Name: Varunaivibrio sulfuroxidans DSM 101688
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 132624

Type strain:

Species: Varunaivibrio sulfuroxidans

Culture col. no.: DSM 101688, JCM 31027, TC 8

Strain history: C. Vetriani; Rutgers Univ., USA; TC8.

NCBI tax ID(s): 1773489 (species)

SI-ID 405343

DSM 101688

Section

Varunaivibrio sulfuroxidans DSM 101688 is a facultative anaerobe, chemoautotroph, mesophilic bacterium that was isolated from sediment from a submarine coastal gas vent.

Gram-negative
motile
vibrio-shaped
chemoautotroph
facultative anaerobe
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	*Rhodospirillales*
	Family	*Thalassospiraceae*
	Genus	*Varunaivibrio*
	Species	**Varunaivibrio sulfuroxidans**
	Full Scientific Name (LPSN)	Varunaivibrio sulfuroxidans Patwardhan and Vetriani 2016

Information on morphological and physiological properties Morphology

[Ref.: #43161]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.999

[Ref.: #43161]	Cell length	1-1.5 µm

[Ref.: #43161]	Cell width	0.6 µm

[Ref.: #43161]	Cell shape	vibrio-shaped

[Ref.: #43161]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %92.817

Information on culture and growth conditions Culture and growth conditions

[Ref.: #24413]

Culture medium

SULFURIMONAS MJ MEDIUM (DSMZ Medium 1011)

[Ref.: #24413]

Culture medium growth

[Ref.: #24413]

Culture medium link

Medium recipe at MediaDive

[Ref.: #24413]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #24413]	growth	30 °C
[Ref.: #43161]	optimum	30 °C
[Ref.: #43161]	growth	20-35 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #24413]	Temperature range	mesophilic
[Ref.: #43161]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #43161]			optimum	6.0-7.0
[Ref.: #43161]			growth	4.5-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43161]	Oxygen tolerance	facultative anaerobe
[Ref.: #43161]	Oxygen tolerance	microaerophile

[Ref.: #43161]	Nutrition type	chemoautotroph
[Ref.: #43161]	Nutrition type	chemoheterotroph
[Ref.: #43161]	Nutrition type	chemoorganoheterotroph
[Ref.: #43161]	Nutrition type	chemolithoheterotroph

[Ref.: #43161]	Type of spore	spore
[Ref.: #43161]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.996

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43161]		NaCl		growth	5-45	g/L
[Ref.: #43161]		NaCl		optimum	15-20	g/L

[Ref.: #67770]

Observation

quinones: Q-9, Q-8

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43161]	carbon dioxide ChEBI	+	carbon source
[Ref.: #43161]	casamino acids	+	carbon source
[Ref.: #43161]	citrate ChEBI	+	carbon source
[Ref.: #43161]	dioxygen ChEBI	+	electron acceptor
[Ref.: #43161]	elemental sulfur ChEBI	+	electron donor
[Ref.: #43161]	ferric iron ChEBI	+	electron acceptor
[Ref.: #43161]	L-glutamine ChEBI	+	carbon source
[Ref.: #43161]	lactate ChEBI	+	carbon source
[Ref.: #43161]	nitrate ChEBI	+	electron acceptor
[Ref.: #43161]	peptone	+	carbon source
[Ref.: #43161]	pyruvate ChEBI	+	carbon source
[Ref.: #43161]	thiosulfate ChEBI	+	electron donor
[Ref.: #43161]	tryptone	+	carbon source
[Ref.: #43161]	yeast extract	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration
[Ref.: #43161]	ampicillin ChEBI	yes	100000	µg/mL
[Ref.: #43161]	chloramphenicol ChEBI	yes	100000	µg/mL
[Ref.: #43161]	kanamycin ChEBI	yes	100000	µg/mL
[Ref.: #43161]	streptomycin ChEBI	yes	100000	µg/mL

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #43161]		catalase	-	1.11.1.6

