Name: Rhizobium lupini 3C231
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 13606

Type strain:

Species: Rhizobium lupini

Strain Designation: 3C231

Culture col. no.: DSM 30140, ATCC 10319, JCM 20681, IAM 12610, NBRC 100381, VKM B-1965

Strain history: IAM 12610 <-- ATCC 10319 <-- L. W. Erdman 3C231 (Rhizobium lupini).

NCBI tax ID(s): 375 (species)

SI-ID 35204

ATCC 10319, DSM 30140, IFO 14781, IAM 12610, VKM B-1965, NBRC 100381, NBRC 14781, KACC 10747, BCRC 17460, CCRC 17460, JCM 20681

Special Collections

DSMZ
JCM

Section

Rhizobium lupini 3C231 is a Gram-negative bacterium that was isolated from source of the original strain: lupin root nodules.

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	*Rhizobiaceae*
	Genus	*Rhizobium*
	Species	**Rhizobium lupini**
	Full Scientific Name (LPSN)	Rhizobium lupini (Schroeter 1886) Eckhardt et al. 1931 (Approved Lists 1980)

Synonym

"Phytomyxa lupini"

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %97.769

[Ref.: #9161]

Incubation period

1-2 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #9161]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #9161]

Culture medium growth

[Ref.: #9161]

Culture medium link

Medium recipe at MediaDive

[Ref.: #9161]

Culture medium composition

expand / minimize

[Ref.: #9161]

Culture medium

RHIZOBIUM MEDIUM (DSMZ Medium 98)

[Ref.: #9161]

Culture medium growth

[Ref.: #9161]

Culture medium link

Medium recipe at MediaDive

[Ref.: #9161]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #9161]			growth	30 °C
[Ref.: #67770]			growth	25 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]

Ability of spore formation

no Confidence in %100

	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]	esculin ChEBI	-	hydrolysis	* 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
	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.: #9161]	catalase	+	1.11.1.6
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #9161]	cytochrome-c oxidase	+	1.9.3.1
[Ref.: #68369]	gelatinase	-		* 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.: #9161]	24111	+	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+
[Ref.: #9161]	24110	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.

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

[Ref.: #9161]	Sample type/isolated from	source of the original strain: lupin (Lupinus angustifolius) root nodules

[Ref.: #67770]	Sample type/isolated from	Lupine (Lupinus angustifolius)
[Ref.: #67770]	Host species	Lupinus angustifolius
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root nodule

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB681156 (>99% sequence identity) for Bradyrhizobium from Microbeatlas

Aquatic Samples	2827
Soil Samples	5001
Animal Samples	4320
Plant Samples	739
Total Samples	12887

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

[Ref.: #9161]

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.: #9161]	Bradyrhizobium lupini strain DSM 30140 16S ribosomal RNA, partial sequence	NR044869	1482	GenBank ENA	136996 tax ID
[Ref.: #20218]	Bradyrhizobium sp. USDA 3051 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial sequence	EU834723	1220	GenBank ENA	546898 tax ID	*
[Ref.: #20218]	Rhizobium lupini 16S rRNA gene, type strain DSM 30140T	X87273	1484	GenBank ENA	136996 tax ID	*
[Ref.: #20218]	Rhizobium lupini gene for 16S rRNA, partial sequence, strain: NBRC 100381	AB681156	1414	GenBank ENA	136996 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Bradyrhizobium lupini strain DSM 30140	136996.3	wgs	PATRIC	136996 tax ID	*
[Ref.: #66792]	Bradyrhizobium lupini DSM 30140	2861120366	draft	JGI IMG/M	136996 tax ID	*

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Bradyrhizobium lupini strain DSM 30140 PATRIC: 136996.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Bradyrhizobium lupini strain DSM 30140 PATRIC: 136996.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	97.769	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	94.07	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	80.045	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	83.089	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	98.499	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	75.088	no

Availability in culture collections External links

[Ref.: #9161]

Culture collection no.

DSM 30140, ATCC 10319, JCM 20681, IAM 12610, NBRC 100381, VKM B-1965

[Ref.: #82793]

SI-ID 35204

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Revision of the taxonomic status of the species Rhizobium lupini and reclassification as Bradyrhizobium lupini comb. nov.	Peix A, Ramirez-Bahena MH, Flores-Felix JD, Alonso de la Vega P, Rivas R, Mateos PF, Igual JM, Martinez-Molina E, Trujillo ME, Velazquez E	Int J Syst Evol Microbiol	10.1099/ijs.0.000082	2015	*
Pathogenicity	Cytokine induction by lipopolysaccharide (LPS) corresponds to lethal toxicity and is inhibited by nontoxic Rhodobacter capsulatus LPS.	Loppnow H, Libby P, Freudenberg M, Krauss JH, Weckesser J, Mayer H	Infect Immun	10.1128/iai.58.11.3743-3750.1990	1990	*
	Occurrence of lipid A variants with 27-hydroxyoctacosanoic acid in lipopolysaccharides from members of the family Rhizobiaceae.	Bhat UR, Mayer H, Yokota A, Hollingsworth RI, Carlson RW	J Bacteriol	10.1128/jb.173.7.2155-2159.1991	1991	*

References

#9161

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 30140

#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 .

#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 )

#82793

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-ID35204.1 )

* These data were automatically processed and therefore are not curated

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Bradyrhizobium lupini strain DSM 30140

Bradyrhizobium lupini strain DSM 30140

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