Bradyrhizobium

Bradyrhizobium species are Gram-negative bacilli (rod-shaped) with a single subpolar or polar flagellum. They are common soil-dwelling micro-organisms that can form symbiotic relationships with leguminous plant species where they fix nitrogen in exchange for carbohydrates from the plant. Like other rhizobia, many members of this genus have the ability to fix atmospheric nitrogen into forms readily available for other organisms to use. Bradyrhizobia are also major components of forest soil microbial communities, where strains isolated from these soils are not typically capable of nitrogen fixation or nodulation.{{cite journal |last1=VanInsberghe|first1=David|last2=Maas|first2=Kendra|last3=Cardenas|first3=Erick|last4=Strachan|first4=Cameron|last5=Hallam|first5=Steven|last6=Mohn|first6=William|title=Non-symbiotic Bradyrhizobium ecotypes dominate North American forest soils|journal=The ISME Journal|year=2015|volume=9|issue=11|pages=2435–2441|doi=10.1038/ismej.2015.54|pmid=25909973|pmc=4611507}} They are slow-growing in contrast to Rhizobium species, which are considered fast-growing rhizobia. In a liquid medium, Bradyrhizobium species take 3–5 days to create a moderate turbidity and 6–8 hours to double in population size. They tend to grow best with pentoses as carbon sources.{{cite book |isbn=978-0-387-94134-9|author=P. Somasegaran |year=1994|title=Handbook for rhizobia: Methods in legume–rhizobium technology|place=New York|publisher=Springer-Verlag|pages=1–6, 167}} Some strains (for example, USDA 6 and CPP) are capable of oxidizing carbon monoxide aerobically.{{cite journal |last=Gary|first=King|title=Molecular and culture-based analyses of aerobic carbon monoxide oxidizer diversity|journal=Applied and Environmental Microbiology|year=2003|volume=69|issue=12|pages=7257–7265|doi=10.1128/aem.69.12.7257-7265.2003|pmid=14660374|pmc=309980}}

Bradyrhizobium comprises the following species:{{cite web |url=https://lpsn.dsmz.de/genus/bradyrhizobium |title=List of Prokaryotic names with Standing in Nomenclature —Bradyrhizobium |accessdate=May 23, 2021}}

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• B. agreste Klepa et al. 2021{{cite journal |vauthors=Klepa MS, Ferraz Helene LC, O'Hara G, Hungria M | year = 2021 | title = Bradyrhizobium agreste sp. nov., Bradyrhizobium glycinis sp. nov. and Bradyrhizobium diversitatis sp. nov., isolated from a biodiversity hotspot of the genus Glycine in Western Australia | journal = Int J Syst Evol Microbiol | volume = 71| issue=3| doi = 10.1099/ijsem.0.004742 | pmid = 33709900| pmc = 8375429 | doi-access = free }}
• B. algeriense Ahnia et al. 2019
• B. americanum Ramírez-Bahena et al. 2017
• B. amphicarpaeae Bromfield et al. 2019
• B. arachidis Wang et al. 2013
• B. archetypum Helene et al. 2020
• B. australiense Helene et al. 2020
• B. betae Rivas et al. 2004
• B. cajani Araújo et al. 2017
• B. canariense Vinuesa et al. 2005

