Hyphomicrobiales

Hyphomicrobiales
Agrobacterium (SEM image)
Scientific classification
Domain:	Bacteria
Kingdom:	Pseudomonadati
Phylum:	Pseudomonadota
Class:	Alphaproteobacteria
Order:	Hyphomicrobiales Douglas 1957 (Approved Lists 1980)
Families [1]
See text
Synonyms [2]
RhizobialesKuykendall 2006

The Hyphomicrobiale' (synonym 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 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, an important tool in genetic engineering.

Taxonomy

Accepted families

• Aestuariivirgaceae Li et al. 2019
• Afifellaceae Hördt et al. 2020
• Ahrensiaceae Hördt et al. 2020
• Alsobacteraceae Sun et al. 2018
• Amorphaceae Hördt et al. 2020
• Ancalomicrobiaceae Dahal et al. 2018
• Aurantimonadaceae Hördt et al. 2020
• Bartonellaceae Gieszczykiewicz 1939 (Approved Lists 1980)
• Beijerinckiaceae Garrity et al. 2006
• Blastochloridaceae Hördt et al. 2020
• Boseaceae Hördt et al. 2020
• Breoghaniaceae Hördt et al. 2020
• Brucellaceae Breed et al. 1957 (Approved Lists 1980)
• Chelatococcaceae Dedysh et al. 2016
• Cohaesibacteraceae Hwang and Cho 2008
• Devosiaceae Hördt et al. 2020
• Hyphomicrobiaceae Babudieri 1950 (Approved Lists 1980)
• Kaistiaceae Hördt et al. 2020
• Lichenibacteriaceae Pankratov et al. 2020
• Lichenihabitantaceae Noh et al. 2019
• Methylobacteriaceae Garrity et al. 2006
• Methylocystaceae Bowman 2006
• Nitrobacteraceae corrig. Buchanan 1917 (Approved Lists 1980)
• Notoacmeibacteraceae Huang et al. 2017
• Parvibaculaceae Hördt et al. 2020
• Phreatobacteraceae Hördt et al. 2020
• Phyllobacteriaceae Mergaert and Swings 2006
• Pleomorphomonadaceae Hördt et al. 2020
• Pseudoxanthobacteraceae Hördt et al. 2020
• Rhabdaerophilaceae Ming et al. 2020
• Rhizobiaceae Conn 1938 (Approved Lists 1980)
• Rhodobiaceae Garrity et al. 2006
• Roseiarcaceae Kulichevskaya et al. 2014
• Salinarimonadaceae Cole et al. 2018
• Segnochrobactraceae Akter et al. 2020
• Stappiaceae Hördt et al. 2020
• Tepidamorphaceae Hördt et al. 2020
• Xanthobacteraceae Lee et al. 2005

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] [a]}

Hyphomicrobiales Parvibaculaceae Hyphomicrobiaceae Amorphaceae Rhodobiaceae Afifellaceae Cohaesibacteraceae Breoghaniaceae Stappiaceae Devosiaceae Aurantimonadaceae Ahrensiaceae Notoacmeibacteraceae Phyllobacteriaceae Rhizobiaceae Bartonellaceae Phyllobacterium [b] Brucellaceae Tepidamorphaceae Kaistiaceae Pseudoxanthobacteraceae Prosthecomicrobium [c] 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

• Lar1

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.
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.
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.
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.