. Microbiol. 64 (Pt 2): 462–468. doi:10.1099/ijs.0.053397-0. PMID   24096357.
9. Doronina NV, Poroshina MN, Kaparullina EN, Ezhov VA, Trotsenko YA. (2013). "Methyloligella halotolerans gen. nov., sp. nov. and Methyloligella solikamskensis sp. nov., two non-pigmented halotolerant obligately methylotrophic bacteria isolated from the Ural saline environments". Syst. Appl. Microbiol. 36 (3): 148–154. doi:10.1016/j.syapm.2012.12.001. PMID   23351489.
10. J.P. Euzéby. "Proteobacteria (scroll down for Rhizobiales)". List of Prokaryotic names with Standing in Nomenclature . Archived from the original on 2013-01-27. Retrieved 2012-05-02.
11. "Rhizobiales". National Center for Biotechnology Information . Retrieved 2012-05-02.
12. Collapsed from the tree built by PATRIC Archived 2016-03-15 at the Wayback Machine . Access date: 2012-05-02.
13. Demanèche S, Kay E, Gourbière F, Simonet P (2001). "Natural transformation of Pseudomonas fluorescens and Agrobacterium tumefaciens in soil". Appl. Environ. Microbiol. 67 (6): 2617–21. doi:10.1128/AEM.67.6.2617-2621.2001. PMC   92915 . PMID   11375171.
14. O'Connor M, Wopat A, Hanson RS (1977). "Genetic transformation in Methylobacterium organophilum". J. Gen. Microbiol. 98 (1): 265–72. doi: 10.1099/00221287-98-1-265 . PMID   401866.
15. Raina JL, Modi VV (1972). "Deoxyribonucleate binding and transformation in Rhizobium japonicum". J. Bacteriol. 111 (2): 356–60. doi:10.1128/JB.111.2.356-360.1972. PMC   251290 . PMID   4538250.

Further reading

• Kuykendall, L. D. and Dazzo, F.B. 2005. Allorhizobium. In Brenner, Krieg, Staley and Garrity (Editors), The Alpha-, Beta-, Delta- and Epsilonproteobacteria, The Proteobacteria, Part C, Bergey’s Manual of Systematic Bacteriology, 2nd. Ed., Vol. 2, Springer, New York, NY, pp. 345–346.
• Kuykendall, L. D. 2005 Genus Azorhizobium. In Brenner, Krieg, Staley and Garrity (Editors), The Alpha-, Beta-, Delta- and Epsilonproteobacteria, The Proteobacteria, Part C, Bergey’s Manual of Systematic Bacteriology, 2nd. Ed.,Vol. 2, Springer, New York, NY, pp. 505–506.
• Kuykendall, L.D. 2005. Genus Bradyrhizobium, family Bradyrhizobiaceae. In: Bergey's Manual of Systematic Bacteriology, 2nd Edition, 2nd Volume. George Garrity, (Ed.) Springer–Verlag, New York, NY, pp. 438–443.
• Chen, W. X., E.T. Wang, and L.D. Kuykendall. 2005. Genus Mesorhizobium, Family Photobacteriaceae. In: Bergey's Manual of Systematic Bacteriology, 2nd Edition, 2nd Volume. George Garrity, (Ed.) Springer–Verlag, New York, NY, pp. 403–408.,
• Kuykendall, L.D., J.M. Young, E. Martínez-Romero, A. Kerr, and H. Sawada. 2005. Genus Rhizobium, a highly divergent genus in a revised family, the Rhizobiaceae. In: Bergey's Manual of Systematic Bacteriology, 2nd Edition, 2nd Volume. George Garrity, (Ed.) Springer–Verlag, New York, NY, pp. 324–340.