Rhizobiales

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 Bartonella (pathogen) and Agrobacterium (genetic engineering).

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature[2] and National Center for Biotechnology Information[3] and the phylogeny is based on whole-genome sequences.[4]











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




Hyphomicrobiaceae pro parte


Cucumibacter Hwang and Cho 2008

Maritalea Hwang et al. 2009

Pelagibacterium Xu et al. 2011

Amorphus Zeevi Ben Yosef et al. 2008

Pleomorphomonas Hwang et al. 2009[lower-alpha 2]

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

Balneimonas corrig. Takeda et al. 2004[lower-alpha 4]
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

Methylocystis (ex Whittenbury et al. 1970) Bowman et al. 1993 emend. Dedysh et al. 2007

Methylosinus (ex Whittenbury et al. 1970) Bowman et al. 1993







Hyphomicrobiaceae pro parte

Hyphomicrobium Stutzer and Hartleb 1899

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)



Natural genetic transformation

Natural genetic transformation has been reported in at least three Rhizobiales species: Agrobacterium tumefaciens,[5] Methylobacterium organophilum,[6] and Bradyrhizobium japonicum.[7] 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.


Notes

  1. 1 2 These families have been proposed but not yet validly published according to the rules of the Bacteriological Code.
  2. ↑ Pleomorphomonas is currently included in Methylocystaceae.
  3. ↑ Kaistia is currently included in Rhizobiaceae.
  4. ↑ Balneimonas is currently included in Bradyrhizobiaceae.
  5. ↑ Meganema is currently included in Methylobacteriaceae.

References

  1. 1 2 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.
  2. ↑ J.P. Euzéby. "Proteobacteria (scroll down for Rhizobiales)". List of Prokaryotic names with Standing in Nomenclature. Retrieved 2012-05-02.
  3. ↑ "Rhizobiales". National Center for Biotechnology Information. Retrieved 2012-05-02.
  4. ↑ Collapsed from the tree built by PATRIC. Access date: 2012-05-02.
  5. ↑ 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.
  6. ↑ 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.
  7. ↑ Raina JL, Modi VV (1972). "Deoxyribonucleate binding and transformation in Rhizobium jpaonicum". J. Bacteriol. 111 (2): 356–60. PMC 251290Freely accessible. PMID 4538250.

Further reading

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