Strain identifier
BacDive ID: 17024
Type strain: 
Species: Pyrobaculum islandicum
Strain Designation: GEO3
Strain history: DSM 4184 <-- K. O. Stetter and G. Huber GEO3.
NCBI tax ID(s): 384616 (strain), 2277 (species)
version 8.1 (current version)
General
@ref: 1610
BacDive-ID: 17024
DSM-Number: 4184
keywords: genome sequence, 16S sequence, Archaea, anaerobe, spore-forming, hyperthermophilic, Gram-negative
description: Pyrobaculum islandicum GEO3 is an anaerobe, spore-forming, hyperthermophilic archaeon that was isolated from water, geothermal power plant.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 2277 | species |
| 384616 | strain |
strain history
| @ref | history |
|---|---|
| 1610 | <- K. O. Stetter, Univ. Regensburg, Germany; GEO3 <- R. Huber {1984} |
| 67770 | DSM 4184 <-- K. O. Stetter and G. Huber GEO3. |
doi: 10.13145/bacdive17024.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/thermoproteota
- domain: Archaea
- phylum: Thermoproteota
- class: Thermoprotei
- order: Thermoproteales
- family: Thermoproteaceae
- genus: Pyrobaculum
- species: Pyrobaculum islandicum
- full scientific name: Pyrobaculum islandicum Huber et al. 1988
@ref: 1610
domain: Archaea
phylum: Crenarchaeota
class: Thermoprotei
order: Thermoproteales
family: Thermoproteaceae
genus: Pyrobaculum
species: Pyrobaculum islandicum
full scientific name: Pyrobaculum islandicum Huber et al. 1988
strain designation: GEO3
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.876
Culture and growth conditions
culture medium
- @ref: 1610
- name: PYROBACULUM MEDIUM (DSMZ Medium 390)
- growth: yes
- link: https://mediadive.dsmz.de/medium/390
- composition: Name: PYROBACULUM MEDIUM (DSMZ Medium 390) Composition: Na2S2O3 x 5 H2O 1.9802 g/l (NH4)2SO4 1.28713 g/l Trypticase peptone 0.49505 g/l Na2S x 9 H2O 0.49505 g/l KH2PO4 0.277228 g/l MgSO4 x 7 H2O 0.247525 g/l Yeast extract 0.19802 g/l CaCl2 x 2 H2O 0.0693069 g/l FeCl3 x 6 H2O 0.019802 g/l Na2B4O7 x 10 H2O 0.00445545 g/l MnCl2 x 4 H2O 0.00178218 g/l Sodium resazurin 0.00049505 g/l ZnSO4 x 7 H2O 0.000217822 g/l CuCl2 x 2 H2O 4.95049e-05 g/l Na2MoO4 x 2 H2O 2.9703e-05 g/l VOSO4 x 2 H2O 2.9703e-05 g/l CoSO4 x 7 H2O 9.90099e-06 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range | confidence |
|---|---|---|---|---|---|
| 1610 | positive | growth | 95 | hyperthermophilic | |
| 67770 | positive | growth | 95 | hyperthermophilic | |
| 69480 | thermophilic | 99.999 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 1610 | anaerobe | |
| 69480 | anaerobe | 99.998 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 100 |
| 69480 | no | 99.978 |
observation
- @ref: 67770
- observation: quinones: MK-6(H12)
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 1610 | water, geothermal power plant | Krafla | Iceland | ISL | Europe |
| 67770 | Hot water from the Krafla geothermal power plant | Iceland | ISL | Europe |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Industrial | #Plant (Factory) |
| #Environmental | #Aquatic |
Safety information
risk assessment
- @ref: 1610
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 67770
- description: Pyrobaculum islandicum 16S ribosomal RNA gene
- accession: L07511
- length: 1474
- database: ena
- NCBI tax ID: 2277
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Pyrobaculum islandicum DSM 4184 | GCA_000015205 | complete | ncbi | 384616 |
| 66792 | Pyrobaculum islandicum DSM 4184 | 639633053 | complete | img | 384616 |
| 66792 | Pyrobaculum islandicum DSM 4184 | 384616.10 | complete | patric | 384616 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 1610 | 47.0 | |
| 1610 | 45.0 | |
| 67770 | 45 | thermal denaturation, midpoint method (Tm) |
| 67770 | 47 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| motile | no | 73.277 | no |
| flagellated | no | 95.374 | no |
| gram-positive | no | 96.779 | no |
| anaerobic | yes | 99.498 | yes |
| halophile | no | 84.145 | no |
| spore-forming | no | 96.599 | no |
| thermophile | yes | 100 | yes |
| glucose-util | yes | 70.916 | no |
| aerobic | no | 96.777 | no |
| glucose-ferment | no | 72.778 | no |
External links
@ref: 1610
culture collection no.: DSM 4184, JCM 9189
straininfo link
- @ref: 86025
- straininfo: 47807
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Enzymology | 11823469 | Dye-linked D-proline dehydrogenase from hyperthermophilic archaeon Pyrobaculum islandicum is a novel FAD-dependent amino acid dehydrogenase. | Satomura T, Kawakami R, Sakuraba H, Ohshima T | J Biol Chem | 10.1074/jbc.M112272200 | 2002 | Amino Acid Sequence, Base Sequence, Chromatography, Ion Exchange, Coloring Agents/*chemistry, DNA Probes, Electrophoresis, Polyacrylamide Gel, Enzyme Stability, Molecular Sequence Data, Proline Oxidase/chemistry/isolation & purification/*metabolism, Sequence Homology, Amino Acid, Thermoproteaceae/*enzymology | Genetics |
| Phylogeny | 24346234 | Quartet analysis of putative horizontal gene transfer in Crenarchaeota. | Ching TH, Yoza BA, Li QX | J Mol Evol | 10.1007/s00239-013-9607-7 | 2013 | Computational Biology, Crenarchaeota/classification/*genetics, Ferredoxins/genetics, *Gene Transfer, Horizontal, Phylogeny, RNA, Ribosomal/genetics, RNA, Ribosomal, 16S/genetics |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 1610 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4184) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-4184 | |||
| 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 | |||
| 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/ | ||||
| 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) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 86025 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID47807.1 | StrainInfo: A central database for resolving microbial strain identifiers |