Strain identifier

BacDive ID: 132624

Type strain: Yes

Species: Varunaivibrio sulfuroxidans

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

NCBI tax ID(s): 1773489 (species)

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General

@ref: 24413

BacDive-ID: 132624

DSM-Number: 101688

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, chemoautotroph, mesophilic, Gram-negative, motile, vibrio-shaped

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

NCBI tax id

  • NCBI tax id: 1773489
  • Matching level: species

strain history

@refhistory
24413<- C. Vetriani, Rutgers, State Univ. New Jersey, New Brunswick, USA; TC8 <- S. Patwardhan {2014}
67770C. Vetriani; Rutgers Univ., USA; TC8.

doi: 10.13145/bacdive132624.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodospirillales
  • family: Thalassospiraceae
  • genus: Varunaivibrio
  • species: Varunaivibrio sulfuroxidans
  • full scientific name: Varunaivibrio sulfuroxidans Patwardhan and Vetriani 2016

@ref: 24413

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodospirillales

family: Thalassospiraceae

genus: Varunaivibrio

species: Varunaivibrio sulfuroxidans

full scientific name: Varunaivibrio sulfuroxidans Patwardhan and Vetriani 2016

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43161negative1-1.5 µm0.6 µmvibrio-shapedyes
69480negative99.999
69480yes92.817

Culture and growth conditions

culture medium

  • @ref: 24413
  • name: SULFURIMONAS MJ MEDIUM (DSMZ Medium 1011)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1011
  • composition: Name: SULFURIMONAS MJ MEDIUM (DSMZ Medium 1011; with strain-specific modifications) Composition: MgCl2 x 6 H2O 4.13452 g/l KNO3 1.97824 g/l NaHCO3 1.48368 g/l Na2S2O3 x 5 H2O 1.48368 g/l KCl 0.326409 g/l NH4Cl 0.24728 g/l K2HPO4 0.138477 g/l MgSO4 x 7 H2O 0.0296736 g/l Nitrilotriacetic acid 0.0148368 g/l Fe(NH4)2(SO4)2 x 6 H2O 0.0098912 g/l NaCl 0.0098912 g/l MnSO4 x H2O 0.0049456 g/l CoSO4 x 7 H2O 0.00178042 g/l ZnSO4 x 7 H2O 0.00178042 g/l CaCl2 x 2 H2O 0.00098912 g/l FeSO4 x 7 H2O 0.00098912 g/l NiCl2 x 6 H2O 0.000296736 g/l AlK(SO4)2 x 12 H2O 0.000197824 g/l CuSO4 x 5 H2O 9.8912e-05 g/l Pyridoxine hydrochloride 9.8912e-05 g/l Na2MoO4 x 2 H2O 9.8912e-05 g/l H3BO3 9.8912e-05 g/l p-Aminobenzoic acid 4.9456e-05 g/l (DL)-alpha-Lipoic acid 4.9456e-05 g/l Calcium D-(+)-pantothenate 4.9456e-05 g/l Nicotinic acid 4.9456e-05 g/l Riboflavin 4.9456e-05 g/l Thiamine HCl 4.9456e-05 g/l Folic acid 1.97824e-05 g/l Biotin 1.97824e-05 g/l Na2WO4 x 2 H2O 3.95648e-06 g/l Na2SeO3 x 5 H2O 2.96736e-06 g/l Vitamin B12 9.8912e-07 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
43161positiveoptimum30mesophilic
43161positivegrowth20-35
24413positivegrowth30mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
43161positivegrowth4.5-8.5alkaliphile
43161positiveoptimum6.0-7.0

