Name: Variovorax gossypii JM-310
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 131560

Type strain:

Species: Variovorax gossypii

Strain Designation: JM-310, JM 310

Culture col. no.: DSM 100435, CCM 8614, CIP 110912, LMG 28869

Strain history: CIP <- 2015, P. Kämpfer, Giessen Univ., Giessen, Germany: strain JM 310

NCBI tax ID(s): 1679495 (species)

SI-ID 406461

DSM 100435, CIP 110912

Special Collections

Section

Variovorax gossypii JM-310 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from healthy internal root tissue of 4-week-old cotton .

colony-forming
Gram-negative
motile
rod-shaped
aerobe
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	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Comamonadaceae*
	Genus	*Variovorax*
	Species	**Variovorax gossypii**
	Full Scientific Name (LPSN)	Variovorax gossypii Kämpfer et al. 2015

Information on morphological and physiological properties Morphology

[Ref.: #23102]	Gram stain	negative
[Ref.: #119715]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %93.5

[Ref.: #23102]	Cell length	1.5-3.0 µm

[Ref.: #23102]	Cell width	0.3-0.5 µm

[Ref.: #23102]	Cell shape	rod-shaped
[Ref.: #119715]	Cell shape	rod-shaped

[Ref.: #23102]	Motility	yes
[Ref.: #119715]	Motility	no

[Ref.: #23102]	Colony color	beige
[Ref.: #23102]	Colony shape	circular
[Ref.: #23102]	Cultivation medium used	nutrient agar

Information on culture and growth conditions Culture and growth conditions

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Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

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Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

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Culture medium

R2A MEDIUM (DSMZ Medium 830)

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Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

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Culture medium

Nutrient agar (NA)

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Culture medium growth

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Culture medium

Reasoner's 2A agar (R2A)

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Culture medium growth

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Culture medium

trypticase soy agar

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Culture medium growth

[Ref.: #41883]

Culture medium

MEDIUM 72- for trypto casein soja agar

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Culture medium growth

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Culture medium composition

expand / minimize

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Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

[Ref.: #119715]

Culture medium

CIP Medium 72

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Culture medium growth

[Ref.: #119715]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #22787]		growth	28 °C
[Ref.: #23102]		growth	11.0-36.0 °C
[Ref.: #23102]	no	growth	<4.0 °C
[Ref.: #23102]	no	growth	>45.0 °C
[Ref.: #41883]		growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #23102]

