Rhizobium leguminosarum (DSM 6040, ATCC 14479, 3D1K2)

Name: Rhizobium leguminosarum (DSM 6040, ATCC 14479, 3D1K2)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13593

Type strain

Strain Designation 3D1K2

Culture col. no. DSM 6040 ATCC 14479 3D1K2

NCBI tax ID(s) 384

Special Collections DSMZ

History DSMZ <- ATCC <- U.M. Means, 3D1K2

Links

Rhizobium leguminosarum 3D1K2 is a bacterium of the family Rhizobiaceae.

genome sequence Bacteria

Name and taxonomic classification

SI-ID 36091

ATCC 14479,DSM 6040,KCTC 2362

@ref 20215

Last LPSN update 2026-05-29 08:28:05

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Rhizobiaceae

Genus Rhizobium

Species Rhizobium leguminosarum

Full scientific name Rhizobium leguminosarum (Frank 1879) Frank 1889 (Approved Lists 1980)

Synonyms (3)

Rhizobium indigoferae
Rhizobium trifolii
"Schinzia leguminosarum"

BacDive ID	Other strains from **Rhizobium leguminosarum** (15)	Type strain
138443	R. leguminosarum 3Hoq18, CIP 106959, ATCC 10004, IAM 12609, ... (type strain)
13588	R. leguminosarum DSM 1980, TAL 381
13590	R. leguminosarum ANU618, pBR1AN, DSM 5206
13591	R. leguminosarum LPR5035, pRtr5a::Tn5, DSM 5207
13592	R. leguminosarum RCR 3622, DSM 6039, ATCC 35179, PDDCC 6745
13594	R. leguminosarum 3D1q25a, DSM 6041, ATCC 14484
13595	R. leguminosarum NZ 29, DSM 6042, ATCC 35180, PDDCC 1309
13596	R. leguminosarum DSM 6043, ATCC 35172, PDDCC 5943, NZP 5225
13597	R. leguminosarum 175F1, DSM 6044, ATCC 35282
13598	R. leguminosarum 92A3, DSM 6045, ATCC 35643, TAL 634
13599	R. leguminosarum 3HOa1, DSM 30133, ATCC 11444
13600	R. leguminosarum 3D1k5, DSM 30138, ATCC 10328
13601	R. leguminosarum 3D1r1, DSM 30139, ATCC 14481
13602	R. leguminosarum 3D1k22a, DSM 30141, ATCC 14480, JCM 20684, ...
13603	R. leguminosarum 580, DSM 30143, DSM 60273

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	95.545
125438	negative	98.833

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
2212	RHIZOBIUM MEDIUM (DSMZ Medium 98)		Medium recipe at MediaDive	Name: RHIZOBIUM MEDIUM (DSMZ Medium 98) Composition: air-dried garden soil 80.0 g/l Agar 15.0 g/l Mannitol 10.0 g/l Yeast extract 1.0 g/l Na2CO3 0.2 g/l Distilled water
2212	NUTRIENT AGAR (DSMZ Medium 1)		Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
2212	positive	growth	22
2212	positive	growth	26

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	98.258

Spore formation

@ref	Spore formation	Confidence
125439		98.849

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68369	17634 ChEBI	D-glucose	-	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68369	gelatinase	-		from API 20NE
68369	urease	-	3.5.1.5	from API 20NE

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
2212	-	-	-	-	-	+/-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	+

Isolation, sampling and environmental information

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
2212	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM329040v1 assembly for Rhizobium leguminosarum ATCC 14479	complete	GCA_003290405	384.95	2859840839	384	97.03

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM329040v1 assembly for Rhizobium leguminosarum ATCC 14479
BV-BRC: 384.95

