Strain identifier
BacDive ID: 16873
Type strain: 
Species: Thermococcus siculi
Strain Designation: RG-20
Strain history: <- G. Antranikian, Techn. Univ. Hamburg-Harburg; RG-20
NCBI tax ID(s): 72803 (species)
version 8.1 (current version)
General
@ref: 4708
BacDive-ID: 16873
DSM-Number: 12349
keywords: genome sequence, 16S sequence, Archaea, anaerobe, hyperthermophilic, Gram-negative
description: Thermococcus siculi RG-20 is an anaerobe, hyperthermophilic, Gram-negative archaeon that was isolated from deep-sea thermal vent.
NCBI tax id
- NCBI tax id: 72803
- Matching level: species
strain history
- @ref: 4708
- history: <- G. Antranikian, Techn. Univ. Hamburg-Harburg; RG-20
doi: 10.13145/bacdive16873.20230509.8.1
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 siculi
- full scientific name: Thermococcus siculi Grote et al. 2000
@ref: 4708
domain: Archaea
phylum: Euryarchaeota
class: Thermococci
order: Thermococcales
family: Thermococcaceae
genus: Thermococcus
species: Thermococcus siculi
full scientific name: Thermococcus siculi Grote et al. 2000
strain designation: RG-20
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.806
Culture and growth conditions
culture medium
- @ref: 4708
- name: MARINE THERMOCOCCUS MEDIUM (DSMZ Medium 760)
- growth: yes
- link: https://mediadive.dsmz.de/medium/760
- composition: Name: 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
culture temp
| @ref | growth | type | temperature | range | confidence |
|---|---|---|---|---|---|
| 4708 | positive | growth | 85 | hyperthermophilic | |
| 69480 | thermophilic | 99.999 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 4708 | anaerobe | |
| 69480 | anaerobe | 98.709 |
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.176
Isolation, sampling and environmental information
isolation
- @ref: 4708
- sample type: deep-sea thermal vent
- geographic location: Mid-Okinawa Trough, southwest Pacific Ocean
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Hydrothermal vent |
| #Environmental | #Aquatic | #Marine |
| #Condition | #Thermophilic (>45°C) |
Safety information
risk assessment
- @ref: 4708
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Thermococcus siculi gene for 16S rRNA, partial sequence, strain:DSM 12349 | AB055126 | 1422 | ena | 72803 |
| 20218 | Thermococcus siculi 16S rRNA gene, strain DSM 12349 Type | AJ291808 | 1326 | ena | 72803 |
| 20218 | Thermococcus siculi strain DSM 12349 16S ribosomal RNA gene, partial sequence | AY099185 | 1442 | ena | 72803 |
| 20218 | Thermococcus siculi strain DSM 12349 16S-23S ribosomal RNA intergenic spacer region, complete sequence | AY099221 | 181 | ena | 72803 |
| 4708 | Thermococcus siculi gene for 16S rRNA | AB010893 | 897 | ena | 72803 |
| 4708 | Thermococcus siculi partial 16S rRNA gene, strain DSM 12349 | AJ298870 | 1326 | ena | 72803 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Thermococcus siculi RG-20 | GCA_002214505 | complete | ncbi | 72803 |
| 66792 | Thermococcus siculi RG-20 | 2758568024 | complete | img | 72803 |
GC content
- @ref: 4708
- GC-content: 55.8±0.1
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 88 | no |
| flagellated | no | 96.066 | no |
| gram-positive | no | 95.681 | no |
| anaerobic | yes | 98.682 | yes |
| aerobic | no | 97.637 | yes |
| halophile | no | 77.187 | no |
| spore-forming | no | 97.558 | no |
| glucose-util | yes | 78.03 | no |
| thermophile | yes | 100 | yes |
| motile | no | 78.319 | no |
| glucose-ferment | no | 58.396 | no |
External links
@ref: 4708
culture collection no.: DSM 12349, ATCC BAA 270
straininfo link
- @ref: 85881
- straininfo: 44341
literature
- topic: Phylogeny
- Pubmed-ID: 10086845
- title: Thermococcus siculi sp. nov., a novel hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent at the Mid-Okinawa Trough.
- authors: Grote R, Li L, Tamaoka J, Kato C, Horikoshi K, Antranikian G
- journal: Extremophiles
- DOI: 10.1007/s007920050099
- year: 1999
- mesh: DNA, Archaeal, DNA, Ribosomal/genetics, Hot Temperature, Hydrogen-Ion Concentration, Lipids/chemistry, Microbial Sensitivity Tests, Microscopy, Electron, Phylogeny, RNA, Ribosomal, 16S/genetics, Salts, Thermococcus/chemistry/genetics/growth & development/*isolation & purification, Water Microbiology
- topic2: Stress
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 4708 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12349) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-12349 | |||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 85881 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID44341.1 | StrainInfo: A central database for resolving microbial strain identifiers |