Name: Rhizobium leguminosarum 3D1K2
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13593

Type strain:

Species: Rhizobium leguminosarum

Strain Designation: 3D1K2

Culture col. no.: DSM 6040, ATCC 14479

Strain history: <- ATCC <- U.M. Means, 3D1K2

NCBI tax ID(s): 384 (species)

SI-ID 36091

ATCC 14479, DSM 6040, KCTC 2362

Other strains from Rhizobium leguminosarum

Section

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

motile
psychrophilic
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	*Rhizobiaceae*
	Genus	*Rhizobium*
	Species	**Rhizobium leguminosarum**
	Full Scientific Name (LPSN)	Rhizobium leguminosarum (Frank 1879) Frank 1889 (Approved Lists 1980)

	Synonym	"Schinzia* leguminosarum"*
	Synonym	Rhizobium trifolii

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.975

[Ref.: #69480]	Motility	yes Confidence in %93.891

Information on culture and growth conditions Culture and growth conditions

[Ref.: #2212]

Culture medium

RHIZOBIUM MEDIUM (DSMZ Medium 98)

[Ref.: #2212]

Culture medium growth

[Ref.: #2212]

Culture medium link

Medium recipe at MediaDive

[Ref.: #2212]

Culture medium composition

expand / minimize

[Ref.: #2212]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #2212]

Culture medium growth

[Ref.: #2212]

Culture medium link

Medium recipe at MediaDive

[Ref.: #2212]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #2212]			growth	22 °C
[Ref.: #2212]			growth	26 °C

[Ref.: #2212]	Temperature range	psychrophilic
[Ref.: #2212]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.995

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE

API® 20NE:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #2212]	24583	-	-	-	-	-	+/-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	+

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

[Ref.: #2212]

Biosafety level

Risk group (German classification)
According to TRBA 466

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

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rhizobium leguminosarum ATCC 14479	GCA_003290405	complete	GenBank	384 tax ID	*
[Ref.: #66792]	Rhizobium leguminosarum strain ATCC 14479	384.95	complete	PATRIC	384 tax ID	*
[Ref.: #66792]	Rhizobium leguminosarum ATCC 14479	2859840839	complete	JGI IMG/M	384 tax ID	*

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Rhizobium leguminosarum ATCC 14479 NCBI: GCA_003290405.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhizobium leguminosarum ATCC 14479 NCBI: GCA_003290405.1
[Ref.: #69480]	motile	yes	86.338	no
[Ref.: #69480]	flagellated	no	79.024	no
[Ref.: #69480]	gram-positive	no	98.149	no
[Ref.: #69480]	anaerobic	no	98.079	no
[Ref.: #69480]	aerobic	yes	91.338	no
[Ref.: #69480]	halophile	no	94.774	no
[Ref.: #69480]	spore-forming	no	93.575	no
[Ref.: #69480]	glucose-util	yes	85.422	yes
[Ref.: #69480]	thermophile	no	99.611	no
[Ref.: #69480]	glucose-ferment	no	89.665	yes

Availability in culture collections External links

[Ref.: #2212]

Culture collection no.

DSM 6040, ATCC 14479

[Ref.: #82780]

SI-ID 36091

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 .

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#82780

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-ID36091.1 )

* These data were automatically processed and therefore are not curated

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Rhizobium leguminosarum ATCC 14479

Rhizobium leguminosarum ATCC 14479

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