Name: Bradyrhizobium elkanii DSM 11554
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 1811

Type strain:

Species: Bradyrhizobium elkanii

Culture col. no.: DSM 11554, ATCC 49852, USDA 76, JCM 20971, IAM 13629

Strain history: IAM 13629 <-- USDA 76.

NCBI tax ID(s): 398525 (strain), 29448 (species)

SI-ID 1340

LMG 6134, ATCC 49852, DSM 11554, IFO 14791, CECT 4650, NBRC 14791, BCRC 15790, CCRC 15790, IAM 13629, ICMP 13638, ICMP 13195, KACC 10647, JCM 20971

Special Collections

DSMZ
JCM

Other strains from Bradyrhizobium elkanii

Section

Bradyrhizobium elkanii DSM 11554 is a bacterium that was isolated from soybean Glycine max.

16S sequence
Bacteria

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 culture and growth conditions Culture and growth conditions

[Ref.: #4416]

Culture medium

RHIZOBIUM MEDIUM (DSMZ Medium 98)

[Ref.: #4416]

Culture medium growth

[Ref.: #4416]

Culture medium link

Medium recipe at MediaDive

[Ref.: #4416]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #4416]			growth	30 °C
[Ref.: #67770]			growth	25 °C

Information on physiology and metabolism Physiology and metabolism

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	quinate degradation	100	2 of 2
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	gallate degradation	100	5 of 5
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	4-hydroxymandelate degradation	100	9 of 9
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	3-chlorocatechol degradation	100	5 of 5
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	resorcinol degradation	100	2 of 2
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	propanol degradation	100	7 of 7
[Ref.: #66794]	glycolate and glyoxylate degradation	100	6 of 6
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	lactate fermentation	100	4 of 4
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	CO2 fixation in Crenarchaeota	100	9 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	NAD metabolism	94.44	17 of 18
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	leucine metabolism	92.31	12 of 13
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	glutamate and glutamine metabolism	89.29	25 of 28
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	methionine metabolism	88.46	23 of 26
[Ref.: #66794]	flavin biosynthesis	86.67	13 of 15
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	citric acid cycle	85.71	12 of 14
[Ref.: #66794]	phenol degradation	85	17 of 20
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	83.33	10 of 12
[Ref.: #66794]	alanine metabolism	82.76	24 of 29
[Ref.: #66794]	vitamin B12 metabolism	82.35	28 of 34
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	glutathione metabolism	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	degradation of pentoses	78.57	22 of 28
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	non-pathway related	76.32	29 of 38
[Ref.: #66794]	tryptophan metabolism	76.32	29 of 38
[Ref.: #66794]	degradation of sugar acids	76	19 of 25
[Ref.: #66794]	toluene degradation	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	purine metabolism	74.47	70 of 94
[Ref.: #66794]	3-phenylpropionate degradation	73.33	11 of 15
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	ascorbate metabolism	72.73	16 of 22
[Ref.: #66794]	oxidative phosphorylation	72.53	66 of 91
[Ref.: #66794]	tyrosine metabolism	71.43	10 of 14
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	sulfate reduction	69.23	9 of 13
[Ref.: #66794]	androgen and estrogen metabolism	68.75	11 of 16
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	sulfoquinovose degradation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	pyrimidine metabolism	62.22	28 of 45
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	O-antigen biosynthesis	60	3 of 5
[Ref.: #66794]	vitamin K metabolism	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	lysine metabolism	59.52	25 of 42
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	58.82	10 of 17
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	isoprenoid biosynthesis	53.85	14 of 26
[Ref.: #66794]	degradation of hexoses	50	9 of 18
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	arachidonic acid metabolism	50	9 of 18
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	alginate biosynthesis	50	2 of 4
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	carnitine metabolism	50	4 of 8
[Ref.: #66794]	phenylpropanoid biosynthesis	46.15	6 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	allantoin degradation	44.44	4 of 9
[Ref.: #66794]	chlorophyll metabolism	44.44	8 of 18
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	carotenoid biosynthesis	40.91	9 of 22
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	daunorubicin biosynthesis	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #4416]	Sample type/isolated from	soybean Glycine max
[Ref.: #4416]	Host species	Glycine max
[Ref.: #4416]	Country	USA
[Ref.: #4416]	Country ISO 3 Code	USA
[Ref.: #4416]	Continent	North America
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Fruit (Seed)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence U35000 (>99% sequence identity) for Bradyrhizobium from Microbeatlas

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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #4416]

Biosafety level

Risk group (German classification)
According to TRBA 466

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

16S Sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #20218]	Bradyrhizobium elkanii 16S ribosomal RNA gene, partial sequence	AF362942	1042	GenBank ENA	29448 tax ID	*
[Ref.: #20218]	Bradyrhizobium elkanii strain LMG 6134 16S ribosomal RNA gene, partial sequence; internal transcribed spacer, complete sequence; and 23S ribosomal RNA, partial sequence	AF345254	854	GenBank ENA	29448 tax ID	*
[Ref.: #20218]	Bradyrhizobium elkanii gene for 16S ribosomal RNA, partial sequence, strain: NBRC 14791	AB509378	1414	GenBank ENA	29448 tax ID	*
[Ref.: #20218]	Bradyrhizobium elkanii genes for 16S-23S ribosomal RNA intergenic spacer, tRNA-Ile, tRNA-Ala, partial and complete sequence, strain: NBRC 14791	AB509379	833	GenBank ENA	29448 tax ID	*
[Ref.: #20218]	Bradyrhizobium elkanii DNA, 16S-23S ITS1 region, tRNA-Ile, tRNA-Ala, strain: USDA 76	AB100747	809	GenBank ENA	29448 tax ID	*
[Ref.: #20218]	Bradyrhizobium elkanii strain USDA 76 16S ribosomal RNA gene, partial sequence	HQ233240	1340	GenBank ENA	29448 tax ID	*
[Ref.: #20218]	Bradyrhizobium japonicum (USDA 76) 16S ribosomal RNA (partial)	M55490	264	GenBank ENA	375 tax ID	*
[Ref.: #20218]	Bradyrhizobium elkanii 16S ribosomal RNA gene, partial sequence; tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, complete sequence	U35000	5136	GenBank ENA	29448 tax ID	*