• B. centrosematis corrig. Ramírez-Bahena et al. 2017
• B. cosmicum Wasai-Hara et al. 2020
• B. cytisi Chahbourne et al. 2011
• B. daqingense Wang JY et al. 2012
• B. denitrificans (Hirsch and Müller 1986) van Berkum et al. 2011
• B. diazoefficiens Delamuta et al 2013
• B. diversitatis Serenato Klepa et al. 2021
• B. elkanii Kuykendall et al. 1993
• B. embrapense Delamuta et al.2015
• B. erythrophlei Yao et al. 2015
• B. ferriligni Yao et al. 2015
• B. frederickii de Oliveira Urquiaga et al. 2019
• B. ganzhouense Lu et al. 2014
• B. glycinis Serenato Klepa et al. 2021
• B. guangdongense Li et al. 2015
• B. guangxiense Li et al. 2015
• B. hipponense Rejili et al. 2020
• B. huanghuaihaiense Zhang et al. 2012
• B. icense Durán et al. 2014
• B. ingae da Silva et al. 2014
• B. iriomotense Islam et al. 2010
• B. ivorense Fossou et al. 2020
• B. japonicum (Kirchner 1896) Jordan 1982
• symbiovar genistearum{{cite journal |pmid=20452160|year=2010|last1=Kalita|first1=M|title=Genista tinctoria microsymbionts from Poland are new members of Bradyrhizobium japonicum bv. genistearum|journal=Systematic and Applied Microbiology|volume=33|issue=5|pages=252–9|last2=Małek|first2=W|doi=10.1016/j.syapm.2010.03.005}}
• symbiovar glycinearum
• B. jicamae Ramírez-Bahena et al. 2009
• B. kavangense Lasse gronemeyer et al. 2015
• B. lablabi Chang et al. 2011
• B. liaoningense Xu et al. 1995
• B. lupini Peix et al. 2015
• B. manausense Silva et al. 2014
• B. mercantei Helene et al. 2017
• B. murdochi Helene et al. 2020
• B. namibiense Grönemeyer et al. 2017
• B. nanningense Li et al. 2020
• B. neotropicale Zilli et al. 2014
• B. niftali Klepa et al. 2019
• B. nitroreducens Jang et al. 2020
• B. oligotrophicum (Ohta and Hattori 1985) Ramírez-Bahena et al. 2013
• B. ottawaense Yu et al. 2014
• B. pachyrhizi Ramírez-Bahena et al. 2009
• B. paxllaeri Durán et al. 2014
• B. retamae Guerrouj et al. 2013
• B. rifense Chahboune et al. 2012
• B. ripae Bünger et al. 2018
• B. shewense Aserse et al. 2018
• B. stylosanthis Marçon Delamuta et al. 2016
• B. subterraneum Gronemeyer et al. 2015
• B. symbiodeficiens Bromfield et al. 2020
• B. tropiciagri Delamuta et al. 2015
• B. vignae Grönemeyer et al. 2016
• B. viridifuturi Helene et al. 2015
• B. yuanmingense Yao et al. 2002

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The following species have been published, but not validated according to the Bacteriological Code.

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• "B. brasilense" Martins da Costa et al. 2017
• "B. campsiandrae" Cabral Michel et al. 2021
• "B. centrolobii" Michel et al. 2017
• "B. forestalis" Martins da Costa et al. 2018
• "B. guangzhouense" Li et al. 2019
• "B. macuxiense" Michel et al. 2017
• "B. sacchari" de Matos et al. 2017
• "Photorhizobium thompsonianum" Eaglesham et al. 1990{{cite book |vauthors= Eaglesham AR, Ellis JM, Evans WR, Fleishman DE, Hungria M, Hardy KW |year= 1990 |chapter= The first photosynthetic N₂-fixing Rhizobium: Characteristics |title= Nitrogen Fixation: Achievements and Objectives |veditors= Gresshoff PM, Koth LE, Stacey G, Newton WE |pages= 805–811 |publisher= Springer |location= Boston, MA |isbn= 978-1-4684-6434-4 |doi= 10.1007/978-1-4684-6432-0_69}}
• "B. uaiense" Cabral Michel et al. 2020
• "B. valentinum" Durán et al. 2014
• "B. zhanjiangense" Li et al. 2019

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The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN). The phylogeny is based on whole-genome analysis.{{cite journal |last1=Hördt |first1=Anton |last2=López |first2=Marina García |last3=Meier-Kolthoff |first3=Jan P. |last4=Schleuning |first4=Marcel |last5=Weinhold |first5=Lisa-Maria |last6=Tindall |first6=Brian J. |last7=Gronow |first7=Sabine |last8=Kyrpides |first8=Nikos C. |last9=Woyke |first9=Tanja |last10=Göker |first10=Markus |title=Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria |journal=Frontiers in Microbiology |date=7 April 2020 |volume=11 |pages=468 |doi=10.3389/fmicb.2020.00468|pmid=32373076 |pmc=7179689 |doi-access=free }}