Oxygen tolerance

aerobe

[Ref.: #23102]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %91.04
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #23102]		NaCl		growth	1.0-3.0	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #23102]	2-oxoglutarate ChEBI	+	carbon source
[Ref.: #23102]	3-hydroxybenzoate ChEBI	-	carbon source
[Ref.: #23102]	3-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #23102]	4-hydroxybenzoate ChEBI	-	carbon source
[Ref.: #23102]	acetate ChEBI	+	carbon source
[Ref.: #23102]	adipate ChEBI	+	carbon source
[Ref.: #23102]	arbutin ChEBI	-	carbon source
[Ref.: #23102]	azelaate ChEBI	+	carbon source
[Ref.: #23102]	beta-alanine ChEBI	+	carbon source
[Ref.: #23102]	cellobiose ChEBI	-	builds acid from
[Ref.: #23102]	cellobiose ChEBI	-	carbon source
[Ref.: #23102]	cis-aconitate ChEBI	-	carbon source
[Ref.: #23102]	citrate ChEBI	-	carbon source
[Ref.: #23102]	D-arabitol ChEBI	-	builds acid from
[Ref.: #23102]	D-fructose ChEBI	+	carbon source
[Ref.: #23102]	D-galactose ChEBI	-	carbon source
[Ref.: #23102]	D-glucose ChEBI	+	builds acid from
[Ref.: #23102]	D-glucose ChEBI	+	carbon source
[Ref.: #23102]	D-mannitol ChEBI	+	builds acid from
[Ref.: #23102]	D-mannitol ChEBI	+	carbon source
[Ref.: #23102]	D-mannose ChEBI	+	carbon source
[Ref.: #23102]	D-ribose ChEBI	+	carbon source
[Ref.: #23102]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #23102]	D-sorbitol ChEBI	+	carbon source
[Ref.: #23102]	D-xylose ChEBI	-	builds acid from
[Ref.: #23102]	D-xylose ChEBI	+	carbon source
[Ref.: #23102]	erythritol ChEBI	-	builds acid from
[Ref.: #23102]	esculin ChEBI	+	hydrolysis
[Ref.: #23102]	fumarate ChEBI	+	carbon source
[Ref.: #23102]	galactitol ChEBI	-	builds acid from
[Ref.: #23102]	gamma-aminobutyric acid ChEBI	+	carbon source
[Ref.: #23102]	gluconate ChEBI	+	carbon source
[Ref.: #23102]	glutaric acid ChEBI	+	carbon source
[Ref.: #23102]	glycerol ChEBI	-	carbon source
[Ref.: #23102]	itaconate ChEBI	-	carbon source
[Ref.: #23102]	L-alanine ChEBI	+	carbon source
[Ref.: #23102]	L-arabinose ChEBI	+	builds acid from
[Ref.: #23102]	L-arabinose ChEBI	+	carbon source
[Ref.: #23102]	L-aspartate ChEBI	+	carbon source
[Ref.: #23102]	L-histidine ChEBI	+	carbon source
[Ref.: #23102]	L-leucine ChEBI	+	carbon source
[Ref.: #23102]	L-ornithine ChEBI	+	carbon source
[Ref.: #23102]	L-phenylalanine ChEBI	-	carbon source
[Ref.: #23102]	L-proline ChEBI	+	carbon source
[Ref.: #23102]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #23102]	L-rhamnose ChEBI	-	carbon source
[Ref.: #23102]	L-serine ChEBI	+	carbon source
[Ref.: #23102]	L-tryptophan ChEBI	+	carbon source
[Ref.: #23102]	lactose ChEBI	-	builds acid from
[Ref.: #23102]	maltitol ChEBI	-	carbon source
[Ref.: #23102]	maltose ChEBI	-	builds acid from
[Ref.: #23102]	maltose ChEBI	-	carbon source
[Ref.: #23102]	melibiose ChEBI	-	builds acid from
[Ref.: #23102]	melibiose ChEBI	+	carbon source
[Ref.: #23102]	mesaconate ChEBI	-	carbon source
[Ref.: #23102]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from
[Ref.: #23102]	myo-inositol ChEBI	-	builds acid from
[Ref.: #23102]	myo-inositol ChEBI	-	carbon source
[Ref.: #23102]	N-acetylgalactosamine ChEBI	-	carbon source
[Ref.: #23102]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #23102]	phenylacetate ChEBI	-	carbon source
[Ref.: #23102]	propionate ChEBI	+	carbon source
[Ref.: #23102]	putrescine ChEBI	-	carbon source
[Ref.: #23102]	pyruvate ChEBI	+	carbon source
[Ref.: #23102]	raffinose ChEBI	-	builds acid from
[Ref.: #23102]	ribitol ChEBI	-	carbon source
[Ref.: #23102]	ribitol ChEBI	+	builds acid from
[Ref.: #23102]	salicin ChEBI	-	builds acid from
[Ref.: #23102]	salicin ChEBI	-	carbon source
[Ref.: #23102]	suberic acid ChEBI	-	carbon source
[Ref.: #23102]	sucrose ChEBI	-	builds acid from
[Ref.: #23102]	sucrose ChEBI	-	carbon source
[Ref.: #23102]	trans-aconitate ChEBI	-	carbon source
[Ref.: #23102]	trehalose ChEBI	-	builds acid from
[Ref.: #23102]	trehalose ChEBI	-	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #23102]	alpha-glucosidase	-	3.2.1.20
[Ref.: #23102]	beta-galactosidase	-	3.2.1.23
[Ref.: #23102]	catalase	+	1.11.1.6
[Ref.: #23102]	cytochrome oxidase	+	1.9.3.1

