Strain identifier
BacDive ID: 4201
Type strain: 
Species: Staphylothermus marinus
Strain Designation: F1
Strain history: DSM 3639 <-- K. O. Stetter and G. Fiala F1.
NCBI tax ID(s): 399550 (strain), 2280 (species)
version 8.1 (current version)
General
@ref: 1429
BacDive-ID: 4201
DSM-Number: 3639
keywords: genome sequence, 16S sequence, Archaea, anaerobe, hyperthermophilic
description: Staphylothermus marinus F1 is an anaerobe, hyperthermophilic archaeon that was isolated from geothermally heated marine sediment.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 399550 | strain |
| 2280 | species |
strain history
| @ref | history |
|---|---|
| 1429 | <- K.O. Stetter and G. Fiala, F1 |
| 67770 | DSM 3639 <-- K. O. Stetter and G. Fiala F1. |
doi: 10.13145/bacdive4201.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/thermoproteota
- domain: Archaea
- phylum: Thermoproteota
- class: Thermoprotei
- order: Desulfurococcales
- family: Desulfurococcaceae
- genus: Staphylothermus
- species: Staphylothermus marinus
- full scientific name: Staphylothermus marinus Stetter and Fiala 1986
@ref: 1429
domain: Archaea
phylum: Crenarchaeota
class: Thermoprotei
order: Desulfurococcales
family: Desulfurococcaceae
genus: Staphylothermus
species: Staphylothermus marinus
full scientific name: Staphylothermus marinus Stetter and Fiala 1986
strain designation: F1
type strain: yes
Culture and growth conditions
culture medium
- @ref: 1429
- name: PYROCOCCUS MEDIUM (DSMZ Medium 377)
- growth: yes
- link: https://mediadive.dsmz.de/medium/377
- composition: Name: PYROCOCCUS MEDIUM (DSMZ Medium 377) Composition: Sulfur 30.0 g/l Peptone 5.0 g/l MgCl2 x 6 H2O 2.75 g/l Yeast extract 1.0 g/l KH2PO4 0.5 g/l Na2S x 9 H2O 0.5 g/l KCl 0.33 g/l NaBr 0.05 g/l MgSO4 x 7 H2O 0.03 g/l Nitrilotriacetic acid 0.015 g/l NaCl 0.01 g/l (NH4)2SO4 0.01 g/l SrCl2 x 6 H2O 0.007 g/l Citric acid 0.005 g/l MnSO4 x H2O 0.005 g/l CoSO4 x 7 H2O 0.0018 g/l ZnSO4 x 7 H2O 0.0018 g/l CaCl2 x 2 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Sodium resazurin 0.0005 g/l NiCl2 x 6 H2O 0.0003 g/l AlK(SO4)2 x 12 H2O 0.0002 g/l CuSO4 x 5 H2O 0.0001 g/l Na2MoO4 x 2 H2O 0.0001 g/l H3BO3 0.0001 g/l KI 5e-05 g/l Na2WO4 x 2 H2O 4e-06 g/l Na2SeO3 x 5 H2O 3e-06 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 1429 | positive | growth | 88 | hyperthermophilic |
| 67770 | positive | growth | 90 | hyperthermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 1429
- oxygen tolerance: anaerobe
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 1429 | geothermally heated marine sediment | Vulcano island | Italy | ITA | Europe |
| 67770 | Geothermally heated sea floor at Vulcano | Italy | ITA | Europe |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Aquatic | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_188783.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17883;96_69637;97_90438;98_122924;99_188783&stattab=map
- Last taxonomy: Staphylothermus marinus subclade
- 16S sequence: X99560
- Sequence Identity:
- Total samples: 1
- aquatic counts: 1
Safety information
risk assessment
- @ref: 1429
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20218
- description: S.marinus 16S rRNA gene
- accession: X99560
- length: 1442
- database: ena
- NCBI tax ID: 399550
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Staphylothermus marinus F1 | GCA_000015945 | complete | ncbi | 399550 |
| 66792 | Staphylothermus marinus F1, DSM 3639 | 640069332 | complete | img | 399550 |
| 66792 | Staphylothermus marinus F1 | 399550.11 | complete | patric | 399550 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 1429 | 35.0 | |
| 67770 | 35.3 | high performance liquid chromatography (HPLC) |
| 67770 | 34.9 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 60.288 | no |
| flagellated | no | 91.932 | no |
| gram-positive | no | 94.171 | no |
| anaerobic | yes | 98.754 | no |
| halophile | no | 77.317 | no |
| spore-forming | no | 97.644 | no |
| thermophile | yes | 100 | no |
| glucose-util | yes | 84.362 | no |
| aerobic | no | 96.179 | no |
| glucose-ferment | no | 54.985 | no |
External links
@ref: 1429
culture collection no.: DSM 3639, JCM 9404, ATCC 43588
straininfo link
- @ref: 73701
- straininfo: 47743
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 1429 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3639) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-3639 | |||
| 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) | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 69479 | João 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 73701 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID47743.1 | StrainInfo: A central database for resolving microbial strain identifiers |