Availability in culture collections External links

[Ref.: #4416]

Culture collection no.

DSM 11554, ATCC 49852, USDA 76, JCM 20971, IAM 13629

[Ref.: #71457]

SI-ID 1340

Literature:

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

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Bradyrhizobium ripae sp. nov., a nitrogen-fixing symbiont isolated from nodules of wild legumes in Namibia.	Bunger W, Gronemeyer JL, Sarkar A, Reinhold-Hurek B	Int J Syst Evol Microbiol	10.1099/ijsem.0.002955	2018	*
Enzymology	Bacterial exopolysaccharides as a modern biotechnological tool for modification of fungal laccase properties and metal ion binding.	Osinska-Jaroszuk M, Jaszek M, Starosielec M, Sulej J, Matuszewska A, Janczarek M, Bancerz R, Wydrych J, Wiater A, Jarosz-Wilkolazka A	Bioprocess Biosyst Eng	10.1007/s00449-018-1928-x	2018	*
Metabolism	A Proteomic Network for Symbiotic Nitrogen Fixation Efficiency in Bradyrhizobium elkanii.	Cooper B, Campbell KB, Beard HS, Garrett WM, Mowery J, Bauchan GR, Elia P	Mol Plant Microbe Interact	10.1094/MPMI-10-17-0243-R	2018	*
Genetics	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	Bradyrhizobium erythrophlei sp. nov. and Bradyrhizobium ferriligni sp. nov., isolated from effective nodules of Erythrophleum fordii.	Yao Y, Sui XH, Zhang XX, Wang ET, Chen WX	Int J Syst Evol Microbiol	10.1099/ijs.0.000183	2015	*
Phylogeny	Bradyrhizobium valentinum sp. nov., isolated from effective nodules of Lupinus mariae-josephae, a lupine endemic of basic-lime soils in Eastern Spain.	Duran D, Rey L, Navarro A, Busquets A, Imperial J, Ruiz-Argueso T	Syst Appl Microbiol	10.1016/j.syapm.2014.05.002	2014	*
Phylogeny	Bradyrhizobium lablabi sp. nov., isolated from effective nodules of Lablab purpureus and Arachis hypogaea.	Chang YL, Wang JY, Wang ET, Liu HC, Sui XH, Chen WX	Int J Syst Evol Microbiol	10.1099/ijs.0.027110-0	2010	*
Genetics	The structure of a novel neutral lipid A from the lipopolysaccharide of Bradyrhizobium elkanii containing three mannose units in the backbone.	Komaniecka I, Choma A, Lindner B, Holst O	Chemistry	10.1002/chem.200902390	2010	*
Enzymology	Changes in population occupancy of Bradyrhizobia under different temperature regimes.	Saeki Y, Ozumi S, Yamamoto A, Umehara Y, Hayashi M, Sigua GC	Microbes Environ	10.1264/jsme2.me10128	2010	*
Phylogeny	Phylogeny and taxonomy of a diverse collection of Bradyrhizobium strains based on multilocus sequence analysis of the 16S rRNA gene, ITS region and glnII, recA, atpD and dnaK genes.	Menna P, Barcellos FG, Hungria M	Int J Syst Evol Microbiol	10.1099/ijs.0.009779-0	2009	*
Phylogeny	Bradyrhizobium pachyrhizi sp. nov. and Bradyrhizobium jicamae sp. nov., isolated from effective nodules of Pachyrhizus erosus.	Ramirez-Bahena MH, Peix A, Rivas R, Camacho M, Rodriguez-Navarro DN, Mateos PF, Martinez-Molina E, Willems A, Velazquez E	Int J Syst Evol Microbiol	10.1099/ijs.0.006320-0	2009	*
Phylogeny	RFLP analysis of the rRNA operon of a Brazilian collection of bradyrhizobial strains from 33 legume species.	Germano MG, Menna P, Mostasso FL, Hungria M	Int J Syst Evol Microbiol	10.1099/ijs.0.02917-0	2006	*
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	*
Phylogeny	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	Phylogenetic analyses of Bradyrhizobium strains nodulating soybean (Glycine max) in Thailand with reference to the USDA strains of Bradyrhizobium.	Ando S, Yokoyama T	Can J Microbiol	10.1139/w99-061	1999	*
Genetics	Common soybean inoculant strains in Brazil are members of Bradyrhizobium elkanii.	Rumjanek NG, Dobert RC, van Berkum P, Triplett EW	Appl Environ Microbiol	10.1128/aem.59.12.4371-4373.1993	1993	*

References

#4416

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 11554

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#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 .

#71457

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-ID1340.1 )

* These data were automatically processed and therefore are not curated

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