Name: Bradyrhizobium elkanii JCM 10832
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 161076

Type strain:

Species: Bradyrhizobium elkanii

Culture col. no.: JCM 10832, USDA 94

Strain history: K. Minamisawa <-- H. H. Keyser USDA 94.

NCBI tax ID(s): 398524 (strain), 29448 (species)

SI-ID 88145

JCM 10832

Special Collections

Other strains from Bradyrhizobium elkanii

Section

Bradyrhizobium elkanii JCM 10832 is a Gram-negative bacterium that was isolated from Root nodules of Glycine max.

Gram-negative
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Nitrobacteraceae*
	Genus	*Bradyrhizobium*
	Species	**Bradyrhizobium elkanii**
	Full Scientific Name (LPSN)	Bradyrhizobium elkanii Kuykendall et al. 1993

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %96

Information on culture and growth conditions Culture and growth conditions

	Temperatures	Kind of temperature		Temperature
[Ref.: #67770]			growth	30 °C

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #67770]	Sample type/isolated from	Root nodules of Glycine max
[Ref.: #67770]	Host species	Glycine max
[Ref.: #67770]	Geographic location (country and/or sea, region)	NC
[Ref.: #67770]	Country	USA
[Ref.: #67770]	Country ISO 3 Code	USA
[Ref.: #67770]	Continent	North America
* marker position based on {}

[Ref.: #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

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Bradyrhizobium japonicum (strain USDA 94) gene for 16S ribosomal RNA	D13429	1456	GenBank ENA	375 tax ID
[Ref.: #67770]	Bradyrhizobium elkanii strain USDA 94 16S ribosomal RNA gene, partial sequence	AF363152	1348	GenBank ENA	29448 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Bradyrhizobium elkanii USDA 94	GCA_000519225	scaffold	GenBank ENA	398524 tax ID

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Bradyrhizobium elkanii USDA 94 USDA 94 NCBI: GCA_000519225.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	96	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	94.481	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	85.997	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	82.324	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	98.5	no
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	70.818	no

Availability in culture collections External links

[Ref.: #67770]

Culture collection no.

JCM 10832, USDA 94

[Ref.: #113189]

SI-ID 88145

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
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	*
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	*
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	*
	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	*
	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	*

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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#113189

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID88145.1 )

* These data were automatically processed and therefore are not curated

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Bradyrhizobium elkanii USDA 94 USDA 94

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