Rhizobium

This article is about the bacterial genus. For the generic term that includes species in other genera, see Rhizobia.
Rhizobium
Rhizobium tropici on an agar plate.
Scientific classification
Kingdom: Bacteria
Phylum: Proteobacteria
Class: Alphaproteobacteria
Order: Rhizobiales
Family: Rhizobiaceae
Genus: Rhizobium
Frank 1889
Type species
Rhizobium leguminosarum
Species[1]

See text.

Rhizobium is a genus of Gram-negative soil bacteria that fix nitrogen. Rhizobium forms an endosymbiotic nitrogen fixing association with roots of legumes and Parasponia.

The bacteria colonize plant cells within root nodules; here the bacteria convert atmospheric nitrogen to ammonia and then provide organic nitrogenous compounds such as glutamine or ureides to the plant. The plant provides the bacteria with organic compounds made by photosynthesis.[2]

History

Beijerinck in the Netherlands was the first to isolate and cultivate a microorganism from the nodules of legumes in 1888. He named it Bacillus radicicola, which is now placed in Bergey's Manual of Determinative Bacteriology under the genus Rhizobium.

Research

Rhizobium forms a symbiotic relationship with certain plants such as legumes. The Rhizobium fixes nitrogen from the air into ammonia, which acts as a natural fertilizer for the plants. Current research is being conducted by Agricultural Research Service microbiologists to discover a way to utilize Rhizobium’s biological nitrogen fixation. This research involves the genetic mapping of various rhizobial species with its respective symbiotic plant species, like alfalfa or soybean. The goal of this research is to increase the plants’ productivity without using fertilizers.

In molecular biology, Rhizobium has also been identified as a contaminant of DNA extraction kit reagents and ultra-pure water systems, which may lead to its erroneous appearance in microbiota or metagenomic datasets.[3] The presence of nitrogen fixing bacteria as contaminants may be due to the use of nitrogen gas in ultra-pure water production to inhibit microbial growth in storage tanks.[4]

Species

  • R. aggregatum (Hirsch and Müller 1986) Kaur et al. 2011[5]
  • R. alamii Berge et al. 2009
  • R. alkalisoli Lu et al. 2009
  • R. alvei Sheu et al.
  • R. azibense Mnasri et al. 2014
  • R. borbori Zhang et al. 2011
  • R. calliandrae Rincón-Rosales et al. 2013
  • R. cauense Liu et al. 2012
  • R. cellulosilyticum García-Fraile et al. 2007
  • R. daejeonense Quan et al. 2005
  • R. endolithicum Parag et al. 2014
  • R. endophyticum López-López et al. 2010
  • R. etli Segovia et al. 1993[6]
    • R. e. sv. mimosae
    • R. e. sv. phaseoli
  • R. fabae Tian et al. 2008
  • R. flavum Gu et al. 2014
  • R. freirei Dall'Agnol et all. 2013
  • R. galegae Lindström 1989
    • R. g. sv. officinalis[7]
    • R. g. sv. orientalis[7]
  • R. gallicum Amarger et al. 1997
    • R. g. sv. gallicum[8]
    • R. g. sv. orientale[9]
    • R. g. sv. phaseoli[8]
  • R. giardinii Amarger et al. 1997
    • R. g. sv. giardinii[8]
    • R. g. sv. phaseoli[8]
  • R. grahamii López-López et al. 2011
  • R. hainanense Chen et al. 1997
  • R. halophytocola Bibi et al. 2012
  • R. halotolerans Diange and Lee 2013[10]
  • R. helanshanense Qin et al. 2012
  • R. herbae Ren et al. 2011[11]
  • R. huautlense Wang et al. 1998
  • R. indigoferae Wei et al. 2002
  • R. jaguaris Rincón-Rosales et al. 2013
  • R. kunmingense Shen et al. 2010
  • R. laguerreae Saïdi et al. 2014
  • R. larrymoorei (Bouzar and Jones 2001) Young 2004[12]
  • R. leguminosarum (Frank 1879) Frank 1889
    • R. l. sv. trifolii
    • R. l. sv. viciae
  • R. lemnae Kittiwongwattana & Thawai 2014
  • R. leucaenae Ribeiro et al. 2011
  • R. loessense Wei et al. 2003
  • R. lupini (Schroeter 1886) Eckhardt et al. 1931
  • R. lusitanum Valverde et al. 2006
  • "Candidatus Rhizobium massiliae" Greub et al. 2004.
  • R. mayense Rincón-Rosales et al. 2013
  • R. mesoamericanum López-López et al. 2011
  • R. mesosinicum Lin et al. 2009
  • R. miluonense Gu et al. 2008
  • R. mongolense Van Berkum et al. 1998[9]
  • R. multihospitium Han et al. 2008
  • R. naphthalenivorans Kaiya et al. 2012
  • R. nepotum Pulawska et al. 2012
  • R. oryzae Peng et al. 2008
  • R. pakistanensis Khalid et al. 2014
  • R. paknamense Kittiwongwattana & Thawai 2013
  • R. paranaense Dall'Agnol et al. 2014
  • R. petrolearium Zhang et al. 2012
  • R. phaseoli Dangeard 1926 emend. Ramírez-Bahena et al. 2008
  • R. phenanthrenilyticum Wen et al. 2011
  • R. pisi Ramírez-Bahena et al. 2008
    • R. p. sv. trifolii[13]
    • R. p. sv. viciae[13]
  • R. pongamiae Kesari et al. 2013[14]
  • R. populi Rozahon et al. 2014
  • R. pseudoryzae Zhang et al. 2011
  • R. pusense Panday et al. 2011
  • R. qilianshanense Xu et al. 2013[15]
  • R. radiobacter (Beijerinck and van Delden 1902) Young et al. 2001[12]
  • R. rhizogenes (Riker et al. 1930) Young et al. 2001[12]
  • R. rhizoryzae Zhang et al. 2014
  • R. rosettiformans Kaur et al. 2011
  • R. rubi (Hildebrand 1940) Young et al. 2001[12]
  • R. selenitireducens corrig. Hunter et al. 2008
  • R. skierniewicense Puławska et al. 2012
  • R. smilacinae Zhang et al. 2014
  • R. soli Yoon et al. 2010
  • R. sophorae Jiao et al. 2014
  • R. sophoriradicis Jiao et al. 2014
  • R. sphaerophysae Xu et al. 2012
  • R. straminoryzae Lin et al. 2014
  • R. subbaraonis Ramana et al. 2013
  • R. sullae Squartini et al. 2002
  • R. taibaishanense Yao et al. 2012
  • R. tarimense Turdahon et al. 2012[16]
  • R. tibeticum Hou et al. 2009
  • R. tropici Martínez-Romero et al. 1991
  • R. tubonense Zhang et al. 2011
  • R. undicola (de Lajudie et al. 1998) Young et al. 2001
  • R. vallis Wang et all. 2011[17]
  • R. vignae Ren et al. 2011
  • R. vitis (Ophel and Kerr 1990) Young et al. 2001[12]
  • R. yanglingense Tan et al. 2001[9]
  • R. yantingense Chen et al. 2014