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	negative	95.55	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.26	no
125439	motility	BacteriaNetⓘ	yes	47.00	no
125439	spore_formation	BacteriaNetⓘ	no	98.85	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rhizobium leguminosarum ATCC 14479
NCBI: GCA_003290405.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.83	no
125438	anaerobic	anaerobicⓘ	no	94.83	no
125438	aerobic	aerobicⓘ	yes	84.20	no
125438	spore-forming	spore-formingⓘ	no	89.75	no
125438	thermophilic	thermophileⓘ	no	99.75	no
125438	flagellated	motile2+ⓘ	yes	74.85	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Pathogenicity	Three separate pathways in Rhizobium leguminosarum maintain phosphatidylcholine biosynthesis, which is required for symbiotic nitrogen fixation with clover.	Kleetz J, Mizza A-S, Shevyreva I, Welter L, Brocks C, Hemschemeier A, Aktas M, Narberhaus F.	Appl Environ Microbiol	10.1128/aem.00590-24	2024
	Rhizobial variation, more than plant variation, mediates plant symbiotic and fitness responses to herbicide stress.	Iriart V, Rarick EM, Ashman TL.	Ecology	10.1002/ecy.4426	2024
Metabolism	Malonate catabolism does not drive N2 fixation in legume nodules.	Karunakaran R, East AK, Poole PS.	Appl Environ Microbiol	10.1128/aem.00919-13	2013
	Skin-penetrating nematodes exhibit life-stage-specific interactions with host-associated and environmental bacteria.	Chavez IN, Brown TM, Assie A, Bryant AS, Samuel BS, Hallem EA.	BMC Biol	10.1186/s12915-021-01153-7	2021
Metabolism	Structure-guided expansion of the substrate range of methylmalonyl coenzyme A synthetase (MatB) of Rhodopseudomonas palustris.	Crosby HA, Rank KC, Rayment I, Escalante-Semerena JC.	Appl Environ Microbiol	10.1128/aem.01733-12	2012
Metabolism	Real-time PCR detection of Brucella abortus: a comparative study of SYBR green I, 5'-exonuclease, and hybridization probe assays.	Newby DT, Hadfield TL, Roberto FF.	Appl Environ Microbiol	10.1128/aem.69.8.4753-4759.2003	2003
Metabolism	Lipid A biosynthesis in Rhizobium leguminosarum: role of a 2-keto-3-deoxyoctulosonate-activated 4' phosphatase.	Price NP, Jeyaretnam B, Carlson RW, Kadrmas JL, Raetz CR, Brozek KA.	Proc Natl Acad Sci U S A	10.1073/pnas.92.16.7352	1995
	Genotypic and Phenotypic Comparisons of Chromosomal Types within an Indigenous Soil Population of Rhizobium leguminosarum bv. trifolii.	Leung K, Strain SR, de Bruijn FJ, Bottomley PJ.	Appl Environ Microbiol	10.1128/aem.60.2.416-426.1994	1994
Metabolism	A phosphotransferase that generates phosphatidylinositol 4-phosphate (PtdIns-4-P) from phosphatidylinositol and lipid A in Rhizobium leguminosarum. A membrane-bound enzyme linking lipid a and ptdins-4-p biosynthesis.	Basu SS, York JD, Raetz CR.	J Biol Chem	10.1074/jbc.274.16.11139	1999
	Variability among Rhizobium Strains Originating from Nodules of Vicia faba.	van Berkum P, Beyene D, Vera FT, Keyser HH.	Appl Environ Microbiol	10.1128/aem.61.7.2649-2653.1995	1995
Metabolism	Isolation and structural identification of the trihydroxamate siderophore vicibactin and its degradative products from Rhizobium leguminosarum ATCC 14479 bv. trifolii.	Wright W, Little J, Liu F, Chakraborty R	Biometals	10.1007/s10534-013-9609-3	2013

References

#2212	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 6040
#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 )
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#68369	Automatically annotated from API 20NE .
#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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Rhizobium leguminosarum (DSM 6040, ATCC 14479, 3D1K2)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20NE

Isolation, sampling and environmental information

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003290405

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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