Hyphomicrobiales

The Hyphomicrobiales are an order of Gram-negative Alphaproteobacteria.

Hyphomicrobiales
Agrobacterium (SEM image)
Scientific classification
Domain: Bacteria
Phylum: Pseudomonadota
Class: Alphaproteobacteria
Order: Hyphomicrobiales
Douglas 1957 (Approved Lists 1980)
Families[1]

See text

Synonyms[2]
  • Rhizobiales Kuykendall 2006

The rhizobia, which fix nitrogen and are symbiotic with plant roots, appear in several different families. The four families Nitrobacteraceae, Hyphomicrobiaceae, Phyllobacteriaceae, and Rhizobiaceae contain at least several 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

Unassigned Genera

The following genus has not been assigned to a family:

  • Flaviflagellibacter Dong et al. 2019[3]

Provisional Taxa

These taxa have been published, but have not been validated according to the Bacteriological Code:

  • "Nordella" La Scola et al. 2004[4]
  • "Propylenellaceae" Liu et al. 2021[5]
    • "Propylenella" Liu et al. 2021[5]
      • "Propylenella binzhouense" Liu et al. 2021[5]
  • "Thermopetrobacter" Sislak 2013[6]

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature[7] and the phylogeny is based on whole-genome sequences.[2][lower-alpha 1]

 
Hyphomicrobiales
 

Parvibaculaceae

 
 
 

Hyphomicrobiaceae

 
 
 
 
 

Amorphaceae

 
 
 
 

Rhodobiaceae

 
 

Afifellaceae

 
 
 
 

Cohaesibacteraceae

 
 
 

Breoghaniaceae

 
 

Stappiaceae

 
 
 
 
 
 
 

Devosiaceae

 
 
 

Aurantimonadaceae

 
 
 
 
 

Ahrensiaceae

 
 
 

Notoacmeibacteraceae

 
 

Phyllobacteriaceae

 
 
 
 

Rhizobiaceae

 
 
 
 

Bartonellaceae

 
 
 

Phyllobacterium [lower-alpha 2]

 
 

Brucellaceae

 
 
 
 
 
 
 
 
 

Tepidamorphaceae

 
 
 

Kaistiaceae

 
 
 
 

Pseudoxanthobacteraceae

 
 
 

Prosthecomicrobium [lower-alpha 3]

 
 

Pleomorphomonadaceae

 
 
 
 
 
 
 

Blastochloridaceae

 
 

Xanthobacteraceae

 
 
 
 

Phreatobacteraceae

 
 

Nitrobacteraceae

 
 
 
 
 
 

Beijerinckiaceae

 
 
 

Roseiarcaceae

 
 

Methylocystaceae

 
 
 
 
 

Chelatococcaceae

 
 
 

Boseaceae

 
 
 

Salinarimonadaceae

 
 

Methylobacteriaceae

 
 
 
 
 
 
 
 
 
 
 
 
outgroups
 

Rhodobacterales

 
 
 

Parvularculales

 
 

Caulobacterales

 
 
 
 

Natural genetic transformation

Natural genetic transformation has been reported in at least four Hyphomicrobiales species: Agrobacterium tumefaciens,[8] Methylobacterium organophilum,[9] Ensifer adhaerens,[10] and Bradyrhizobium japonicum.[11] 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. Aestuariivirgaceae, Alsobacteraceae, Ancalomicrobiaceae, Lichenibacteriaceae, Lichenihabitantaceae, Rhabdaerophilaceae, and Segnochrobactraceae are not included in this phylogenetic tree.
  2. Phyllobacterium is separate from the rest of Phyllobacteriaceae.
  3. Prosthecomicrobium is separate from the rest of Hyphomicrobiaceae.

