Strain identifier

BacDive ID: 16860

Type strain: Yes

Species: Thermococcus celer

Strain Designation: Vu 13

Strain history: DSM 2476 <-- W. Zillig Vu13.

NCBI tax ID(s): 1293037 (strain), 2264 (species)

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General

@ref: 1089

BacDive-ID: 16860

DSM-Number: 2476

keywords: genome sequence, 16S sequence, Archaea, anaerobe, hyperthermophilic, Gram-negative

description: Thermococcus celer Vu 13 is an anaerobe, hyperthermophilic, Gram-negative archaeon that was isolated from solfataric marine water hole.

NCBI tax id

NCBI tax idMatching level
2264species
1293037strain

strain history

@refhistory
1089<- W. Zillig, Vu 13
67770DSM 2476 <-- W. Zillig Vu13.

doi: 10.13145/bacdive16860.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/archaea
  • keyword: phylum/methanobacteriota
  • domain: Archaea
  • phylum: Methanobacteriota
  • class: Thermococci
  • order: Thermococcales
  • family: Thermococcaceae
  • genus: Thermococcus
  • species: Thermococcus celer
  • full scientific name: Thermococcus celer Zillig 1983

@ref: 1089

domain: Archaea

phylum: Euryarchaeota

class: Thermococci

order: Thermococcales

family: Thermococcaceae

genus: Thermococcus

species: Thermococcus celer

full scientific name: Thermococcus celer Zillig 1983

strain designation: Vu 13

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.922

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1089MARINE THERMOCOCCUS MEDIUM (DSMZ Medium 760)yeshttps://mediadive.dsmz.de/medium/760Name: MARINE THERMOCOCCUS MEDIUM (DSMZ Medium 760) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
1089THERMOCOCCUS CELER MEDIUM (DSMZ Medium 266)yeshttps://mediadive.dsmz.de/medium/266Name: THERMOCOCCUS CELER MEDIUM (DSMZ Medium 266) Composition: NaCl 40.0 g/l Sulfur 5.0 g/l Yeast extract 2.0 g/l (NH4)2SO4 1.3 g/l KH2PO4 0.28 g/l MgSO4 x 7 H2O 0.25 g/l CaCl2 x 2 H2O 0.07 g/l FeCl3 x 6 H2O 0.02 g/l Na2B4O7 x 10 H2O 0.0045 g/l MnCl2 x 4 H2O 0.0018 g/l Resazurin 0.001 g/l ZnSO4 x 7 H2O 0.00022 g/l CuCl2 x 2 H2O 5e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l VOSO4 x 2 H2O 3e-05 g/l CoSO4 x 7 H2O 1e-05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerangeconfidence
1089positivegrowth88hyperthermophilic
67770positivegrowth85hyperthermophilic
69480thermophilic99.999

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
1089anaerobe
69480anaerobe99.464

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.742

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
1089solfataric marine water holeVulcano, Porto LevanteItalyITAEurope
67770Solfataric marine water hole on a beach of VulcanoItalyITAEurope

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Terrestrial#Volcanic

Safety information

risk assessment

  • @ref: 1089
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Thermococcus celer gene for 16S rRNA, partial sequence, strain: JCM 8558AB6035191321ena2264
20218Thermococcus celer strain DSM 2476 16S-23S ribosomal RNA intergenic spacer region, complete sequenceAY099210182ena2264
1089Thermococcus celer strain DSM 2476 16S ribosomal RNA gene, partial sequenceAY0991741433ena1293037
67770T.celer 16S ribosomal RNAM215291486ena2264

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Thermococcus celer Vu 13 = JCM 8558GCA_002214365completencbi1293037
66792Thermococcus celer Vu 13 = JCM 8558GCA_001315845contigncbi1293037
66792Thermococcus celer JCM 85582681813024draftimg1293037
66792Thermococcus celer JCM 85581293037.3wgspatric1293037

GC content

@refGC-contentmethod
108956.6
6777056.9thermal denaturation, midpoint method (Tm)
6777056.3high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes60no
flagellatedno95.901no
gram-positiveno96.911no
anaerobicyes98.867no
aerobicno97.931no
halophileno79.576no
spore-formingno97.005no
glucose-utilyes84.079no
thermophileyes100yes
motileno81.427no
glucose-fermentyes51.303no

External links

@ref: 1089

culture collection no.: DSM 2476, JCM 8558, ATCC 35543

straininfo link

  • @ref: 85868
  • straininfo: 41147

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny8085828Growth requirements of hyperthermophilic sulfur-dependent heterotrophic archaea isolated from a shallow submarine geothermal system with reference to their essential amino acids.Hoaki T, Nishijima M, Kato M, Adachi K, Mizobuchi S, Hanzawa N, Maruyama TAppl Environ Microbiol10.1128/aem.60.8.2898-2904.19941994Amino Acids, Essential/*metabolism, Anaerobiosis, Archaea/genetics/*growth & development/physiology/ultrastructure, Base Composition, Base Sequence, Culture Media, DNA, Ribosomal/analysis, Hot Temperature, Molecular Sequence Data, RNA, Ribosomal, 16S/genetics, Seawater, Sequence Analysis, DNA, *Soil MicrobiologyCultivation
Phylogeny23355695Thermococcus prieurii sp. nov., a hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent.Gorlas A, Alain K, Bienvenu N, Geslin CInt J Syst Evol Microbiol10.1099/ijs.0.026419-02013Base Composition, DNA, Archaeal/genetics, Drug Resistance, Microbial, Hot Temperature, Hydrogen-Ion Concentration, Hydrothermal Vents/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Thermococcus/*classification/genetics/growth & development, Water MicrobiologyStress

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1089Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2476)https://www.dsmz.de/collection/catalogue/details/culture/DSM-2476
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
85868Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID41147.1StrainInfo: A central database for resolving microbial strain identifiers