Bradyrhizobium elkanii (USDA 94, JCM 10832)

Name: Bradyrhizobium elkanii (USDA 94, JCM 10832)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 161076

Type strain

Culture col. no. USDA 94 JCM 10832

NCBI tax ID(s) 398524 29448

Special Collections JCM

History K. Minamisawa <-- H. H. Keyser USDA 94.

Links

Bradyrhizobium elkanii JCM 10832 is a mesophilic prokaryote that was isolated from Root nodules of Glycine max.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 88145

JCM 10832

@ref 20215

Last LPSN update 2026-02-09 11:39:03

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Nitrobacteraceae

Genus Bradyrhizobium

Species Bradyrhizobium elkanii

Full scientific name Bradyrhizobium elkanii Kuykendall et al. 1993

BacDive ID	Other strains from **Bradyrhizobium elkanii** (8)	Type strain
1811	B. elkanii DSM 11554, ATCC 49852, USDA 76, JCM 20971, ... (type strain)
154146	B. elkanii CCUG 52553 B
154187	B. elkanii CCUG 52681 B
154192	B. elkanii CCUG 52706
154403	B. elkanii CCUG 53411
155116	B. elkanii CCUG 56518
155117	B. elkanii CCUG 56519
155425	B. elkanii CCUG 57705

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	99.4
125438	negative	96

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
67770	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	98.6

Spore formation

@ref	Spore formation	Confidence
125439		98

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
67770	Root nodules of Glycine max	Glycine max	NC	USA	USA	North America

Taxonmaps

69479

Global distribution of 16S sequence AF363152 (>99% sequence identity) for Bradyrhizobium from Microbeatlas

Aquatic Samples	4833
Soil Samples	14338
Animal Samples	6732
Plant Samples	3278
Total Samples	29181

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM3058484v1 assembly for Bradyrhizobium elkanii USDA 94	complete	GCA_030584845	398524.11		398524	98.35
67770	ASM51922v1 assembly for Bradyrhizobium elkanii USDA 94	scaffold	GCA_000519225	398524.3	2513237137	398524	43.39

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
67770	Bradyrhizobium elkanii strain USDA 94 16S ribosomal RNA gene, partial sequence	AF363152	1348	29448
67770	Bradyrhizobium japonicum (strain USDA 94) gene for 16S ribosomal RNA	D13429	1456	375
124043	Bradyrhizobium elkanii USDA 94 16S ribosomal RNA gene, partial sequence 16S-23S ribosomal RNA intergenic spacer, complete sequence and 23S ribosomal RNA gene, partial sequence.	MK573761	841	398524
124043	Bradyrhizobium elkanii strain USDA 94 16S ribosomal RNA gene, partial sequence tRNA-Ile and tRNA-Ala genes, complete sequence and 23S ribosomal RNA gene, partial sequence.	AF208518	2687	29448
124043	Bradyrhizobium elkanii DNA, 16S-23S ITS1 region, tRNA-Ile, tRNA-Ala, strain: USDA 94.	AB100748	801	29448
124043	Bradyrhizobium elkanii USDA 94 16S ribosomal RNA gene, partial sequence.	MK782145	1345	398524

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Bradyrhizobium elkanii USDA 94
NCBI: GCA_000519225

