Rhizobium

Rhizobium
	Rhizobium tropici on an agar plate (Tryptone — Yeast extract agar).
Scientific classification
Domain:	Bacteria
Phylum:	Pseudomonadota
Class:	Alphaproteobacteria
Order:	Hyphomicrobiales
Family:	Rhizobiaceae
Genus:	Rhizobium; Frank 1889 (Approved Lists 1980)
Type species
	Rhizobium leguminosarum; (Frank 1879) Frank 1889 (Approved Lists 1980)
Species
	See text

Rhizobium is a genus of Gram-negative soil bacteria that fix nitrogen. Rhizobium species form an endosymbiotic nitrogen-fixing association with roots of (primarily) legumes and other flowering plants.

The bacteria colonize plant cells to form root nodules, where they convert atmospheric nitrogen into ammonia using the enzyme nitrogenase. The ammonia is shared with the host plant in the form of organic nitrogenous compounds such as glutamine or ureides.^[3] The plant, in turn, provides the bacteria with organic compounds made by photosynthesis. This mutually beneficial relationship is true of all of the rhizobia, of which the genus Rhizobium is a typical example.^[4] Rhizobium is also capable of solubilizing phosphate.^[5]

History

Martinus Beijerinck was the first to isolate and cultivate a microorganism from the nodules of legumes in 1888.^[6] 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, fixing nitrogen from the air into ammonia, which acts as a natural fertilizer for the plants. The Agricultural Research Service is conducting research involving the genetic mapping of various rhizobial species with their respective symbiotic plant species, like alfalfa or soybean. The goal of this research is to increase the plants’ productivity without using fertilizers.^[7]

In molecular biology, Rhizobium has been identified as a contaminant of DNA extraction kit reagents and ultrapure water systems, which may lead to its erroneous appearance in microbiota or metagenomic datasets.^[8] 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.^[9]

Species

The genus Rhizobium comprises the following species:^[10]