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	photosynthesis	100	14 of 14
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	vitamin B12 metabolism	82.35	28 of 34
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	purine metabolism	70.21	66 of 94
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	NAD metabolism	66.67	12 of 18
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	pyrimidine metabolism	64.44	29 of 45
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	oxidative phosphorylation	63.74	58 of 91
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	alanine metabolism	62.07	18 of 29
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	vitamin B1 metabolism	61.54	8 of 13
[Ref.: #66794]	lipid metabolism	61.29	19 of 31
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	flavin biosynthesis	60	9 of 15
[Ref.: #66794]	histidine metabolism	58.62	17 of 29
[Ref.: #66794]	tryptophan metabolism	57.89	22 of 38
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	carnitine metabolism	50	4 of 8
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	lysine metabolism	47.62	20 of 42
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	degradation of sugar alcohols	37.5	6 of 16
[Ref.: #66794]	dTDPLrhamnose biosynthesis	37.5	3 of 8
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	degradation of sugar acids	36	9 of 25
[Ref.: #66794]	degradation of pentoses	35.71	10 of 28
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	urea cycle	30.77	4 of 13
[Ref.: #66794]	phenol degradation	30	6 of 20
[Ref.: #66794]	starch degradation	30	3 of 10
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	carotenoid biosynthesis	27.27	6 of 22
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	glycogen biosynthesis	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	sulfate reduction	23.08	3 of 13
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #24413]	Sample type/isolated from	sediment from a submarine coastal gas vent
[Ref.: #24413]	Geographic location (country and/or sea, region)	Tyrrhenian Sea, Tor Caldara
[Ref.: #24413]	Country	Italy
[Ref.: #24413]	Country ISO 3 Code	ITA
[Ref.: #24413]	Continent	Europe
[Ref.: #24413]	Geographic location	41.4858°/12.5897°

[Ref.: #43161]	Sample type/isolated from	surface sediment of an active shallow-water gas vent
[Ref.: #43161]	Sampling date	2013-08
[Ref.: #43161]	Geographic location (country and/or sea, region)	Tor Caldara in the Tyrrhenian Sea, Italy
[Ref.: #43161]	Country	Italy
[Ref.: #43161]	Country ISO 3 Code	ITA
[Ref.: #43161]	Continent	Europe
[Ref.: #43161]	Geographic location	41.0000°/12.0000°

[Ref.: #67770]	Sample type/isolated from	Sulfidic shallow-water marine gas vent located at Tor Caldara in the Tyrrhenian Sea
[Ref.: #67770]	Country	Italy
[Ref.: #67770]	Country ISO 3 Code	ITA
[Ref.: #67770]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment
#Environmental	#Terrestrial	#Coast

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KU294728 (>99% sequence identity) for Varunaivibrio sulfuroxidans subclade from Microbeatlas

Aquatic Samples	108
Soil Samples	11
Animal Samples	10
Plant Samples	4
Total Samples	133

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

[Ref.: #24413]

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.: #24413]	Varunaivibrio sulfuroxidans strain TC8 16S ribosomal RNA gene, partial sequence	KU294728	1360	ENA	1773489 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Varunaivibrio sulfuroxidans DSM 101688	GCA_004341725	contig	GenBank	1773489 tax ID
[Ref.: #66792]	Varunaivibrio sulfuroxidans strain DSM 101688	1773489.15	wgs	PATRIC	1773489 tax ID	*
[Ref.: #66792]	Varunaivibrio sulfuroxidans DSM 101688	2784746782	draft	JGI IMG/M	1773489 tax ID	*

[Ref.: #24413]

GC-content

59.9 mol%

high performance liquid chromatography (HPLC)

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: Varunaivibrio sulfuroxidans strain DSM 101688 PATRIC: 1773489.15
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Varunaivibrio sulfuroxidans strain DSM 101688 PATRIC: 1773489.15
[Ref.: #69480]	motile	yes	92.667	yes
[Ref.: #69480]	gram-positive	no	99.207	no
[Ref.: #69480]	anaerobic	no	93.336	yes
[Ref.: #69480]	aerobic	no	88.051	yes
[Ref.: #69480]	halophile	no	68.735	no
[Ref.: #69480]	spore-forming	no	93.528	yes
[Ref.: #69480]	thermophile	yes	60.562	no
[Ref.: #69480]	glucose-util	yes	61.615	no
[Ref.: #69480]	flagellated	yes	60.628	no
[Ref.: #69480]	glucose-ferment	no	89.664	no

Availability in culture collections External links

[Ref.: #24413]

Culture collection no.

DSM 101688, JCM 31027, TC 8

[Ref.: #90938]

SI-ID 405343

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Varunaivibrio sulfuroxidans gen. nov., sp. nov., a facultatively chemolithoautotrophic, mesophilic alphaproteobacterium from a shallow-water gas vent at Tor Caldara, Tyrrhenian Sea.	Patwardhan S, Vetriani C	Int J Syst Evol Microbiol	10.1099/ijsem.0.001235	2016	*

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 )

#24413

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 101688

#43161

Sushmita Patwardhan and Costantino Vetriani: Varunaivibrio sulfuroxidans gen. nov., sp. nov., a facultatively chemolithoautotrophic, mesophilic alphaproteobacterium from a shallow-water gas vent at Tor Caldara, Tyrrhenian Sea. IJSEM 66: 3579 - 3584 2016 ( DOI 10.1099/ijsem.0.001235 , PubMed 27298285 )

#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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

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

#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 )

#90938

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-ID405343.1 )

* 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 Varunaivibrio sulfuroxidans in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Varunaivibrio sulfuroxidans strain DSM 101688

Varunaivibrio sulfuroxidans strain DSM 101688

Change proposal

Change proposal