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.00	no
125439	motility	BacteriaNetⓘ	yes	70.80	no
125439	gram_stain	BacteriaNetⓘ	negative	99.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bradyrhizobium elkanii USDA 94 USDA 94
NCBI: GCA_000519225.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.00	no
125438	anaerobic	anaerobicⓘ	no	94.48	no
125438	aerobic	aerobicⓘ	yes	86.00	no
125438	spore-forming	spore-formingⓘ	no	82.32	no
125438	thermophilic	thermophileⓘ	no	98.50	no
125438	flagellated	motile2+ⓘ	yes	70.82	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Comparative Analysis Reveals Host Species-Dependent Diversity Among 16 Virulent Bacteriophages Isolated Against Soybean Bradyrhizobium spp.	Morgese EA, Ferrell BD, Toth SC, Polson SW, Wommack KE, Fuhrmann JJ.	Viruses	10.3390/v17111474	2025
	High-quality permanent draft genome sequence of the Bradyrhizobium elkanii type strain USDA 76^T, isolated from Glycine max (L.) Merr.	Reeve W, van Berkum P, Ardley J, Tian R, Gollagher M, Marinova D, Elia P, Reddy TBK, Pillay M, Varghese N, Seshadri R, Ivanova N, Woyke T, Baeshen MN, Baeshen NA, Kyrpides N.	Stand Genomic Sci	10.1186/s40793-017-0238-2	2017
Phylogeny	Isolation and characterization of rhizobia from nodules of Clitoria ternatea in Thailand.	Duangkhet M, Chikoti Y, Thepsukhon A, Thapanapongworakul P, Chungopast S, Tajima S, Nomura M.	Plant Biotechnol (Tokyo)	10.5511/plantbiotechnology.18.0402a	2018
	Bradyrhizobium elkanii nod regulon: insights through genomic analysis.	Passaglia LMP.	Genet Mol Biol	10.1590/1678-4685-gmb-2016-0228	2017
	Genome Sequence of Bradyrhizobium pachyrhizi Strain PAC48T, a Nitrogen-Fixing Symbiont of Pachyrhizus erosus (L.) Urb.	Delamuta JR, Ribeiro RA, Gomes DF, Souza RC, Chueire LM, Hungria M.	Genome Announc	10.1128/genomea.01074-15	2015
Phylogeny	Phylogeny and distribution of Bradyrhizobium symbionts nodulating cowpea (Vigna unguiculata L. Walp) and their association with the physicochemical properties of acidic African soils.	Puozaa DK, Jaiswal SK, Dakora FD.	Syst Appl Microbiol	10.1016/j.syapm.2019.02.004	2019
Metabolism	Comparative conventional and phenomics approaches to assess symbiotic effectiveness of Bradyrhizobia strains in soybean (Glycine max L. Merrill) to drought.	Govindasamy V, George P, Aher L, Ramesh SV, Thangasamy A, Anandan S, Raina SK, Kumar M, Rane J, Annapurna K, Minhas PS.	Sci Rep	10.1038/s41598-017-06441-3	2017
	African origin of Bradyrhizobium populations nodulating Bambara groundnut (Vigna subterranea L. Verdc) in Ghanaian and South African soils.	Puozaa DK, Jaiswal SK, Dakora FD.	PLoS One	10.1371/journal.pone.0184943	2017
	Genetic diversity and geographical distribution of indigenous soybean-nodulating bradyrhizobia in the United States.	Shiro S, Matsuura S, Saiki R, Sigua GC, Yamamoto A, Umehara Y, Hayashi M, Saeki Y.	Appl Environ Microbiol	10.1128/aem.00236-13	2013
	Atypical homodimerization revealed by the structure of the (S)-enantioselective haloalkane dehalogenase DmmarA from Mycobacterium marinum.	Snajdarova K, Marques SM, Damborsky J, Bednar D, Marek M.	Acta Crystallogr D Struct Biol	10.1107/s2059798323006642	2023
Metabolism	A distinct pathway for tetrahymanol synthesis in bacteria.	Banta AB, Wei JH, Welander PV.	Proc Natl Acad Sci U S A	10.1073/pnas.1511482112	2015
	A Genomic Encyclopedia of the Root Nodule Bacteria: assessing genetic diversity through a systematic biogeographic survey.	Reeve W, Ardley J, Tian R, Eshragi L, Yoon JW, Ngamwisetkun P, Seshadri R, Ivanova NN, Kyrpides NC.	Stand Genomic Sci	10.1186/1944-3277-10-14	2015
	Soybean-Nodulating Strains With Low Intrinsic Competitiveness for Nodulation, Good Symbiotic Performance, and Stress-Tolerance Isolated From Soybean-Cropped Soils in Argentina.	Iturralde ET, Covelli JM, Alvarez F, Perez-Gimenez J, Arrese-Igor C, Lodeiro AR.	Front Microbiol	10.3389/fmicb.2019.01061	2019
	Evidence of horizontal transfer of symbiotic genes from a Bradyrhizobium japonicum inoculant strain to indigenous diazotrophs Sinorhizobium (Ensifer) fredii and Bradyrhizobium elkanii in a Brazilian Savannah soil.	Barcellos FG, Menna P, da Silva Batista JS, Hungria M.	Appl Environ Microbiol	10.1128/aem.01823-06	2007
Phylogeny	The aquatic budding bacterium Blastobacter denitrificans is a nitrogen-fixing symbiont of Aeschynomene indica.	van Berkum P, Eardly BD.	Appl Environ Microbiol	10.1128/aem.68.3.1132-1136.2002	2002
Enzymology	Mathematical ecology analysis of geographical distribution of soybean-nodulating Bradyrhizobia in Japan.	Saeki Y, Shiro S, Tajima T, Yamamoto A, Sameshima-Saito R, Sato T, Yamakawa T.	Microbes Environ	10.1264/jsme2.me13079	2013
	New assay for rhizobitoxine based on inhibition of 1-aminocyclopropane-1-carboxylate synthase.	Yasuta T, Satoh S, Minamisawa K.	Appl Environ Microbiol	10.1128/aem.65.2.849-852.1999	1999
	Variability among Soybean Genotypes in Response to Nodulation by a Rhizobitoxine-Producing Strain of Bradyrhizobia	Fuhrmann JJ, Vasilas BL.	Agron J		1994
Phylogeny	Relationships of bradyrhizobia from the legumes Apios americana and Desmodium glutinosum.	Parker MA.	Appl Environ Microbiol	10.1128/aem.65.11.4914-4920.1999	1999
Phylogeny	Evidence from internally transcribed spacer sequence analysis of soybean strains that extant Bradyrhizobium spp. are likely the products of reticulate evolutionary events.	van Berkum P, Fuhrmann JJ.	Appl Environ Microbiol	10.1128/aem.01408-08	2009
	Case of localized recombination in 23S rRNA genes from divergent bradyrhizobium lineages associated with neotropical legumes.	Parker MA.	Appl Environ Microbiol	10.1128/aem.67.5.2076-2082.2001	2001
Phylogeny	Population genomics of Sinorhizobium medicae based on low-coverage sequencing of sympatric isolates.	Bailly X, Giuntini E, Sexton MC, Lower RP, Harrison PW, Kumar N, Young JP.	ISME J	10.1038/ismej.2011.55	2011
Phylogeny	Phylogeny of Sym plasmids of rhizobia by PCR-based sequencing of a nodC segment.	Ueda T, Suga Y, Yahiro N, Matsuguchi T.	J Bacteriol	10.1128/jb.177.2.468-472.1995	1995
Phylogeny	Diversification of lupine Bradyrhizobium strains: evidence from nodulation gene trees.	Stepkowski T, Hughes CE, Law IJ, Markiewicz L, Gurda D, Chlebicka A, Moulin L.	Appl Environ Microbiol	10.1128/aem.02125-06	2007
	A Selective Medium for the Isolation and Quantification of Bradyrhizobium japonicum and Bradyrhizobium elkanii Strains from Soils and Inoculants.	Tong Z, Sadowsky MJ.	Appl Environ Microbiol	10.1128/aem.60.2.581-586.1994	1994
Phylogeny	The diversity of Phaseolus-nodulating rhizobial populations is altered by liming of acid soils planted with Phaseolus vulgaris L. in Brazil.	Andrade DS, Murphy PJ, Giller KE.	Appl Environ Microbiol	10.1128/aem.68.8.4025-4034.2002	2002
