Rhizobiales

The Rhizobiales are an order of Gram-negative Alphaproteobacteria.

Rhizobiales
Agrobacterium (SEM image)
Scientific classification
Domain: Bacteria
Phylum: Proteobacteria
Class: Alphaproteobacteria
Order: Rhizobiales
Kuykendall 2006
Families

See text

Synonyms
  • Hyphomicrobiales Douglas 1957

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

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.

  • Alsobacter Bao et al. 2014[4]
  • Amorphus Zeevi Ben Yosef et al. 2008[5]
  • Bauldia Yee et al. 2010[6]
  • Methylobrevis Poroshina et al. 2015[7]
  • Methyloceanibacter Takeuchi et al. 2014[8]
  • Methyloligella Doronina et al. 2014[9]
  • Vasilyevaea Yee 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

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
  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.CS1 maint: uses authors parameter (link)
  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.CS1 maint: uses authors parameter (link)
  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.CS1 maint: uses authors parameter (link)
  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.CS1 maint: uses authors parameter (link)
  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.CS1 maint: uses authors parameter (link)
  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.CS1 maint: uses authors parameter (link)
  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.
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