Strain identifier
BacDive ID: 4189
Type strain: 
Species: Ignicoccus islandicus
Strain history: <- H. Huber and K. O. Stetter, Univ. Regensburg, Germany; Kol8 <- K. O. Stetter {1989}
NCBI tax ID(s): 940295 (strain), 54259 (species)
version 8.1 (current version)
General
@ref: 4955
BacDive-ID: 4189
DSM-Number: 13165
keywords: genome sequence, 16S sequence, Archaea, anaerobe, chemolithoautotroph, spore-forming, hyperthermophilic, Gram-negative, motile, coccus-shaped
description: Ignicoccus islandicus DSM 13165 is an anaerobe, chemolithoautotroph, spore-forming archaeon that was isolated from sandy sediments.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 940295 | strain |
| 54259 | species |
strain history
- @ref: 4955
- history: <- H. Huber and K. O. Stetter, Univ. Regensburg, Germany; Kol8 <- K. O. Stetter {1989}
doi: 10.13145/bacdive4189.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/thermoproteota
- domain: Archaea
- phylum: Thermoproteota
- class: Thermoprotei
- order: Desulfurococcales
- family: Desulfurococcaceae
- genus: Ignicoccus
- species: Ignicoccus islandicus
- full scientific name: Ignicoccus islandicus Huber et al. 2000
@ref: 4955
domain: Archaea
phylum: Crenarchaeota
class: Thermoprotei
order: Desulfurococcales
family: Desulfurococcaceae
genus: Ignicoccus
species: Ignicoccus islandicus
full scientific name: Ignicoccus islandicus Huber et al. 2000
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell shape | motility | flagellum arrangement | confidence |
|---|---|---|---|---|---|---|
| 23219 | negative | 1.2-3.0 µm | coccus-shaped | yes | polytrichous, monopolar | |
| 69480 | negative | 99.932 |
Culture and growth conditions
culture medium
- @ref: 4955
- name: IGNICOCCUS MEDIUM (DSMZ Medium 897)
- growth: yes
- link: https://mediadive.dsmz.de/medium/897
- composition: Name: IGNICOCCUS MEDIUM (DSMZ Medium 897) Composition: NaCl 13.5417 g/l Sulfur 4.96032 g/l MgSO4 x 7 H2O 3.47222 g/l MgCl2 x 6 H2O 2.72817 g/l Meat extract 0.992063 g/l KH2PO4 0.496032 g/l CaCl2 x 2 H2O 0.376984 g/l KCl 0.327381 g/l (NH4)2SO4 0.248016 g/l Na2S x 9 H2O 0.198413 g/l NaBr 0.0496032 g/l H3BO3 0.014881 g/l SrCl2 x 6 H2O 0.00694444 g/l Sodium resazurin 0.000496032 g/l KI 4.96032e-05 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range | confidence |
|---|---|---|---|---|---|
| 4955 | positive | growth | 90 | hyperthermophilic | |
| 23219 | positive | growth | 70-98 | hyperthermophilic | |
| 23219 | positive | optimum | 90 | hyperthermophilic | |
| 69480 | thermophilic | 99.735 |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 23219 | positive | growth | 3.8-6.5 | acidophile |
| 23219 | positive | optimum | 5.8 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 4955 | anaerobe | |
| 23219 | anaerobe | |
| 69480 | anaerobe | 98.648 |
nutrition type
- @ref: 23219
- type: chemolithoautotroph
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 100 |
| 69480 | no | 99.943 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 23219 | NaCl | positive | growth | 0.3-5.5 % |
| 23219 | NaCl | positive | optimum | 2 % |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 23219 | 17632 | nitrate | - | electron acceptor |
| 23219 | 16189 | sulfate | - | electron acceptor |
| 23219 | 17359 | sulfite | - | electron acceptor |
| 23219 | 16094 | thiosulfate | - | electron acceptor |
Isolation, sampling and environmental information
isolation
- @ref: 4955
- sample type: sandy sediments
- geographic location: Kolbeinsey Ridge north of Iceland
- country: Iceland
- origin.country: ISL
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Sandy |
| #Environmental | #Terrestrial | #Sediment |
Safety information
risk assessment
- @ref: 4955
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 4955
- description: I.islandicus 16S rRNA gene
- accession: X99562
- length: 1469
- database: ena
- NCBI tax ID: 940295
Genome sequences
- @ref: 66792
- description: Ignicoccus islandicus DSM 13165
- accession: GCA_001481685
- assembly level: complete
- database: ncbi
- NCBI tax ID: 940295
GC content
- @ref: 4955
- GC-content: 41
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| flagellated | no | 90.129 | yes |
| gram-positive | no | 96.539 | yes |
| anaerobic | yes | 98.776 | no |
| aerobic | no | 96.89 | yes |
| halophile | no | 87.663 | no |
| spore-forming | no | 97.252 | no |
| glucose-util | yes | 77.507 | no |
| motile | no | 63.856 | no |
| thermophile | yes | 100 | yes |
| glucose-ferment | no | 57.873 | no |
External links
@ref: 4955
culture collection no.: DSM 13165, ATCC 700957, Kol 8
straininfo link
- @ref: 73689
- straininfo: 49425
literature
- topic: Phylogeny
- Pubmed-ID: 11155984
- title: Ignicoccus gen. nov., a novel genus of hyperthermophilic, chemolithoautotrophic Archaea, represented by two new species, Ignicoccus islandicus sp nov and Ignicoccus pacificus sp nov. and Ignicoccus pacificus sp. nov.
- authors: Huber H, Burggraf S, Mayer T, Wyschkony I, Rachel R, Stetter KO
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/00207713-50-6-2093
- year: 2000
- mesh: Base Composition, Culture Media, DNA, Ribosomal/analysis, Desulfurococcaceae/*classification/genetics/*growth & development, Microscopy, Electron, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sulfur/*metabolism, *Temperature
- topic2: Cultivation
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 4955 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13165) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-13165 | |||
| 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 | |||
| 23219 | H Huber, S Burggraf, T Mayer, I Wyschkony, R Rachel, K O Stetter | 10.1099/00207713-50-6-2093 | Ignicoccus gen. nov., a novel genus of hyperthermophilic, chemolithoautotrophic Archaea, represented by two new species, Ignicoccus islandicus sp nov and Ignicoccus pacificus sp nov. and Ignicoccus pacificus sp. nov. | IJSEM 50: 2093-2100 2000 | 11155984 | |
| 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 | |
| 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 | |||
| 73689 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID49425.1 | StrainInfo: A central database for resolving microbial strain identifiers |