References
  1. Parker CT, Garrity GM (1 January 2003). Parker CT, Garrity GM (eds.). "Taxonomic Abstract for the families: Mabikibacteraceae". The NamesforLife Abstracts. NamesforLife, LLC. doi:10.1601/tx.30673.
  2. Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, et al. (2020). "Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria". Frontiers in Microbiology. 11: 468. doi:10.3389/fmicb.2020.00468. PMC 7179689. PMID 32373076.
  3. Dong L, Han MX, Wang D, Liu F, Asem MD, Jiao JY, Xiao M, Salam N, Li WJ. (2019). "Flaviflagellibacter deserti gen. nov., sp. nov., a novel member of the order Rhizobiales isolated from a desert soil". Antonie van Leeuwenhoek. 112 (6): 947–954. doi:10.1007/s10482-019-01228-0. PMID 30637538. S2CID 58006833.{{cite journal}}: CS1 maint: uses authors parameter (link)
  4. La Scola B, Barrassi L, Raoult D. (2004). "A novel alpha-Proteobacterium, Nordella oligomobilis gen. nov., sp. nov., isolated by using amoebal co-cultures". Res Microbiol. 155 (1): 47–51. doi:10.1016/j.resmic.2003.09.012. PMID 14759708.{{cite journal}}: CS1 maint: uses authors parameter (link)
  5. Liu YL, Meng D, Wang F, Gong XF, Gu PF, Fan XY, Du ZJ, Zou JD, Li Q (2021). "Propylenella binzhouense gen. nov., sp. nov. isolated from activated sludge, and proposal of Propylenellaceae fam. nov". Antonie van Leeuwenhoek. 114 (3): 225–233. doi:10.1007/s10482-020-01514-2. PMID 33400070. S2CID 230665484.
  6. Sislak CD (2013). Novel Thermophilic Bacteria Isolated From Marine Hydrothermal Vents (MSc). Portland State University. doi:10.15760/etd.1485. 1486.
  7. Euzéby JP, Parte AC. "Hyphomicrobiales". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved May 15, 2021.{{cite web}}: CS1 maint: uses authors parameter (link)
  8. Demanèche S, Kay E, Gourbière F, Simonet P (June 2001). "Natural transformation of Pseudomonas fluorescens and Agrobacterium tumefaciens in soil". Applied and Environmental Microbiology. 67 (6): 2617–21. Bibcode:2001ApEnM..67.2617D. doi:10.1128/AEM.67.6.2617-2621.2001. PMC 92915. PMID 11375171.
  9. O'Connor M, Wopat A, Hanson RS (January 1977). "Genetic transformation in Methylobacterium organophilum". Journal of General Microbiology. 98 (1): 265–72. doi:10.1099/00221287-98-1-265. PMID 401866.
  10. Zuniga-Soto E, Mullins E, Dedicova B (2015). "Ensifer-mediated transformation: an efficient non-Agrobacterium protocol for the genetic modification of rice". SpringerPlus. 4: 600. doi:10.1186/s40064-015-1369-9. PMC 4628045. PMID 26543735.
  11. Raina JL, Modi VV (August 1972). "Deoxyribonucleate binding and transformation in Rhizobium jpaonicum". Journal of Bacteriology. 111 (2): 356–60. doi:10.1128/JB.111.2.356-360.1972. PMC 251290. PMID 4538250.

Further reading
  • Kuykendall LD, Dazzo FB (2005). "Allorhizobium". In Brenner DJ, Krieg NR, Staley JT, Garrity G (eds.). The Alpha-, Beta-, Delta- and Epsilonproteobacteria, The Proteobacteria, Part C, Bergey's Manual of Systematic Bacteriology. Vol. 2 (2nd ed.). Springer, New York, NY. pp. 345–346. ISBN 978-0-387-24144-9.
  • Kuykendall LD (2005). "Genus Azorhizobium". In Brenner DJ, Krieg NR, Staley JT, Garrity G (eds.). The Alpha-, Beta-, Delta- and Epsilonproteobacteria, The Proteobacteria, Part C, Bergey's Manual of Systematic Bacteriology. Vol. 2 (2nd ed.). Springer, New York, NY. pp. 505–506. ISBN 978-0-387-24144-9.
  • Kuykendall LD (2005). "Genus Bradyrhizobium, family Bradyrhizobiaceae'". In Brenner DJ, Krieg NR, Staley JT, Garrity G (eds.). The Alpha-, Beta-, Delta- and Epsilonproteobacteria, The Proteobacteria, Part C, Bergey's Manual of Systematic Bacteriology. Vol. 2 (2nd ed.). Springer, New York, NY. pp. 438–443. ISBN 978-0-387-24144-9.
  • Kuykendall LD, Young JM, Martínez-Romero, Kerr A, Sawada H (2005). "Genus Rhizobium, a highly divergent genus in a revised family". In Brenner DJ, Krieg NR, Staley JT, Garrity G (eds.). The Alpha-, Beta-, Delta- and Epsilonproteobacteria, The Proteobacteria, Part C, Bergey's Manual of Systematic Bacteriology. Vol. 2 (2nd ed.). Springer, New York, NY. pp. 324–340. ISBN 978-0-387-24144-9.
  • Chen WX, Wang ET, Kuykendall LD (2005). "enus Mesorhizobium, Family Photobacteriaceae.". In Brenner DJ, Krieg NR, Staley JT, Garrity G (eds.). The Alpha-, Beta-, Delta- and Epsilonproteobacteria, The Proteobacteria, Part C, Bergey's Manual of Systematic Bacteriology. Vol. 2 (2nd ed.). Springer, New York, NY. pp. 403–408. ISBN 978-0-387-24144-9.
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