Rhizobiales

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Rhizobiales
Agrobacterium-tumefaciens.png
Agrobacterium (SEM image)
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Domain: Bacteria
Phylum: Proteobacteria
Class: Alphaproteobacteria
Order: Rhizobiales
Kuykendall 2006
Families

See text

Synonyms
  • Hyphomicrobiales Douglas 1957

The Rhizobiales are an order of Gram-negative Alphaproteobacteria.

Contents

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

Provisional families

These families have been proposed but not yet validly published according to the rules of the Bacteriological Code.

Genera incertae sedis

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

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature [10] and National Center for Biotechnology Information [11] and the phylogeny is based on whole-genome sequences. [12]

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" [lower-alpha 1]

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 [lower-alpha 2]

"Kaistiaceae"

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

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" [lower-alpha 4]

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)

Magnetospirillum Schleifer et al. 1992 (outgroup)

Natural genetic transformation

Natural genetic transformation has been reported in at least three Rhizobiales species: Agrobacterium tumefaciens , [13] Methylobacterium organophilum , [14] and Bradyrhizobium japonicum . [15] 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. Cucumibacter , Maritalea , and Pelagibacterium are currently included in Hyphomicrobiaceae.
  2. Pleomorphomonas is currently included in Methylocystaceae.
  3. Kaistia is currently included in Rhizobiaceae.
  4. Rhodomicrobium is currently included in Hyphomicrobiaceae.
  5. Meganema is currently included in Methylobacteriaceae.

Related Research Articles

Rhizobiaceae Family of bacteria

The Rhizobiaceae is a family of proteobacteria comprising multiple subgroups that enhance and hinder plant development. Some bacteria found in the family are used for plant nutrition and collectively make up the rhizobia. Other bacteria such as Agrobacterium tumefaciens and A. rhizogenes severely alter the development of plants in their ability to induce crown galls or hairy roots found on the stem. The family has been of an interest to scientists for centuries in their ability to associate with plants and modify plant development. The Rhizobiaceae are, like all Proteobacteria, Gram-negative. They are aerobic, and the cells are usually rod-shaped. Many species of the Rhizobiaceae are diazotrophs which are able to fix nitrogen and are symbiotic with plant roots.

Rhodobacterales are an order of the Alphaproteobacteria.

Burkholderiaceae Family of bacteria

The Burkholderiaceae are a family of bacteria included in the order Burkholderiales. It includes some pathogenic species, such as Burkholderia mallei (glanders) and Burkholderia pseudomallei (melioidosis).

In taxonomy, Ruegeria is a genus of the Rhodobacteraceae. This genus was formerly known as the marine Agrobacterium before they were reclassified in 1998. It bears in fact the name of Hans-Jürgen Rüger, a German microbiologist, for his contribution to the taxonomy of marine species of Agrobacterium.

In taxonomy, Jannaschia is a genus of the Rhodobacteraceae.

In taxonomy, Leisingera is a genus of the Rhodobacteraceae.

In taxonomy, Loktanella is a genus of the Rhodobacteraceae.

In taxonomy, Marinovum is a genus of the Rhodobacteraceae. Up to now there is only one species of this genus known.

In taxonomy, Oceanicola is a genus of the Rhodobacteraceae.

In taxonomy, Pannonibacter is a genus of the Rhodobacteraceae.

In taxonomy, Phaeobacter is a genus of the Rhodobacteraceae.

In taxonomy, Sulfitobacter is a genus of the Rhodobacteraceae.

In taxonomy, Thalassobacter is a genus of the Rhodobacteraceae. (Proteobacteria)

In taxonomy, Halobiforma is a genus of the Halobacteriaceae. Species include:

Halopiger is a genus of archaeans in the family Halobacteriaceae that have high tolerance to salinity.

In taxonomy, Halosimplex is a genus of the Halobacteriaceae.

In taxonomy, Natrinema is a genus of the Halobacteriaceae.

In taxonomy, Natronorubrum is a genus of the Halobacteriaceae.

The Negativicutes are a class of bacteria in the phylum Firmicutes, whose members have a peculiar cell wall with a lipopolysaccharide outer membrane which stains gram-negative, unlike most other members of the Firmicutes. Although several neighbouring Clostridia species also stain gram-negative, the proteins responsible for the unusual diderm structure of the Negativicutes may have actually been laterally acquired from Proteobacteria. Additional research is required to confirm the origin of the diderm cell envelope in the Negativicutes.

Lentibacillus salicampi is a moderately halophilic bacterium, the type species of its genus. It is Gram-variable, aerobic, endospore-forming and rod-shaped, with type strain SF-20(T).

References

  1. Parker, Charles Thomas; Garrity, George M (1 January 2003). Parker, Charles Thomas; Garrity, George M (eds.). "Taxonomic Abstract for the families". The NamesforLife Abstracts. doi:10.1601/tx.30673.
  2. 1 2 3 4 5 6 7 8 The SILVA database, release 132. Accessed on 5/18/2018. See
  3. 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.
  4. Bao Z, Sato Y, Fujimura R, Ohta H. (2014). "Alsobacter metallidurans gen. nov., sp. nov., a thallium-tolerant soil bacterium in the order Rhizobiales". Int. J. Syst. Evol. Microbiol. 64 (Pt 3): 775–780. doi:10.1099/ijs.0.054783-0. PMID   24221990.CS1 maint: uses authors parameter (link)
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  7. Poroshina MN, Trotsenko YA, Doronina NV. (2015). "Methylobrevis pamukkalensis gen. nov., sp. nov., a halotolerant restricted facultative methylotroph isolated from saline water". Int. J. Syst. Evol. Microbiol. 65 (4): 1321–1327. doi: 10.1099/ijs.0.000105 . PMID   25667389.CS1 maint: uses authors parameter (link)
  8. Takeuchi M, Katayama T, Yamagishi T, Hanada S, Tamaki H, Kamagata Y, Oshima K, Hattori M, Marumo K, Nedachi M, Maeda H, Suwa Y, Sakata S. (2014). "Methyloceanibacter caenitepidi gen. nov., sp. nov., a facultatively methylotrophic bacterium isolated from marine sediments near a hydrothermal vent". Int. J. Syst. Evol. Microbiol. 64 (Pt 2): 462–468. doi:10.1099/ijs.0.053397-0. PMID   24096357.CS1 maint: uses authors parameter (link)
  9. Doronina NV, Poroshina MN, Kaparullina EN, Ezhov VA, Trotsenko YA. (2013). "Methyloligella halotolerans gen. nov., sp. nov. and Methyloligella solikamskensis sp. nov., two non-pigmented halotolerant obligately methylotrophic bacteria isolated from the Ural saline environments". Syst. Appl. Microbiol. 36 (3): 148–154. doi:10.1016/j.syapm.2012.12.001. PMID   23351489.CS1 maint: uses authors parameter (link)
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  12. Collapsed from the tree built by PATRIC Archived 2016-03-15 at the Wayback Machine . Access date: 2012-05-02.
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Further reading