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) [1] and National Center for Biotechnology Information (NCBI)[18] and the phylogeny is based on 16S rRNA-based LTP release 106 by The All-Species Living Tree Project [19]














Rhizobium lusitanum Valverde et al. 2006

Rhizobium rhizogenes (Riker et al. 1930) Young et al. 2001[12]

Rhizobium rubi (Hildebrand 1940) Young et al. 2001[12]


Rhizobium multihospitium Han et al. 2008

Rhizobium tropici Martínez-Romero et al. 1991

Rhizobium miluonense Gu et al. 2008

Rhizobium leguminosarum (Frank 1879) Frank 1889 (Approved Lists 1980) emend. Ramírez-Bahena et al. 2008[20]


Rhizobium endophyticum López-López et al. 2011

Rhizobium tibeticum Hou et al. 2009

Rhizobium etli Segovia et al. 1993

Rhizobium pisi Ramírez-Bahena et al. 2008

Rhizobium phaseoli Dangeard 1926 (Approved Lists 1980) emend. Ramírez-Bahena et al. 2008

Rhizobium fabae Tian et al. 2008

Rhizobium hainanense Chen et al. 1997

Arthrobacter viscosus Gasdorf et al. 1965[21]

Rhizobium alamii Berge et al. 2009

Rhizobium mesosinicum Lin et al. 2009

Rhizobium sullae Squartini et al. 2002

Rhizobium indigoferae Wei et al. 2002

Rhizobium gallicum Amarger et al. 1997

Rhizobium yanglingense Tan et al. 2001

Rhizobium mongolense Van Berkum et al. 1998

Rhizobium oryzae Peng et al. 2008

Rhizobium loessense Wei et al. 2003

Rhizobium tubonense Zhang et al. 2011



Rhizobium cellulosilyticum García-Fraile et al. 2007

Rhizobium soli Yoon et al. 2010

Rhizobium galegae Lindström 1989

Rhizobium vignae Ren et al. 2011

Rhizobium huautlense Wang et al. 1998

Rhizobium alkalisoli Lu et al. 2009




References

  1. ↑ 1.0 1.1 J.P. Euzéby. "Rhizobium". List of Prokaryotic names with Standing in Nomenclature (LPSN) . Retrieved 2012-05-02.
  2. ↑ Sawada H, Kuykendall LD, Young JM (2003). "Changing concepts in the systematics of bacterial nitrogen-fixing legume symbionts". J. Gen. Appl. Microbiol. 49 (3): 155–79. doi:10.1099/ijs.0.026484-0. PMID 21131504.
  3. ↑ Salter, S; Cox, M; Turek, E; Calus, S; Cookson, W; Moffatt, M; Turner, P; Parkhill, J; Loman, N; Walker, A (2014). "Reagent contamination can critically impact sequence-based microbiome analyses". bioRxiv. doi:10.1101/007187.
  4. ↑ Kulakov, L; McAlister, M; Ogden, K; Larkin, M; O'Hanlon, J (2002). "Analysis of Bacteria Contaminating Ultrapure Water in Industrial Systems". Applied and Environmental Microbiology 68: 1548–1555. doi:10.1128/AEM.68.4.1548-1555.2002. PMID 11916667.
  5. ↑ NOTE: This strain was formerly named Blastobacter aggregatus.
  6. ↑ NOTE: This species was formerly known as R. leguminosarum sv. phaseoli.
  7. ↑ 7.0 7.1 Radeva G, Jurgens G, Niemi M, Nick G, Suominen L, Lindström K. (2001). "Description of two biovars in the Rhizobium galegae species: biovar orientalis and biovar officinalis". Syst. Appl. Microbiol. 24 (2): 192–205. doi:10.1078/0723-2020-00029. PMID 11518322.
