Rhizobiales

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Rhizobiales
Bartonella.jpg
Scientific classification e
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 (genetic engineering).

Taxonomy[edit]

Accepted Families[edit]

Provisional Families[edit]

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[1]
  • "Kaistiaceae" Yarza et al. 2014[1]
  • "Labriaceae" Beck et al. 2015[2]
  • "Lutibaculaceae" Yarza et al. 2014[1]
  • "Methyloligellaceae" Yarza et al. 2014[1]
  • "Methylopilaceae" Beck et al. 2015[2]
  • "Pleomorphomonadaceae" Yarza et al. 2014[1]
  • "Rhodomicrobiaceae" Yarza et al. 2014[1]
  • "Stappiaceae" Yarza et al. 2014[1]
  • "Thermopetrobacteraceae" Yarza et al. 2014[1]

Genera incertae sedis[edit]

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

Phylogeny[edit]

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature[9] and National Center for Biotechnology Information[10] and the phylogeny is based on whole-genome sequences.[11]












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"[a]



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[b]




"Kaistiaceae"

Kaistia Im et al. 2005[c]





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"[d]

Rhodomicrobium Duchow and Douglas 1949 (Approved Lists 1980) emend. Imhoff et al. 1984




Rhodobiaceae

Parvibaculum Schleheck et al. 2004




Meganema Thomsen et al. 2006[e]




Sphingomonas Yabuuchi et al. 1990 emend. Yabuuchi et al. 1999 (outgroup)



Magnetospirillum Schleifer et al. 1992 (outgroup)




Natural genetic transformation[edit]

Natural genetic transformation has been reported in at least three Rhizobiales species: Agrobacterium tumefaciens,[12] Methylobacterium organophilum,[13] and Bradyrhizobium japonicum.[14] 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[edit]

Notes[edit]

  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[edit]

  1. ^ a b c d e f g h The SILVA database, release 132. Accessed on 5/18/2018. See
  2. ^ a b 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. 
  3. ^ 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: 775–780. doi:10.1099/ijs.0.054783-0. 
  4. ^ 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: 2704–2709. doi:10.1099/ijs.0.65462-0. 
  5. ^ a b 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: 2960–2966. doi:10.1099/ijs.0.018234-0. PMC 3052453Freely accessible. 
  6. ^ 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: 1321–1327. doi:10.1099/ijs.0.000105. 
  7. ^ 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: 462–468. doi:10.1099/ijs.0.053397-0. 
  8. ^ 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: 148–154. doi:10.1016/j.syapm.2012.12.001. 
  9. ^ 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. 
  10. ^ "Rhizobiales". National Center for Biotechnology Information. Retrieved 2012-05-02. 
  11. ^ Collapsed from the tree built by PATRIC Archived 2016-03-15 at the Wayback Machine.. Access date: 2012-05-02.
  12. ^ 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 92915Freely accessible. PMID 11375171. 
  13. ^ 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. 
  14. ^ Raina JL, Modi VV (1972). "Deoxyribonucleate binding and transformation in Rhizobium japonicum". J. Bacteriol. 111 (2): 356–60. PMC 251290Freely accessible. PMID 4538250. 

Further reading[edit]

  • 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.