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

[Ref.: #22787]	Sample type/isolated from	healthy internal root tissue of 4-week-old cotton (Gossypium hirsutum, cultivar 'DES-119')
[Ref.: #22787]	Host species	Gossypium hirsutum
[Ref.: #22787]	Geographic location (country and/or sea, region)	Alabama, Macon county, Tallassee
[Ref.: #22787]	Country	USA
[Ref.: #22787]	Country ISO 3 Code	USA
[Ref.: #22787]	Continent	North America

[Ref.: #23102]	Sample type/isolated from	endophyte from the healthy internal root tissue of 4-week-old cotton (Gossypium hirsutum, cultivar ‘DES-119’) grown at the Plant Breeding Unit facility
[Ref.: #23102]	Enrichment culture	trypticase soy agar (TSA; Oxoid)
[Ref.: #23102]	Enrichment culture temperature	28.0 ̊C

[Ref.: #119715]	Sample type/isolated from	Plant, Internal root tissue, cotton
[Ref.: #119715]	Country	United States of America
[Ref.: #119715]	Country ISO 3 Code	USA
[Ref.: #119715]	Continent	North America
[Ref.: #119715]	Isolation date	1990-01-02
* marker position based on {}

Isolation sources categories

#Engineered	#Agriculture	#Plantation
#Host	#Other	#Endosymbiont
#Host	#Plants	#Shrub (Scrub)
#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Root (Rhizome)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KR349468 (>99% sequence identity) for Variovorax from Microbeatlas

Aquatic Samples	2157
Soil Samples	3106
Animal Samples	2122
Plant Samples	2332
Total Samples	9717

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

[Ref.: #22787]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #119715]	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.: #22787]	Variovorax gossypii strain JM-310 16S ribosomal RNA gene, partial sequence	KR349468	1437	GenBank ENA	1679495 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Variovorax gossypii DSM 100435	GCA_003965815	contig	GenBank ENA	1679495 tax ID	*
[Ref.: #66792]	Variovorax gossypii strain DSM 100435	1679495.4	wgs	PATRIC	1679495 tax ID	*
[Ref.: #66792]	Variovorax gossypii DSM 100435	2831272406	draft	JGI IMG/M	1679495 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: Variovorax gossypii strain DSM 100435 PATRIC: 1679495.4
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Variovorax gossypii strain DSM 100435 PATRIC: 1679495.4
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	93.5	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	95.457	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	91.04	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	82.505	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	97.212	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	70.589	no

Availability in culture collections External links

[Ref.: #22787]

Culture collection no.

DSM 100435, CCM 8614, CIP 110912, LMG 28869

[Ref.: #89974]

SI-ID 406461

Literature:

Topic	Title	Authors	Journal	DOI	Year
Stress	Improved Medicago sativa Nodulation under Stress Assisted by Variovorax sp. Endophytes.	Flores-Duarte NJ, Perez-Perez J, Navarro-Torre S, Mateos-Naranjo E, Redondo-Gomez S, Pajuelo E, Rodriguez-Llorente ID	Plants (Basel)	10.3390/plants11081091	2022	*
Phylogeny	Variovorax gossypii sp. nov., isolated from Gossypium hirsutum.	Kampfer P, Busse HJ, McInroy JA, Glaeser SP	Int J Syst Evol Microbiol	10.1099/ijsem.0.000581	2015	*
Phylogeny	Variovorax terrae sp. nov. Isolated from Soil with Potential Antioxidant Activity.	Woo CY, Kim J	J Microbiol Biotechnol	10.4014/jmb.2205.05018	2022	*

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 )

#22787

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100435

#23102

Peter Kämpfer,Hans-Jürgen Busse,John A. McInroy,Stefanie P. Glaeser: Variovorax gossypii sp. nov., isolated from Gossypium hirsutum. IJSEM 65: 4335 - 4340 2015 ( DOI 10.1099/ijsem.0.000581 , PubMed 26341669 )

#41883 ; Curators of the CIP;

#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) .

#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 )

#89974

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-ID406461.1 )

#119715 Collection of Institut Pasteur ; Curators of the CIP; CIP 110912
* These data were automatically processed and therefore are not curated

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Variovorax gossypii strain DSM 100435

Variovorax gossypii strain DSM 100435

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