  8. ↑ 8.0 8.1 8.2 8.3 Amarger N, Macheret V, Laguerre G. (1997). "Rhizobium gallicum sp. nov. and Rhizobium giardinii sp. nov., from Phaseolus vulgaris nodules". Int. J. Syst. Bacteriol. 47 (4): 996–1006. doi:10.1099/00207713-47-4-996. PMID 9336898.
  9. ↑ 9.0 9.1 9.2 NOTE: R. gallicum and R. mongolense are 99.2% identical in their rDNA and may be the same species. It has been proposed by Silva et al. that R. mongolense and R. yanglingense be reclassified as R. gallicum sv. orientale.
  10. ↑ Diange, E. A.; Lee, S. S. (2013). "Rhizobium halotolerans sp. nov., Isolated from Chloroethylenes Contaminated Soil". Current Microbiology 66 (6): 599–605. doi:10.1007/s00284-013-0313-x. PMID 23377488.
  11. ↑ Ren DW, Wang ET, Chen WF, Sui XH, Zhang XX, Liu HC, Chen WX (2011). "Rhizobium herbae sp. nov. and *Rhizobium giardinii-related bacteria, minor microsymbionts of various wild legumes in China". Int. J. Syst. Evol. Microbiol. 61 (8): 1912–20. doi:10.1099/ijs.0.024943-0. PMID 20833881.
  12. ↑ 12.0 12.1 12.2 12.3 12.4 12.5 12.6 NOTE: These strains were formerly placed in the genus Agrobacterium.
  13. ↑ 13.0 13.1 Marek-Kozaczuk M, Leszcz A, Wielbo J, Wdowiak-Wróbel S, Skorupska A. (2013). "Rhizobium pisi sv. trifolii K3.22 harboring nod genes of the Rhizobium leguminosarum sv. trifolii cluster". Syst. Appl. Microbiol. 36 (4): 252–8. doi:10.1016/j.syapm.2013.01.005. PMID 23507586.
  14. ↑ Kesari, V.; Ramesh, A. M.; Rangan, L. (2013). "Rhizobium pongamiae sp. nov. From Root Nodules of Pongamia pinnata". BioMed Research International 2013: 1. doi:10.1155/2013/165198.
  15. ↑ Xu, Lin; Zhang, Yong; Deng, Zheng Shan; Zhao, Liang; Wei, Xiu Li; Wei, Ge Hong (2013). "Rhizobium qilianshanense sp. nov., a novel species isolated from root nodule of *Oxytropis ochrocephala Bunge in China". Antonie van Leeuwenhoek 103 (3): 559–565. doi:10.1007/s10482-012-9840-x.
  16. ↑ Turdahon M, Osman G, Hamdun M, Yusuf K, Abdurehim Z, Abaydulla G, Abdukerim M, Fang C, Rahman E (2012). "Rhizobium tarimense sp. nov. isolated from soil in the ancient Khiyik river of Xinjiang, China". Int. J. Syst. Evol. Microbiol. 63 (Pt 7): 2424–9. doi:10.1099/ijs.0.042176-0. PMID 23203621.
  17. ↑ Fang Wang, En Tao Wang, Li Juan Wu, Xin Hua Sui, Ying Li Jr., and Wen Xin Chen (2011). "Rhizobium vallis sp. nov., isolated from nodules of three leguminous species". Int. J. Gen. Syst. Evol. Microbiol. 61 (11): 2582–2588. doi:10.2323/jgam.49.155. PMID 12949698.
  18. ↑ Sayers et al. "Rhizobium/Agrobacterium group". National Center for Biotechnology Information (NCBI) taxonomy database . Retrieved 2012-05-02.
  19. ↑ All-Species Living Tree Project."16S rRNA-based LTP release 106 (full tree)". Silva Comprehensive Ribosomal RNA Database . Retrieved 2012-05-02.
  20. ↑ This is the type species for the genus.
  21. ↑ Arthrobacter viscosus is currently classified in the Micrococcaceae. See Arthrobacter.

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