Metabolism	Multiple Gene Clusters and Their Role in the Degradation of Chlorophenoxyacetic Acids in Bradyrhizobium sp. RD5-C2 Isolated from Non-Contaminated Soil.	Hayashi S, Tanaka S, Takao S, Kobayashi S, Suyama K, Itoh K	Microbes Environ	10.1264/jsme2.ME21016	2021
	Dual-luciferase assay and siRNA silencing for nodD1 to study the competitiveness of Bradyrhizobium diazoefficiens USDA110 in soybean nodulation.	Ramongolalaina C	Microbiol Res	10.1016/j.micres.2020.126488	2020
Metabolism	QTLs underlying the genetic interrelationship between efficient compatibility of Bradyrhizobium strains with soybean and genistein secretion by soybean roots.	Ramongolalaina C, Teraishi M, Okumoto Y	PLoS One	10.1371/journal.pone.0194671	2018
Metabolism	2,4-Dichlorophenoxyacetic acid (2,4-D)- and 2,4,5-trichlorophenoxyacetic acid (2,4,5-T)-degrading gene cluster in the soybean root-nodulating bacterium Bradyrhizobium elkanii USDA94.	Hayashi S, Sano T, Suyama K, Itoh K	Microbiol Res	10.1016/j.micres.2016.04.014	2016
Metabolism	Structural and functional analysis of a novel haloalkane dehalogenase with two halide-binding sites.	Chaloupkova R, Prudnikova T, Rezacova P, Prokop Z, Koudelakova T, Daniel L, Brezovsky J, Ikeda-Ohtsubo W, Sato Y, Kuty M, Nagata Y, Kuta Smatanova I, Damborsky J	Acta Crystallogr D Biol Crystallogr	10.1107/S1399004714009018	2014
Metabolism	A role of Bradyrhizobium elkanii and closely related strains in the degradation of methoxychlor in soil and surface water environments.	Satsuma K, Masuda M, Sato K	Biosci Biotechnol Biochem	10.1271/bbb.130439	2013
Metabolism	Differences in crystallization of two LinB variants from Sphingobium japonicum UT26.	Degtjarik O, Chaloupkova R, Rezacova P, Kuty M, Damborsky J, Kuta Smatanova I	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/S1744309113002467	2013
Phylogeny	Root nodule Bradyrhizobium spp. harbor tfdAalpha and cadA, homologous with genes encoding 2,4-dichlorophenoxyacetic acid-degrading proteins.	Itoh K, Tashiro Y, Uobe K, Kamagata Y, Suyama K, Yamamoto H	Appl Environ Microbiol	10.1128/AEM.70.4.2110-2118.2004	2004
Phenotype	Bradyrhizobium elkanii rtxC gene is required for expression of symbiotic phenotypes in the final step of rhizobitoxine biosynthesis.	Okazaki S, Sugawara M, Minamisawa K	Appl Environ Microbiol	10.1128/AEM.70.1.535-541.2004	2004
	Quantitative and time-course evaluation of nodulation competitiveness of rhizobitoxine-producing Bradyrhizobium elkanii.	Okazaki S, Yuhashi K, Minamisawa K	FEMS Microbiol Ecol	10.1016/S0168-6496(03)00132-6	2003
Metabolism	DNA sequence and mutational analysis of rhizobitoxine biosynthesis genes in Bradyrhizobium elkanii.	Yasuta T, Okazaki S, Mitsui H, Yuhashi K, Ezura H, Minamisawa K	Appl Environ Microbiol	10.1128/AEM.67.11.4999-5009.2001	2001
Phylogeny	DNA sequence of the common nodulation genes of Bradyrhizobium elkanii and their phylogenetic relationship to those of other nodulating bacteria.	Dobert RC, Breil BT, Triplett EW	Mol Plant Microbe Interact	10.1094/mpmi-7-0564	1994
Phylogeny	rRNA and nifD phylogeny of Bradyrhizobium from sites across the Pacific Basin.	Qian J, Kwon SW, Parker MA	FEMS Microbiol Lett	10.1016/S0378-1097(03)00043-0	2003

References

#20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#69479	João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Bradyrhizobium elkanii (USDA 94, JCM 10832)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_030584845

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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