Hyphomicrobiales Explained

The Hyphomicrobiales (synonom 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 (useful 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^[1]

Provisional Taxa

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

• "Nordella" La Scola et al. 2004^[2]
• "Propylenellaceae" Liu et al. 2021^[3]
  • "Propylenella" Liu et al. 2021^[3]
    • "Propylenella binzhouense" Liu et al. 2021^[3]
• "Thermopetrobacter" Sislak 2013^[4]

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature^[5] and the phylogeny is based on whole-genome sequences.

Natural genetic transformation

Natural genetic transformation has been reported in at least four Hyphomicrobiales species: Agrobacterium tumefaciens,^[6] Methylobacterium organophilum,^[7] Ensifer adhaerens,^[8] and Bradyrhizobium japonicum.^[9] 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

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

Notes and References

1. Dong L, Han MX, Wang D, Liu F, Asem MD, Jiao JY, Xiao M, Salam N, Li WJ . Flaviflagellibacter deserti gen. nov., sp. nov., a novel member of the order Rhizobiales isolated from a desert soil . Antonie van Leeuwenhoek . 2019 . 112 . 6 . 947–954. 10.1007/s10482-019-01228-0 . 30637538 . 58006833 .
2. La Scola B, Barrassi L, Raoult D . A novel alpha-Proteobacterium, Nordella oligomobilis gen. nov., sp. nov., isolated by using amoebal co-cultures . Res Microbiol . 2004 . 155 . 1 . 47–51. 10.1016/j.resmic.2003.09.012 . 14759708 . free .
3. Liu YL, Meng D, Wang F, Gong XF, Gu PF, Fan XY, Du ZJ, Zou JD, Li Q . Propylenella binzhouense gen. nov., sp. nov. isolated from activated sludge, and proposal of Propylenellaceae fam. nov. . Antonie van Leeuwenhoek . 2021 . 114 . 3 . 225–233. 10.1007/s10482-020-01514-2 . 33400070 . 230665484 .
4. MSc . Sislak CD . 2013 . Novel Thermophilic Bacteria Isolated From Marine Hydrothermal Vents . Portland State University . 1486 . 10.15760/etd.1485. free .
5. Web site: Euzéby JP, Parte AC . Hyphomicrobiales . May 15, 2021 . List of Prokaryotic names with Standing in Nomenclature (LPSN).
6. Demanèche S, Kay E, Gourbière F, Simonet P . Natural transformation of Pseudomonas fluorescens and Agrobacterium tumefaciens in soil . Applied and Environmental Microbiology . 67 . 6 . 2617–21 . June 2001 . 11375171 . 92915 . 10.1128/AEM.67.6.2617-2621.2001 . 2001ApEnM..67.2617D .
7. O'Connor M, Wopat A, Hanson RS . Genetic transformation in Methylobacterium organophilum . Journal of General Microbiology . 98 . 1 . 265–72 . January 1977 . 401866 . 10.1099/00221287-98-1-265 . free .
8. Zuniga-Soto E, Mullins E, Dedicova B . Ensifer-mediated transformation: an efficient non-Agrobacterium protocol for the genetic modification of rice . SpringerPlus . 4 . 600 . 2015 . 26543735 . 4628045 . 10.1186/s40064-015-1369-9 . free .
9. Raina JL, Modi VV . Deoxyribonucleate binding and transformation in Rhizobium jpaonicum . Journal of Bacteriology . 111 . 2 . 356–60 . August 1972 . 4538250 . 251290 . 10.1128/JB.111.2.356-360.1972 .