Strain identifier
BacDive ID: 16871
Type strain: 
Species: Thermococcus pacificus
Strain Designation: P-4
Strain history: DSM 10394 <-- E. A. Bonch-Osmolovskaya P-4.
NCBI tax ID(s): 71998 (species)
version 9.3 (current version)
General
@ref: 3929
BacDive-ID: 16871
DSM-Number: 10394
keywords: genome sequence, 16S sequence, Archaea, anaerobe, hyperthermophilic
description: Thermococcus pacificus P-4 is an anaerobe, hyperthermophilic archaeon that was isolated from bottom deposits.
NCBI tax id
- NCBI tax id: 71998
- Matching level: species
strain history
| @ref | history |
|---|---|
| 3929 | <- E. A. Bonch-Osmolovskaya, P-4 |
| 67770 | DSM 10394 <-- E. A. Bonch-Osmolovskaya P-4. |
doi: 10.13145/bacdive16871.20250331.9.3
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 pacificus
- full scientific name: Thermococcus pacificus Miroshnichenko et al. 1998
@ref: 3929
domain: Archaea
phylum: Euryarchaeota
class: Thermococci
order: Thermococcales
family: Thermococcaceae
genus: Thermococcus
species: Thermococcus pacificus
full scientific name: Thermococcus pacificus Miroshnichenko et al. 1998
strain designation: P-4
type strain: yes
Morphology
cell morphology
- @ref: 125439
- gram stain: negative
- confidence: 94
Culture and growth conditions
culture medium
- @ref: 3929
- 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 |
|---|---|---|---|
| 3929 | positive | growth | 85 |
| 67770 | positive | growth | 85 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 3929 | anaerobe | |
| 125439 | anaerobe | 99.8 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 125439 | no | 91.3 |
| 125438 | no | 92.604 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 3929 | bottom deposits | Bay of Plenty | New Zealand | NZL | Australia and Oceania |
| 67770 | Geothermally heated bottom deposits of the Bay of Plenty | New Zealand | NZL | Australia and Oceania |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
Safety information
risk assessment
- @ref: 3929
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Thermococcus pacificus 16S rRNA gene, strain DSM 10394 Type | AJ291811 | 1314 | nuccore | 71998 |
| 20218 | Thermococcus pacificus strain DSM 10394 16S ribosomal RNA gene, partial sequence | AY099182 | 1436 | nuccore | 71998 |
| 20218 | Thermococcus pacificus strain DSM 10394 16S-23S ribosomal RNA intergenic spacer region, complete sequence | AY099218 | 181 | nuccore | 71998 |
| 20218 | Thermococcus pacificus gene for 16S rRNA, partial sequence, strain:JCM 10553 | AB055124 | 1421 | nuccore | 71998 |
| 3929 | Thermococcus pacificus 16S rRNA gene | Y16227 | 1335 | nuccore | 71998 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Thermococcus pacificus P-4 | GCA_002214485 | complete | ncbi | 71998 |
| 66792 | Thermococcus pacificus P-4 | 2758568025 | complete | img | 71998 |
GC content
- @ref: 67770
- GC-content: 53.3
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 67.385 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 87.13 | yes |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 87.162 | yes |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 92.604 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | yes | 78.232 | no |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 80.958 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 91.3 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | no | 66.8 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 94 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | anaerobe | 99.8 |
External links
@ref: 3929
culture collection no.: DSM 10394, ATCC 700653, JCM 10553
straininfo link
- @ref: 85879
- straininfo: 44059
literature
- topic: Phylogeny
- Pubmed-ID: 9542072
- title: Thermococcus gorgonarius sp. nov. and Thermococcus pacificus sp. nov.: heterotrophic extremely thermophilic archaea from New Zealand submarine hot vents.
- authors: Miroshnichenko ML, Gongadze GM, Rainey FA, Kostyukova AS, Lysenko AM, Chernyh NA, Bonch-Osmolovskaya EA
- journal: Int J Syst Bacteriol
- DOI: 10.1099/00207713-48-1-23
- year: 1998
- mesh: Cell Membrane/chemistry, DNA, Archaeal/analysis, Hot Temperature, Microscopy, Electron, Molecular Sequence Data, New Zealand, RNA, Archaeal/analysis, RNA, Ribosomal, 16S/analysis, Seawater/*microbiology, Thermococcus/*classification/genetics/ultrastructure
- topic2: Stress
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 3929 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10394) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-10394 | |||
| 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) | |||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 85879 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID44059.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |