Name: Variovorax soli GH9-3
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 3016

Type strain:

Species: Variovorax soli

Strain Designation: GH9-3

Culture col. no.: DSM 18216, KACC 11579, CIP 110194

Strain history: CIP <- 2010, KACC <- S.-H. Yoo: strain GH9-3

NCBI tax ID(s): 376815 (species)

SI-ID 297364

DSM 18216, KACC 11579, CIP 110194

Other strains from Variovorax soli

V. soli SF005835(FSU),

Section

Variovorax soli GH9-3 is an obligate aerobe, mesophilic, Gram-negative bacterium that forms irregular colonies and was isolated from greenhouse soil cultivated with lettuce.

colony-forming
Gram-negative
motile
rod-shaped
mesophilic
obligate aerobe
16S sequence
Bacteria

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 soli**
	Full Scientific Name (LPSN)	Variovorax soli Kim et al. 2006

Information on morphological and physiological properties Morphology

[Ref.: #23099]	Gram stain	negative
[Ref.: #122669]	Gram stain	negative

[Ref.: #23099]	Cell length	1.0-1.5 µm

[Ref.: #23099]	Cell width	0.5-0.7 µm

[Ref.: #23099]	Cell shape	rod-shaped
[Ref.: #122669]	Cell shape	rod-shaped

[Ref.: #23099]	Motility	yes
[Ref.: #122669]	Motility	yes

[Ref.: #23099]	Colony color	light yellow
[Ref.: #23099]	Colony shape	irregular
[Ref.: #23099]	Incubation period	2 days
[Ref.: #23099]	Cultivation medium used	R2A agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7371]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #7371]

Culture medium growth

[Ref.: #7371]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7371]

Culture medium composition

expand / minimize

[Ref.: #23099]

Culture medium

MacConkey agar (Difco)

[Ref.: #23099]

Culture medium growth

[Ref.: #23099]

Culture medium

nutrient agar (Difco)

[Ref.: #23099]

Culture medium growth

[Ref.: #23099]

Culture medium

Reasoner's 2A agar (R2A)

[Ref.: #23099]

Culture medium growth

[Ref.: #23099]

Culture medium

trypticase soy agar (Difco)

[Ref.: #23099]

Culture medium growth

[Ref.: #40349]

Culture medium

MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromati

[Ref.: #40349]

Culture medium growth

[Ref.: #40349]

Culture medium composition

expand / minimize

[Ref.: #122669]

Culture medium

CIP Medium 566

[Ref.: #122669]

Culture medium growth

[Ref.: #122669]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #7371]	growth	30 °C
[Ref.: #23099]	growth	10.0-35.0 °C
[Ref.: #23099]	optimum	30.0 °C
[Ref.: #40349]	growth	30 °C

[Ref.: #7371]	Temperature range	mesophilic
[Ref.: #23099]	Temperature range	mesophilic
[Ref.: #40349]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #23099]			optimum	7.0
[Ref.: #23099]			growth	5.0-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #122669]

Oxygen tolerance

obligate aerobe

[Ref.: #23099]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #23099]		NaCl		growth	0.0-3.0	%
[Ref.: #23099]		NaCl	no	growth	>3.0	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #23099]	2-dehydro-D-gluconate ChEBI	+	growth
[Ref.: #23099]	3-hydroxybenzoate ChEBI	+	growth
[Ref.: #23099]	3-hydroxybutyrate ChEBI	+	growth
[Ref.: #23099]	4-hydroxybenzoate ChEBI	+	growth
[Ref.: #23099]	5-dehydro-D-gluconate ChEBI	-	growth
[Ref.: #23099]	adipate ChEBI	+	growth
[Ref.: #23099]	carboxymethylcellulose ChEBI	-	hydrolysis
[Ref.: #23099]	casein	-	hydrolysis
[Ref.: #23099]	D-glucose ChEBI	+	growth
[Ref.: #23099]	D-mannitol ChEBI	+	growth
[Ref.: #23099]	D-mannose ChEBI	-	growth
[Ref.: #23099]	D-ribose ChEBI	-	growth
[Ref.: #23099]	D-sorbitol ChEBI	+	growth
[Ref.: #23099]	decanoate ChEBI	-	growth
[Ref.: #23099]	disodium malate ChEBI	-	growth
[Ref.: #23099]	dna ChEBI	-	hydrolysis
[Ref.: #23099]	esculin ChEBI	-	hydrolysis
[Ref.: #23099]	gelatin ChEBI	-	hydrolysis
[Ref.: #23099]	glucose ChEBI	-	fermentation
[Ref.: #23099]	glycogen ChEBI	-	growth
[Ref.: #23099]	itaconate ChEBI	-	growth
[Ref.: #23099]	L-alanine ChEBI	-	growth
[Ref.: #23099]	L-arabinose ChEBI	+	growth
[Ref.: #23099]	L-fucose ChEBI	-	growth
[Ref.: #23099]	L-histidine ChEBI	+	growth
[Ref.: #23099]	L-proline ChEBI	-	growth
[Ref.: #23099]	L-rhamnose ChEBI	-	growth
[Ref.: #23099]	L-serine ChEBI	-	growth
[Ref.: #23099]	lactate ChEBI	+	growth
[Ref.: #23099]	malate ChEBI	+	growth
[Ref.: #23099]	maltose ChEBI	-	growth
[Ref.: #23099]	melibiose ChEBI	-	growth
[Ref.: #23099]	myo-inositol ChEBI	-	growth
[Ref.: #23099]	N-acetylglucosamine ChEBI	-	growth
[Ref.: #23099]	nitrate ChEBI	+	reduction
[Ref.: #122669]	nitrate ChEBI	+	reduction
[Ref.: #122669]	nitrite ChEBI	-	reduction
[Ref.: #23099]	phenylacetate ChEBI	+	growth
[Ref.: #23099]	potassium gluconate ChEBI	+	growth
[Ref.: #23099]	propionate ChEBI	+	growth
[Ref.: #23099]	salicin ChEBI	-	growth
[Ref.: #23099]	sodium acetate ChEBI	-	growth
[Ref.: #23099]	sodium citrate ChEBI	-	growth
[Ref.: #23099]	starch ChEBI	-	hydrolysis
[Ref.: #23099]	suberic acid ChEBI	+	growth
[Ref.: #23099]	sucrose ChEBI	-	growth
[Ref.: #23099]	tyrosine ChEBI	+	hydrolysis
[Ref.: #23099]	urea ChEBI	+	hydrolysis
[Ref.: #23099]	valerate ChEBI	+	growth
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #23099]		indole ChEBI	no
[Ref.: #122669]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #23099]	acid phosphatase	+	3.1.3.2
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #23099]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #23099]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #23099]	alpha-fucosidase	-	3.2.1.51
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #23099]	alpha-galactosidase	-	3.2.1.22
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #23099]	alpha-glucosidase	-	3.2.1.20
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #23099]	alpha-mannosidase	-	3.2.1.24
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #23099]	arginine dihydrolase	-	3.5.3.6
[Ref.: #23099]	beta-galactosidase	-	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #23099]	beta-glucuronidase	-	3.2.1.31
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #23099]	catalase	+	1.11.1.6
[Ref.: #122669]	catalase	+	1.11.1.6
[Ref.: #23099]	cystine arylamidase	-	3.4.11.3
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #23099]	cytochrome oxidase	+	1.9.3.1
[Ref.: #23099]	esterase (C 4)	+
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #23099]	esterase lipase (C 8)	+
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #23099]	leucine arylamidase	+	3.4.11.1
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #23099]	lipase (C 14)	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #23099]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #23099]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #122669]	oxidase	+
[Ref.: #23099]	trypsin	-	3.4.21.4
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #23099]	urease	-	3.5.1.5
[Ref.: #122669]	urease	+	3.5.1.5
[Ref.: #23099]	valine arylamidase	-
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

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

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #122669]	12430	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-

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

[Ref.: #7371]	Sample type/isolated from	greenhouse soil cultivated with lettuce
[Ref.: #7371]	Geographic location (country and/or sea, region)	Wanju region
[Ref.: #7371]	Country	Republic of Korea
[Ref.: #7371]	Country ISO 3 Code	KOR
[Ref.: #7371]	Continent	Asia

[Ref.: #122669]	Sample type/isolated from	Environment, Greenhouse soil
[Ref.: #122669]	Geographic location (country and/or sea, region)	Wanju region
[Ref.: #122669]	Country	Republic of Korea
[Ref.: #122669]	Country ISO 3 Code	KOR
[Ref.: #122669]	Continent	Asia

[Ref.: #23099]	Enrichment culture	R2A agar
[Ref.: #23099]	Enrichment culture duration	3 days
[Ref.: #23099]	Enrichment culture temperature	30.0 ̊C
* marker position based on {}

Isolation sources categories

#Engineered	#Agriculture	#Greenhouse
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence DQ432053 (>99% sequence identity) for Variovorax soli from Microbeatlas

Aquatic Samples	448
Soil Samples	914
Animal Samples	1066
Plant Samples	323
Total Samples	2751

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

[Ref.: #7371]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #122669]	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.: #7371]	Variovorax soli strain GH9-3 16S ribosomal RNA gene, partial sequence	DQ432053	1478	ENA	1321611 tax ID

[Ref.: #7371]	GC-content	67.1 mol%
[Ref.: #23099]	GC-content	67.1 mol%	high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #7371]

Culture collection no.

DSM 18216, KACC 11579, CIP 110194

[Ref.: #72538]

SI-ID 297364

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
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 guangxiensis sp. nov., an aerobic, 1-aminocyclopropane-1-carboxylate deaminase producing bacterium isolated from banana rhizosphere.	Gao JL, Yuan M, Wang XM, Qiu TL, Li JW, Liu HC, Li XA, Chen J, Sun JG	Antonie Van Leeuwenhoek	10.1007/s10482-014-0304-3	2014	*
Phylogeny	Variovorax defluvii sp. nov., isolated from sewage.	Jin L, Kim KK, Ahn CY, Oh HM	Int J Syst Evol Microbiol	10.1099/ijs.0.035295-0	2011	*
Phylogeny	Xenophilus aerolatus sp. nov., isolated from air.	Kim SJ, Kim YS, Weon HY, Anandham R, Noh HJ, Kwon SW	Int J Syst Evol Microbiol	10.1099/ijs.0.013185-0	2009	*
Phylogeny	Variovorax boronicumulans sp. nov., a boron-accumulating bacterium isolated from soil.	Miwa H, Ahmed I, Yoon J, Yokota A, Fujiwara T	Int J Syst Evol Microbiol	10.1099/ijs.0.65315-0	2008	*
Phylogeny	Variovorax soli sp. nov., isolated from greenhouse soil.	Kim BY, Weon HY, Yoo SH, Lee SY, Kwon SW, Go SJ, Stackebrandt E	Int J Syst Evol Microbiol	10.1099/ijs.0.64390-0	2006	*

References

#7371

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18216

#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 )

#23099

Byung-Yong Kim,Hang-Yeon Weon,Seung-Hee Yoo,Seon-Young Lee,Soon-Wo Kwon,Seung-Joo Go,Erko Stackebrandt: Variovorax soli sp. nov., isolated from greenhouse soil. IJSEM 56: 2899 - 2901 2006 ( DOI 10.1099/ijs.0.64390-0 , PubMed 17158995 )

#40349 ; Curators of the CIP;

#68382

Automatically annotated from API zym .

#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 .

#72538

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-ID297364.1 )

#122669 Collection of Institut Pasteur ; Curators of the CIP; CIP 110194
* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Variovorax soli in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF