Name: Rhizobium leguminosarum 3D1k22a
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 13602

Type strain:

Species: Rhizobium leguminosarum

Strain Designation: 3D1k22a

Culture col. no.: DSM 30141, ATCC 14480, JCM 20684, IAM 12613, NBRC 14784

Strain history: IAM 12613 <-- ATCC 14480 <-- U. M. Means 3D1k22a.

NCBI tax ID(s): 384 (species)

SI-ID 4783

LMG 8820, ATCC 14480, DSM 30141, IFO 14784, IAM 12613, CECT 4116, CCRC 13519, KCTC 1536, NBRC 14784, BCRC 13519, CCT 4179, CCT 5089, KACC 10746, JCM 20684

Special Collections

DSMZ
JCM

Other strains from Rhizobium leguminosarum

Section

When using BacDive for research please cite our paper

Rhizobium leguminosarum 3D1k22a is a mesophilic bacterium of the family Rhizobiaceae.

mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	09-12-2024 (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
	Synonym	Rhizobium indigoferae

Information on morphological and physiological properties Morphology

[Ref.: #125439]	Gram stain	negative Confidence in %98.2
[Ref.: #125438]	Gram stain	negative Confidence in %99

Information on culture and growth conditions Culture and growth conditions

[Ref.: #9165]

Culture medium

RHIZOBIUM MEDIUM (DSMZ Medium 98)

[Ref.: #9165]

Culture medium growth

[Ref.: #9165]

Culture medium link

Medium recipe at MediaDive

[Ref.: #9165]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #9165]			growth	26 °C
[Ref.: #67770]			growth	25 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #125439]

Oxygen tolerance

aerobe Confidence in %97.5

[Ref.: #125439]

Ability of spore formation

no Confidence in %96.9

	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]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate 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]	beta-glucosidase	+	3.2.1.21	* 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.: #9165]	26792	-	-	-	-	+	+	-	+	-	+/-	+/-	-	+	+/-	-	-	-	+/-	-	-	+

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

[Ref.: #69479]

Global distribution of 16S sequence AY509900 (>99% sequence identity) for Rhizobium from Microbeatlas

Aquatic Samples	531
Soil Samples	4296
Animal Samples	942
Plant Samples	1878
Total Samples	7647

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

[Ref.: #9165]

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:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #9165]	Rhizobium leguminosarum strain ATCC 14480 16S ribosomal RNA gene, partial sequence	AY509900	1475	GenBank ENA	384 tax ID
[Ref.: #124043]	Rhizobium leguminosarum gene for 16S rRNA, partial sequence, strain: NBRC 14784.	AB680663	1406	GenBank ENA	384 tax ID	*
[Ref.: #20218]	Rhizobium leguminosarum strain DSM 30141 16S ribosomal RNA gene, partial sequence; internal transcribed spacer, complete sequence; and 23S ribosomal RNA, partial sequence	AF345272	1161	GenBank ENA	384 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rhizobium leguminosarum DSM 30141	GCA_014138565	scaffold	GenBank ENA	384 tax ID	*
[Ref.: #66792]	Rhizobium leguminosarum strain DSM 30141	384.400	wgs	PATRIC	384 tax ID	*
[Ref.: #66792]	Rhizobium trifolii DSM 30141	2861129306	draft	JGI IMG/M	384 tax ID	*

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rhizobium leguminosarum DSM 30141 NCBI: GCA_014138565.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	99	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	94.738	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	86.853	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	86.902	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	99.75	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	75.659	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Rhizobium leguminosarum DSM 30141 NCBI: GCA_014138565
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	96.9
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	56.7
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	98.2
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	aerobe	97.5

Availability in culture collections External links

[Ref.: #9165]

Culture collection no.

DSM 30141, ATCC 14480, JCM 20684, IAM 12613, NBRC 14784

[Ref.: #82789]

SI-ID 4783

Literature:

	Title	Authors	Journal	DOI	Year
Phylogeny	Phylogenetic diversity based on rrs, atpD, recA genes and 16S-23S intergenic sequence analyses of rhizobial strains isolated from Vicia faba and Pisum sativum in Peru.	Santillana N, Ramirez-Bahena MH, Garcia-Fraile P, Velazquez E, Zuniga D	Arch Microbiol	10.1007/s00203-007-0313-y	2007	*
	Exogenous ACC Deaminase Is Key to Improving the Performance of Pasture Legume-Rhizobial Symbioses in the Presence of a High Manganese Concentration.	Paco A, da-Silva JR, Torres DP, Glick BR, Brigido C	Plants (Basel)	10.3390/plants9121630	2020	*

References

#9165

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 30141

#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 )

#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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68369

Automatically annotated from API 20NE .

#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 .

#82789

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-ID4783.1 )

#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 .

* These data were automatically processed and therefore are not curated

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Rhizobium leguminosarum DSM 30141

Rhizobium leguminosarum DSM 30141

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