Strain identifier

BacDive ID: 16885

Type strain: Yes

Species: Thermococcus gammatolerans

Strain Designation: EJ3

Strain history: E. Jolivet EJ3.

NCBI tax ID(s): 187878 (species)

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General

@ref: 5769

BacDive-ID: 16885

DSM-Number: 15229

keywords: genome sequence, 16S sequence, Archaea, anaerobe, hyperthermophilic

description: Thermococcus gammatolerans EJ3 is an anaerobe, hyperthermophilic archaeon that was isolated from hydrothermal chimney sample.

NCBI tax id

  • NCBI tax id: 187878
  • Matching level: species

strain history

@refhistory
5769<- E. Jolivet; EJ3
67770E. Jolivet EJ3.

doi: 10.13145/bacdive16885.20230509.8.1

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 gammatolerans
  • full scientific name: Thermococcus gammatolerans Jolivet et al. 2003

@ref: 5769

domain: Archaea

phylum: Euryarchaeota

class: Thermococci

order: Thermococcales

family: Thermococcaceae

genus: Thermococcus

species: Thermococcus gammatolerans

full scientific name: Thermococcus gammatolerans Jolivet et al. 2003

strain designation: EJ3

type strain: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5769MARINE 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
5769YPS MEDIUM (DSMZ Medium 990)yeshttps://mediadive.dsmz.de/medium/990Name: YPS MEDIUM (DSMZ Medium 990) Composition: Sea Salt 35.0 g/l Elemental sulphur 5.0 g/l Peptone 4.0 g/l PIPES 3.46 g/l Yeast extract 1.0 g/l NH4Cl 0.5 g/l KH2PO4 0.35 g/l Na2S x 9 H2O 0.25 g/l CaCl2 0.2 g/l FeCl3 0.0067 g/l Na2WO4 0.0029 g/l Resazurin 0.0001 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
5769positivegrowth88hyperthermophilic
67770positivegrowth85hyperthermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 5769
  • oxygen tolerance: anaerobe

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationlatitudelongitude
5769hydrothermal chimney sampleGuaymas Basin, 27°01'N and 111°24'W at a depth of 2,616m27.0167-111.4
67770Chimney from a hydrothermal site in Guaymas Basin

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Hydrothermal vent
#Condition#Thermophilic (>45°C)

Safety information

risk assessment

  • @ref: 5769
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 5769
  • description: Thermococcus gammatolerans 16S ribosomal RNA gene, partial sequence
  • accession: AF479014
  • length: 1370
  • database: ena
  • NCBI tax ID: 593117

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Thermococcus gammatolerans EJ3 EJ3; DSM 15229GCA_000022365completencbi593117
66792Thermococcus gammatolerans EJ3644736411completeimg593117
66792Thermococcus gammatolerans EJ3593117.10completepatric593117

GC content

@refGC-contentmethod
576951.3
6777051.3thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno81.261no
flagellatedno96.07no
gram-positiveno95.986no
anaerobicyes98.948yes
aerobicno97.145yes
halophileno68.79no
spore-formingno96.596no
thermophileyes100yes
glucose-utilyes75.373no
glucose-fermentno61.36no

External links

@ref: 5769

culture collection no.: DSM 15229, JCM 11827

straininfo link

  • @ref: 85891
  • straininfo: 101006

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12807211Thermococcus gammatolerans sp. nov., a hyperthermophilic archaeon from a deep-sea hydrothermal vent that resists ionizing radiation.Jolivet E, L'Haridon S, Corre E, Forterre P, Prieur DInt J Syst Evol Microbiol10.1099/ijs.0.02503-02003Culture Media, DNA, Archaeal/analysis, DNA, Ribosomal/analysis, Dose-Response Relationship, Radiation, *Gamma Rays, *Hot Temperature, Molecular Sequence Data, Phenotype, RNA, Ribosomal, 16S/genetics, *Radiation Tolerance, Seawater/*microbiology, Sequence Analysis, DNA, Thermococcus/*classification/genetics/growth & development/isolation & purification/*radiation effectsCultivation
Phylogeny24556637Thermococcus nautili sp. nov., a hyperthermophilic archaeon isolated from a hydrothermal deep-sea vent.Gorlas A, Croce O, Oberto J, Gauliard E, Forterre P, Marguet EInt J Syst Evol Microbiol10.1099/ijs.0.060376-02014Base Composition, DNA, Archaeal/genetics, Hydrothermal Vents/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Pacific Ocean, *Phylogeny, Plasmids/genetics, RNA, Ribosomal, 16S/genetics, Thermococcus/*classification/genetics/isolation & purificationGenetics

Reference

@idauthorscataloguedoi/urltitle
5769Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15229)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15229
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
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/
85891Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID101006.1StrainInfo: A central database for resolving microbial strain identifiers