Hyphomicrobiales

Hyphomicrobiales
Agrobacterium (SEM image)
Scientific classification
Domain:	Bacteria
Phylum:	Pseudomonadota
Class:	Alphaproteobacteria
Order:	Hyphomicrobiales 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
• 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
• "Kaistiaceae" Yarza et al. 2014
• "Labriaceae" Beck et al. 2015
• "Lutibaculaceae" Yarza et al. 2014
• "Methyloligellaceae" Yarza et al. 2014
• "Methylopilaceae" Beck et al. 2015
• "Pleomorphomonadaceae" Yarza et al. 2014
• "Rhodomicrobiaceae" Yarza et al. 2014
• "Stappiaceae" Yarza et al. 2014
• "Thermopetrobacteraceae" Yarza et al. 2014

Genera incertae sedis

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

• Alsobacter Bao et al. 2014
• Amorphus Zeevi Ben Yosef et al. 2008
• Bauldia Yee et al. 2010
• Methylobrevis Poroshina et al. 2015
• Methyloceanibacter Takeuchi et al. 2014
• Methyloligella Doronina et al. 2014
• Vasilyevaea Yee et al. 2010

Phylogeny

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

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" 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 "Kaistiaceae" Kaistia Im et al. 2005 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" Rhodomicrobium Duchow and Douglas 1949 (Approved Lists 1980) emend. Imhoff et al. 1984 Rhodobiaceae Parvibaculum Schleheck et al. 2004 Meganema Thomsen et al. 2006 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, Methylobacterium organophilum, and Bradyrhizobium japonicum. 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

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.