Rhizobium

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.

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
Domain: Bacteria
Phylum: Pseudomonadota
Class: Alphaproteobacteria
Order: Hyphomicrobiales
Family: Rhizobiaceae
Genus: Rhizobium
Frank 1889 (Approved Lists 1980)[1][2]
Type species
Rhizobium leguminosarum
(Frank 1879) Frank 1889 (Approved Lists 1980)
Species

See text

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

History

Martinus Beijerinck 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, fixing 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 use Rhizobium’s biological nitrogen fixation. This research involves 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.[5]

In molecular biology, Rhizobium has also 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.[6] 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.[7]

Species

The genus Rhizobium comprises the following species:[8]

  • 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[9]
  • "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[10]
  • Rhizobium populi Rozahon et al. 2014
  • "Rhizobium populisoli" Shen et al. 2021
  • Rhizobium puerariae Boonsnongcheep et al. 2016
  • "Rhizobium qilianshanense" Xu et al. 2013[11]
  • "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[12]
  • 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[13]
  • Rhizobium zeae Celador-Lera et al. 2017

Species in "parentheses" have been described, but not validated according to the Bacteriological Code.[8]

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN).[8] The phylogeny is based on whole-genome analysis.[14]

 
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
  1. This species belongs in Pararhizobium, but hasn't been formally transferred, yet.
  2. These species belong in Neorhizobium, but haven't been formally transferred, yet.
  3. This species belongs in Peteryoungia, but hasn't been formally transferred, yet.

References
  1. Frank B. (1889). "Über die Pilzsymbiose der Leguminosen". Berichte der Deutschen Botanischen Gesellschaft. 7: 332–346.
  2. Skerman VBD, McGowan V, Sneath PHA. (1980). "Approved lists of bacterial names". Int J Syst Bacteriol. 30: 225–420. doi:10.1099/00207713-30-1-225.{{cite journal}}: CS1 maint: uses authors parameter (link)
  3. Sawada H, Kuykendall LD, Young JM (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.
  4. 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.
  5. "Marvelous Microbe Collections Accelerate Discoveries To Protect People, Plants—and More!". Agricultural Research. United States Department of Agriculture. January 2010. Retrieved 10 August 2018.
  6. Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, 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. PMC 4228153. PMID 25387460.
  7. Kulakov LA, McAlister MB, Ogden KL, Larkin MJ, O'Hanlon JF (April 2002). "Analysis of bacteria contaminating ultrapure water in industrial systems". Applied and Environmental Microbiology. 68 (4): 1548–55. doi:10.1128/AEM.68.4.1548-1555.2002. PMC 123900. PMID 11916667.
  8. Euzéby JP, Parte AC. "Rhizobiaceae". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved September 16, 2022.{{cite web}}: CS1 maint: uses authors parameter (link)
  9. Diange EA, Lee SS (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.
  10. Kesari V, Ramesh AM, Rangan L (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.
  11. Xu L, Zhang Y, Deng ZS, Zhao L, Wei XL, Wei GH (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.
  12. Wang F, Wang ET, Wu LJ, Sui XH, Li Y, Chen WX (November 2011). "Rhizobium vallis sp. nov., isolated from nodules of three leguminous species". International Journal of Systematic and Evolutionary Microbiology. 61 (Pt 11): 2582–2588. doi:10.1099/ijs.0.026484-0. PMID 21131504.
  13. Silva C, Vinuesa P, Eguiarte LE, Souza V, Martínez-Romero E (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.
  14. 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.
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