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|1={{clade

|label1=Bradyrhizobium

|1={{clade

|1=Bradyrhizobium oligotrophicum

|2={{clade

|1={{clade

|1=Bradyrhizobium manausense

|2={{clade

|1=Bradyrhizobium neotropicale

|2={{clade

|1={{clade

|1=Bradyrhizobium yuanmingense

|2={{clade

|1=Bradyrhizobium ottawaense

|2=Bradyrhizobium shewense

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|2={{clade

|1={{clade

|1=Bradyrhizobium stylosanthis

|2=Bradyrhizobium arachidis

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|2={{clade

|1=Bradyrhizobium diazoefficiens

|2=Bradyrhizobium japonicum

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|2={{clade

|1={{clade

|1={{clade

|1=Bradyrhizobium retamae

|2=Bradyrhizobium icense

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|2={{clade

|1=Bradyrhizobium lablabi

|2={{clade

|1=Bradyrhizobium jicamae

|2=Bradyrhizobium paxllaeri

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|2={{clade

|1={{clade

|1=Bradyrhizobium elkanii

|2=Bradyrhizobium pachyrhizi

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|2={{clade

|1=Bradyrhizobium mercantei

|2={{clade

|1=Bradyrhizobium embrapense

|2={{clade

|1=Bradyrhizobium tropiciagri

|2=Bradyrhizobium viridifuturi

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|label2=outgroup

|2=Rhodopseudomonas

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Nodules are growths on the roots of leguminous plants where the bacteria reside. The plant roots secrete amino acids and sugars into the rhizosphere. The rhizobia move toward the roots and attach to the root hairs. The plant then releases flavonoids, which induce the expression of nod genes within the bacteria. The expression of these genes results in the production of enzymes called Nod factors that initiate root hair curling. During this process, the rhizobia are curled up with the root hair. The rhizobia penetrate the root hair cells with an infection thread that grows through the root hair into the main root. This causes the infected cells to divide and form a nodule. The rhizobia can now begin nitrogen fixation.{{cn|date=March 2025}}

Over 55 genes are known to be associated with nodulation.{{cite journal |doi=10.1111/j.1574-6968.1995.tb07441.x|title=Bradyrhizobium japonicum nodulation genetics|year=1995|last1=Stacey|first1=Gary|journal=FEMS Microbiology Letters|volume=127|pages=1–9|pmid=7737469|issue=1–2|doi-access=free}} NodD is essential for the expression of the other nod genes.{{cite journal |doi=10.1016/0038-0717(95)98622-U|title=Signal exchange in the Bradyrhizobium–soybean symbiosis|year=1995|last1=Stacey|first1=G|journal=Soil Biology and Biochemistry|volume=27|pages=473–483|last2=Sanjuan|first2=J.|last3=Luka|first3=S.|last4=Dockendorff|first4=T.|last5=Carlson|first5=R.W.|issue=4–5}} The two different nodD genes are: nodD₁ and nodD₂. Only nodD₁ is needed for successful nodulation.

Bradyrhizobium and other rhizobia take atmospheric nitrogen and fix it into ammonia (NH₃) or ammonium (NH₄⁺). Plants cannot use atmospheric nitrogen; they must use a combined or fixed form of the element. After photosynthesis, nitrogen fixation (or uptake) is the most important process for the growth and development of plants.{{cite journal |doi=10.1016/S0378-4290(97)00022-1|title=Molecular dissection and improvement of the nodule symbiosis in legumes|year=1997|last1=Caetanoanolles|first1=G|journal=Field Crops Research|volume=53|issue=1–3|pages=47–68}} The levels of ureide nitrogen in a plant correlate with the amount of fixed nitrogen the plant takes up.{{cite journal |author1=van Berkum, P. |author2=Sloger, C. |author3=Weber, D. F. |author4=Cregan, P. B. |author5=Keyser, H. H. |year=1985|title=Relationship between Ureide N and N₂ Fixation, Aboveground N Accumulation, Acetylene Reduction, and Nodule Mass in Greenhouse and Field Studies with Glycine max (L.) Merr|journal=Plant Physiol.|volume=77|pages=53–58|doi=10.1104/pp.77.1.53|pmid=16664027|issue=1|pmc=1064455}}

Nif and fix are important genes involved in nitrogen fixation among Bradyrhizobium species. Nif genes are very similar to genes found in Klebsiella pneumoniae, a free-living diazotroph. The genes found in bradyrhizobia have similar function and structure to the genes found in K. pneumoniae. Fix genes are important for symbiotic nitrogen fixation and were first discovered in rhizobia species. The nif and fix genes are found in at least two different clusters on the chromosome. Cluster I contains most of the nitrogen fixation genes. Cluster II contains three fix genes located near nod genes.{{cite journal |pmid=2200721|year=1990|last1=Hennecke|first1=H|title=Nitrogen fixation genes involved in the Bradyrhizobium japonicum–soybean symbiosis|volume=268|issue=2|pages=422–6|journal=FEBS Letters|doi=10.1016/0014-5793(90)81297-2|s2cid=43001831 |doi-access=free}}