Rhizobium acidisoli Román-Ponce et al. 2016
Rhizobium aegyptiacum Shamseldin et al. 2016
Rhizobium aethiopicum Aserse et al. 2017
Rhizobium alamii Berge et al. 2009
"Rhizobium album" Hang et al. 2019
"Rhizobium albus" Li et al. 2017
Rhizobium altiplani Baraúna et al. 2016
Rhizobium alvei Sheu et al. 2015
Rhizobium anhuiense Zhang et al. 2015
Rhizobium aquaticum Máthé et al. 2019
"Rhizobium arachis" Wang et al. 2001
Rhizobium arenae Zhang et al. 2017^{[Note 1]}
Rhizobium arsenicireducens Mohapatra et al. 2020
Rhizobium azooxidifex Behrendt et al. 2016
Rhizobium bangladeshense Rashid et al. 2015
Rhizobium binae Rashid et al. 2015
Rhizobium calliandrae Rincón-Rosales et al. 2013
Rhizobium capsici Lin et al. 2015
Rhizobium cauense Liu et al. 2015
Rhizobium cellulosilyticum García-Fraile et al. 2007^{[Note 2]}
Rhizobium changzhiense Zhang et al. 2021
Rhizobium chutanense Huo et al. 2019
"Rhizobium cremeum" Yang et al. 2022
"Rhizobium croatiense" Rajnovic et al. 2022
"Rhizobium deserti" Liu et al. 2020^{[Note 2]}
Rhizobium dioscoreae Ouyabe et al. 2020
Rhizobium ecuadorense Ribeiro et al. 2015
Rhizobium endophyticum López-López et al. 2010
Rhizobium esperanzae Cordeiro et al. 2017
Rhizobium etli Segovia et al. 1993
Rhizobium favelukesii Torres Tejerizo et al. 2016
"Rhizobium flavescens" Su et al. 2021
Rhizobium freirei Dall'Agnol et al. 2013
Rhizobium gallicum Amarger et al. 1997
Rhizobium gei Shi et al. 2016
"Rhizobium glycinendophyticum" Wang et al. 2020^{[Note 3]}
Rhizobium grahamii López-López et al. 2011
Rhizobium hainanense Chen et al. 1997
Rhizobium halophytocola Bibi et al. 2012
"Rhizobium halotolerans" Diange and Lee 2013^[11]
"Rhizobium hedysari" Casella et al. 1986
"Rhizobium hedysari" Xu et al. 2017
"Rhizobium hedysarum" Casella et al. 1984
Rhizobium helianthi Wei et al. 2015
Rhizobium hidalgonense Yan et al. 2020
"Rhizobium indicum" Rahi et al. 2020
Rhizobium indigoferae Wei et al. 2002
Rhizobium jaguaris Rincón-Rosales et al. 2013
"Rhizobium kunmingense" Shen et al. 2010
Rhizobium laguerreae Saïdi et al. 2014
Rhizobium leguminosarum (Frank 1879) Frank 1889 (Approved Lists 1980)
Rhizobium lemnae Kittiwongwattana & Thawai 2014
Rhizobium lentis Rashid et al. 2015
Rhizobium leucaenae Ribeiro et al. 2011
Rhizobium lusitanum Valverde et al. 2006
"Candidatus Rhizobium massiliense" Greub et al. 2004.
Rhizobium mayense Rincón-Rosales et al. 2013
Rhizobium mesoamericanum López-López et al. 2011
Rhizobium mesosinicum Lin et al. 2009
Rhizobium metallidurans Grison et al. 2015
Rhizobium miluonense Gu et al. 2008
Rhizobium mongolense van Berkum et al. 1998
Rhizobium multihospitium Han et al. 2008
Rhizobium oryzicola Zhang et al. 2015
"Rhizobium oryzihabitans" Zhao et al. 2020
Rhizobium pakistanense corrig. Khalid et al. 2015^{[Note 2]}
"Rhizobium panacihumi" Kang et al. 2019
Rhizobium paranaense Dall'Agnol et al. 2014
Rhizobium phaseoli Dangeard 1926 (Approved Lists 1980)
"Rhizobium phenanthrenilyticum" Wen et al. 2011
Rhizobium pisi Ramírez-Bahena et al. 2008
"Rhizobium pongamiae" Kesari et al. 2013^[12]
Rhizobium populi Rozahon et al. 2014
"Rhizobium populisoli" Shen et al. 2021
Rhizobium puerariae Boonsnongcheep et al. 2016
"Rhizobium qilianshanense" Xu et al. 2013^[13]
"Rhizobium quercicola" Wang et al. 2022
"Rhizobium redzepovicii" Rajnovic et al. 2022
Rhizobium rhizogenes (Riker et al. 1930) Young et al. 2001
"Rhizobium rhizolycopersici" Thin et al. 2021
Rhizobium rhizoryzae Zhang et al. 2014
Rhizobium ruizarguesonis Jorrin et al. 2020
Rhizobium smilacinae Zhang et al. 2014^{[Note 2]}
Rhizobium soli Yoon et al. 2010
Rhizobium sophorae Jiao et al. 2014
Rhizobium sophoriradicis Jiao et al. 2014
Rhizobium straminoryzae Lin et al. 2014
Rhizobium sullae Squartini et al. 2002
"Rhizobium terrae" Ruan et al. 2020
Rhizobium tibeticum Hou et al. 2009
Rhizobium tropici Martínez-Romero et al. 1991
Rhizobium tubonense Zhang et al. 2011
Rhizobium tumorigenes Kuzmanović et al. 2019
Rhizobium vallis Wang et al. 2011^[14]
Rhizobium viscosum (Gasdorf et al. 1965) Flores-Félix et al. 2017
Rhizobium wenxiniae Gao et al. 2017^{[Note 2]}
Rhizobium yanglingense Tan et al. 2001^[15]
Rhizobium zeae Celador-Lera et al. 2017

Species in "parentheses" have been described, but not validated according to the Bacteriological Code.^[10]

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN).^[10] The phylogeny is based on whole-genome analysis.^[16]

Rhizobium

Rhizobium tubonense

Rhizobium rhizogenes

	Rhizobium jaguaris

	Rhizobium leucaenae

Rhizobium lusitanum

	Rhizobium miluonense

	Rhizobium freirei

Rhizobium tropici

	Rhizobium hainanense

	Rhizobium multihospitium

	Rhizobium altiplani

	Rhizobium grahamii

	Rhizobium favelukesii

	Rhizobium tibeticum

	Rhizobium loessense

	Rhizobium mongolense

	Rhizobium leguminosarum

	Rhizobium laguerreae

Rhizobium aethiopicum

	Rhizobium esperanzae

	Rhizobium etli

outgroups

	Allorhizobium

	Ciceribacter

Agrobacterium

	Pseudorhizobium

	Neorhizobium

Notes

^ This species belongs in Pararhizobium, but hasn't been formally transferred, yet.
^ ^a ^b ^c ^d ^e These species belong in Neorhizobium, but haven't been formally transferred, yet.
^ This species belongs in Peteryoungia, but hasn't been formally transferred, yet.

References

^ Frank, B. (1889). "Über die Pilzsymbiose der Leguminosen". Berichte der Deutschen Botanischen Gesellschaft. 7: 332–346.
^ Skerman, VB; McGowan, V; Sneath, PH (1980). "Approved lists of bacterial names". International Journal of Systematic Bacteriology. 30: 225–420. doi:10.1099/00207713-30-1-225.
^ Thilakarathna, Malinda S.; Raizada, Manish N. (2018-01-01). "Visualizing Glutamine Accumulation in Root Systems Involved in the Legume–Rhizobia Symbiosis by Placement on Agar Embedded with Companion Biosensor Cells". Phytobiomes Journal. 2 (3): 117–128. doi:10.1094/PBIOMES-07-18-0031-TA.
^ Sawada, Hiroyuki; Kuykendall, L. David; Young, John M. (June 2003). "Changing concepts in the systematics of bacterial nitrogen-fixing legume symbionts". The Journal of General and Applied Microbiology. 49 (3): 155–79. doi:10.2323/jgam.49.155. PMID 12949698.
^ Sridevi, M; Mallaiah, KV (March 2009). "Phosphate solubilization by Rhizobium strains". Indian Journal of Microbiology. 49 (1): 98–102. doi:10.1007/s12088-009-0005-1. PMC 3450048. PMID 23100757.
^ Beijerinck, Martinus W. (1888). "Die Bacteriender Papilionaceenknöllchen". Bot.Ztg. 46.
^ "Marvelous Microbe Collections Accelerate Discoveries To Protect People, Plants—and More!". Agricultural Research. United States Department of Agriculture. January 2010. Retrieved 10 August 2018.
^ Salter, Susannah J.; Cox, Michael J.; Turek, Elena M.; Calus, Szymon T.; Cookson, William O.; Moffatt, Miriam F.; et al. (November 2014). "Reagent and laboratory contamination can critically impact sequence-based microbiome analyses". BMC Biology. 12: 87. bioRxiv 10.1101/007187. doi:10.1186/s12915-014-0087-z. ISSN 1741-7007. PMC 4228153. PMID 25387460.
^ Kulakov, Leonid A.; McAlister, Morven B.; Ogden, Kimberly L.; Larkin, Michael J.; O'Hanlon, John F. (April 2002). "Analysis of bacteria contaminating ultrapure water in industrial systems". Applied and Environmental Microbiology. 68 (4): 1548–1555. doi:10.1128/AEM.68.4.1548-1555.2002. PMC 123900. PMID 11916667.
^ ^a ^b ^c Euzéby, JP; Parte, AC. "Rhizobiaceae". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved September 16, 2022.
^ Diange, Eboa Adolf; Lee, Sang-Seob (June 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. S2CID 17809044.
^ Kesari, Vigya; Ramesh, Aadi Moolam; Rangan, Latha (2013). "Rhizobium pongamiae sp. nov. from root nodules of Pongamia pinnata". BioMed Research International. 2013: 165198. doi:10.1155/2013/165198. PMC 3783817. PMID 24078904.
^ Xu, Lin; Zhang, Yong; Deng, Zheng Shan; Zhao, Liang; Wei, Xiu Li; Wei, Ge Hong (March 2013). "Rhizobium qilianshanense sp. nov., a novel species isolated from root nodule of Oxytropis ochrocephala Bunge in China". Antonie van Leeuwenhoek. 103 (3): 559–65. doi:10.1007/s10482-012-9840-x. PMID 23142858. S2CID 18660422.
^ Wang, Fang; Wang, En Tao; Wu, Li Juan; Sui, Xin Hua; Li, Ying Li; Chen, Wen Xin (November 2011). "Rhizobium vallis sp. nov., isolated from nodules of three leguminous species". International Journal of Systematic and Evolutionary Microbiology. 61 (11): 2582–2588. doi:10.1099/ijs.0.026484-0. PMID 21131504.
^ Silva, Claudia; Vinuesa, Pablo; Eguiarte, Luis E; Souza, Valeria; Martínez-Romero, Esperanza (November 2005). "Evolutionary genetics and biogeographic structure of Rhizobium gallicum sensu lato, a widely distributed bacterial symbiont of diverse legumes". Molecular Ecology. 14 (13): 4033–50. doi:10.1111/j.1365-294X.2005.02721.x. PMID 16262857. S2CID 16668742.
^ Hördt, Anton; López, Marina García; Meier-Kolthoff, Jan P.; Schleuning, Marcel; Weinhold, Lisa-Maria; Tindall, Brian J.; Gronow, Sabine; Kyrpides, Nikos C.; Woyke, Tanja; Göker, Markus (7 April 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.