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43161facultative anaerobe
43161microaerophile

nutrition type

@reftype
43161chemoautotroph
43161chemoheterotroph
43161chemoorganoheterotroph
43161chemolithoheterotroph

spore formation

@reftype of sporespore formationconfidence
43161sporeno
69481no100
69480no99.996

halophily

@refsaltgrowthtested relationconcentration
43161NaClpositivegrowth5-45 g/L
43161NaClpositiveoptimum15-20 g/L

observation

  • @ref: 67770
  • observation: quinones: Q-9, Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4316116094thiosulfate+electron donor
4316133403elemental sulfur+electron donor
4316116526carbon dioxide+carbon source
4316117632nitrate+electron acceptor
4316115379dioxygen+electron acceptor
4316129034ferric iron+electron acceptor
4316124996lactate+carbon source
43161peptone+carbon source
43161tryptone+carbon source
43161casamino acids+carbon source
43161yeast extract+carbon source
4316116947citrate+carbon source
4316115361pyruvate+carbon source
4316118050L-glutamine+carbon source

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.
4316128971ampicillinyesyes100000 µg/mL
4316117698chloramphenicolyesyes100000 µg/mL
431616104kanamycinyesyes100000 µg/mL
4316117076streptomycinyesyes100000 µg/mL

enzymes

  • @ref: 43161
  • value: catalase
  • activity: -
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudesampling date
24413sediment from a submarine coastal gas ventTyrrhenian Sea, Tor CaldaraItalyITAEurope41.485812.5897
43161surface sediment of an active shallow-water gas ventTor Caldara in the Tyrrhenian Sea, ItalyItalyITAEurope41122013-08
67770Sulfidic shallow-water marine gas vent located at Tor Caldara in the Tyrrhenian SeaItalyITAEurope

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Coast

taxonmaps

  • @ref: 69479
  • File name: preview.99_131186.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_430;96_51027;97_65734;98_87770;99_131186&stattab=map
  • Last taxonomy: Varunaivibrio sulfuroxidans subclade
  • 16S sequence: KU294728
  • Sequence Identity:
  • Total samples: 133
  • soil counts: 11
  • aquatic counts: 108
  • animal counts: 10
  • plant counts: 4

Safety information

risk assessment

  • @ref: 24413
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24413
  • description: Varunaivibrio sulfuroxidans strain TC8 16S ribosomal RNA gene, partial sequence
  • accession: KU294728
  • length: 1360
  • database: ena
  • NCBI tax ID: 1773489

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Varunaivibrio sulfuroxidans strain DSM 1016881773489.15wgspatric1773489
66792Varunaivibrio sulfuroxidans DSM 1016882784746782draftimg1773489
67770Varunaivibrio sulfuroxidans DSM 101688GCA_004341725contigncbi1773489

GC content

  • @ref: 24413
  • GC-content: 59.9
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes92.667yes
gram-positiveno99.207no
anaerobicno93.336yes
aerobicno88.051yes
halophileno68.735no
spore-formingno93.528yes
thermophileyes60.562no
glucose-utilyes61.615no
flagellatedyes60.628no
glucose-fermentno89.664no

External links

@ref: 24413

culture collection no.: DSM 101688, JCM 31027, TC 8

straininfo link

  • @ref: 90938
  • straininfo: 405343

literature

  • topic: Phylogeny
  • Pubmed-ID: 27298285
  • title: Varunaivibrio sulfuroxidans gen. nov., sp. nov., a facultatively chemolithoautotrophic, mesophilic alphaproteobacterium from a shallow-water gas vent at Tor Caldara, Tyrrhenian Sea.
  • authors: Patwardhan S, Vetriani C
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001235
  • year: 2016
  • mesh: Alphaproteobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Chemoautotrophic Growth, DNA, Bacterial/genetics, Hydrothermal Vents/*microbiology, Italy, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
24413Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-101688Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 101688)
43161Sushmita Patwardhan and Costantino VetrianiVarunaivibrio sulfuroxidans gen. nov., sp. nov., a facultatively chemolithoautotrophic, mesophilic alphaproteobacterium from a shallow-water gas vent at Tor Caldara, Tyrrhenian Sea10.1099/ijsem.0.001235IJSEM 66: 3579-3584 201627298285
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69479João 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 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
90938Reimer, 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 identifiers10.60712/SI-ID405343.1