Name: Rhizobium metallidurans ChimEc512
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 131342

Type strain:

Species: Rhizobium metallidurans

Strain Designation: ChimEc512

Culture col. no.: DSM 26575, CIP 110550

Strain history: CIP <- 2012, C. Grison, CEFE CNRS, Montpellier, France: strain ChimEc512

NCBI tax ID(s): 1265931 (species)

SI-ID 403805

DSM 26575, CIP 110550

Section

Rhizobium metallidurans ChimEc512 is a mesophilic, Gram-negative bacterium that was isolated from root nodules of the zinc-hyperaccumulating legume Anthyllis vulneraria growing on a heavy metal contaminated mining site.

Gram-negative
mesophilic
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 metallidurans**
	Full Scientific Name (LPSN)	Rhizobium metallidurans Grison et al. 2015

Information on morphological and physiological properties Morphology

[Ref.: #120920]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.977

[Ref.: #120920]	Cell shape	rod-shaped

[Ref.: #120920]	Motility	no

[Ref.: #22569]	Type of hemolysis	gamma
[Ref.: #22569]	Incubation period	1-2 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #22569]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #22569]

Culture medium growth

[Ref.: #22569]

Culture medium link

Medium recipe at MediaDive

[Ref.: #22569]

Culture medium composition

expand / minimize

[Ref.: #120920]

Culture medium

CIP Medium 72

[Ref.: #120920]

Culture medium growth

[Ref.: #120920]

Culture medium link

Medium recipe provided by DSMZ

	Temperatures	Kind of temperature		Temperature
[Ref.: #22569]			growth	30 °C

[Ref.: #22569]

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]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* 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.: #22569]	catalase	+	1.11.1.6
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #22569]	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.: #22569]	24925	+	-	-	-	-	+	-	+	+	+	+	+	+	+	-	-	-	+	-	-	+
[Ref.: #22569]	24464	+	-	-	-	-	+	-	+	+	+	+	+	+	+	+/-	-	-	+	-	-	+
[Ref.: #22569]	23949	+	-	-	-	+/-	+	-	+	+	+	+	+	+	+	-	-	-	+	-	-	not determinedn.d.

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

[Ref.: #22569]	Sample type/isolated from	root nodules of the zinc-hyperaccumulating legume Anthyllis vulneraria growing on a heavy metal contaminated mining site
[Ref.: #22569]	Host species	Anthyllis vulneraria
[Ref.: #22569]	Geographic location (country and/or sea, region)	Gard County, Les Avinières
[Ref.: #22569]	Country	France
[Ref.: #22569]	Country ISO 3 Code	FRA
[Ref.: #22569]	Continent	Europe

[Ref.: #120920]	Geographic location (country and/or sea, region)	Saint Laurent le Minier
[Ref.: #120920]	Country	France
[Ref.: #120920]	Country ISO 3 Code	FRA
[Ref.: #120920]	Continent	Europe
[Ref.: #120920]	Isolation date	2012
* marker position based on {}

Isolation sources categories

#Engineered	#Contamination	#Heavy metal
#Engineered	#Other	#Mine
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root nodule

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence JX678769 (>99% sequence identity) for Rhizobium from Microbeatlas

Aquatic Samples	672
Soil Samples	1930
Animal Samples	982
Plant Samples	1204
Total Samples	4788

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

[Ref.: #22569]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #120920]	Biosafety level	1	Risk group (French classification)

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.: #22569]	Rhizobium metallidurans strain ChimEc512 16S ribosomal RNA gene, partial sequence	JX678769	1475	ENA	1265931 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rhizobium metallidurans DSM 26575	GCA_014196505	scaffold	GenBank	1265931 tax ID	*
[Ref.: #66792]	Rhizobium metallidurans strain DSM 26575	1265931.3	wgs	PATRIC	1265931 tax ID	*
[Ref.: #66792]	Rhizobium metallidurans DSM 26575	2829912830	draft	JGI IMG/M	1265931 tax ID	*

[Ref.: #22569]

GC-content

58.9 mol%

thermal denaturation, midpoint method (Tm)

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 metallidurans DSM 26575 NCBI: GCA_014196505.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhizobium metallidurans DSM 26575 NCBI: GCA_014196505.1
[Ref.: #69480]	flagellated	no	82.445	no
[Ref.: #69480]	gram-positive	no	98.195	no
[Ref.: #69480]	anaerobic	no	97.932	no
[Ref.: #69480]	aerobic	yes	92.419	no
[Ref.: #69480]	halophile	no	92.727	no
[Ref.: #69480]	spore-forming	no	93.859	no
[Ref.: #69480]	glucose-util	yes	92.806	yes
[Ref.: #69480]	thermophile	no	98.743	no
[Ref.: #69480]	motile	yes	84.602	no
[Ref.: #69480]	glucose-ferment	no	88.795	yes

Availability in culture collections External links

[Ref.: #22569]

Culture collection no.

DSM 26575, CIP 110550

[Ref.: #89783]

SI-ID 403805

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rhizobium metallidurans sp. nov., a symbiotic heavy metal resistant bacterium isolated from the Anthyllis vulneraria Zn-hyperaccumulator.	Grison CM, Jackson S, Merlot S, Dobson A, Grison C	Int J Syst Evol Microbiol	10.1099/ijs.0.000130	2015	*

References

#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 )

#22569

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26575

#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 .

#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 )

#89783

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-ID403805.1 )

#120920 Collection of Institut Pasteur ; Curators of the CIP; CIP 110550
* These data were automatically processed and therefore are not curated

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Rhizobium metallidurans DSM 26575

Rhizobium metallidurans DSM 26575

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