This genus of bacteria can form either specific or general symbioses; one species of Bradyrhizobium may only be able to nodulate one legume species, whereas other Bradyrhizobium species may be able to nodulate several legume species. Ribosomal RNA is highly conserved in this group of microbes, making Bradyrhizobium extremely difficult to use as an indicator of species diversity. DNA–DNA hybridizations have been used instead and show more diversity. However, few phenotypic differences are seen, so not many species have been named.{{cn|date=March 2025}}

Some strains are photosynthetic, these Bradyrhizobium often form nodules in the stems of semi-aquatic Aeschynomene legumes, and have also been found in the nodal roots of African wild rice Oryza breviligulata.{{cite journal |last1=Chaintreuil |first1=Clémence |last2=Giraud |first2=Eric |last3=Prin |first3=Yves |last4=Lorquin |first4=Jean |last5=Bâ |first5=Amadou |last6=Gillis |first6=Monique |last7=de Lajudie |first7=Philippe |last8=Dreyfus |first8=Bernard |date=December 2000 |title=Photosynthetic Bradyrhizobia Are Natural Endophytes of the African Wild Rice Oryza breviligulata |url=https://www.researchgate.net/publication/12229861 |journal=Applied and Environmental Microbiology |volume=66 |issue=12 |pages=5437–5447 |pmc=92479 |doi=10.1128/AEM.66.12.5437-5447.2000 |pmid=11097925 |bibcode=2000ApEnM..66.5437C |access-date=7 May 2021|doi-access=free }}

Grain legumes are cultivated on about 1.5 million km² of land per year. The amount of nitrogen fixed annually is about 44–66 million tons worldwide, providing almost half of all nitrogen used in agriculture.{{cite journal |doi=10.1016/j.soilbio.2005.08.018|title=Sampling effects on the assessment of genetic diversity of rhizobia associated with soybean and common bean|year=2006|last1=Alberton|first1=O|last2=Kaschuk|first2=G|last3=Hungria|first3=M|journal=Soil Biology and Biochemistry|volume=38|pages=1298–1307|issue=6}} Commercial inoculants of Bradyrhizobium are available.

Bradyrhizobium 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.{{cite bioRxiv |last1=Salter|first1=S|last2=Cox|first2=M|last3=Turek|first3=E|last4=Calus|first4=S|last5=Cookson|first5=W|last6=Moffatt|first6=M|last7=Turner|first7=P|last8=Parkhill|first8=J|last9=Loman|first9=N|last10=Walker|first10=A|title=Reagent contamination can critically impact sequence-based microbiome analyses |date=2014|biorxiv=10.1101/007187}} The presence of nitrogen-fixing bacteria as contaminants may be due to the use of nitrogen gas in ultrapure water production to inhibit microbial growth in storage tanks.{{cite journal |last1=Kulakov|first1=L|last2=McAlister|first2=M|last3=Ogden|first3=K|last4=Larkin|first4=M|last5=O'Hanlon|first5=J|title=Analysis of Bacteria Contaminating Ultrapure Water in Industrial Systems|journal=Applied and Environmental Microbiology|date=2002|volume=68|issue=4|pages=1548–1555|doi=10.1128/AEM.68.4.1548-1555.2002|pmid=11916667|pmc=123900|bibcode=2002ApEnM..68.1548K}}

• Bradyrhizobium betae was isolated from tumor-like root deformations on sugar beets; they have an unknown symbiotic status.{{cite journal |doi=10.1016/j.syapm.2008.12.005|title=Multilocus sequence analysis of the genus Bradyrhizobium|year=2009|last1=Rivas|first1=Raul|last2=Martens|first2=Miet|last3=De Lajudie|first3=Philippe|last4=Willems|first4=Anne|journal=Systematic and Applied Microbiology|volume=32|pages=101–10|pmid=19201125|issue=2}}
• Bradyrhizobium elkanii, Bradyrhizobium diazoefficiens, and Bradyrhizobium liaoningense establish symbiosis with soybeans.
• Bradyrhizobium japonicum nodulates soybeans, cowpeas, mung beans, and siratro.
• Bradyrhizobium yuanmingense nodulates Lespedeza.
• Bradyrhizobium canariense nodulates genistoid legumes endemic to the Canary Islands. It has also been found in lupin and serradella nodules in western Australia and southern Africa.

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Category:Bacteria genera

Category:Nitrobacteraceae