Strain identifier
BacDive ID: 13526
Type strain: 
Species: Pyrodictium occultum
Strain Designation: PL-19
Strain history: DSM 2709 <-- K. O. Stetter PL-19.
NCBI tax ID(s): 2309 (species)
version 8.1 (current version)
General
@ref: 1209
BacDive-ID: 13526
DSM-Number: 2709
keywords: genome sequence, 16S sequence, Archaea, anaerobe, hyperthermophilic
description: Pyrodictium occultum PL-19 is an anaerobe, hyperthermophilic archaeon that was isolated from submarine solfataric field.
NCBI tax id
- NCBI tax id: 2309
- Matching level: species
strain history
| @ref | history |
|---|---|
| 1209 | <- K.O. Stetter, PL-19 |
| 67770 | DSM 2709 <-- K. O. Stetter PL-19. |
doi: 10.13145/bacdive13526.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/thermoproteota
- domain: Archaea
- phylum: Thermoproteota
- class: Thermoprotei
- order: Desulfurococcales
- family: Pyrodictiaceae
- genus: Pyrodictium
- species: Pyrodictium occultum
- full scientific name: Pyrodictium occultum Stetter et al. 1984
@ref: 1209
domain: Archaea
phylum: Crenarchaeota
class: Thermoprotei
order: Desulfurococcales
family: Pyrodictiaceae
genus: Pyrodictium
species: Pyrodictium occultum
full scientific name: Pyrodictium occultum Stetter et al. 1984
strain designation: PL-19
type strain: yes
Culture and growth conditions
culture medium
- @ref: 1209
- name: PYRODICTIUM MEDIUM (DSMZ Medium 283)
- growth: yes
- link: https://mediadive.dsmz.de/medium/283
- composition: Name: PYRODICTIUM MEDIUM (DSMZ Medium 283; with strain-specific modifications) Composition: Sulfur 29.2683 g/l MgCl2 x 6 H2O 2.68293 g/l Na2S x 9 H2O 0.487805 g/l KH2PO4 0.487805 g/l KCl 0.321951 g/l Yeast extract 0.195122 g/l NaBr 0.0487805 g/l MgSO4 x 7 H2O 0.0292683 g/l Nitrilotriacetic acid 0.0146341 g/l (NH4)2SO4 0.0097561 g/l NaCl 0.0097561 g/l SrCl2 x 6 H2O 0.00682927 g/l MnSO4 x H2O 0.00487805 g/l Citric acid 0.00487805 g/l CoSO4 x 7 H2O 0.0017561 g/l ZnSO4 x 7 H2O 0.0017561 g/l FeSO4 x 7 H2O 0.00097561 g/l CaCl2 x 2 H2O 0.00097561 g/l Sodium resazurin 0.000487805 g/l NiCl2 x 6 H2O 0.000292683 g/l AlK(SO4)2 x 12 H2O 0.000195122 g/l H3BO3 9.7561e-05 g/l Na2MoO4 x 2 H2O 9.7561e-05 g/l CuSO4 x 5 H2O 9.7561e-05 g/l KI 4.87805e-05 g/l Na2WO4 x 2 H2O 3.90244e-06 g/l Na2SeO3 x 5 H2O 2.92683e-06 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 1209 | positive | growth | 97 | hyperthermophilic |
| 67770 | positive | growth | 95 | hyperthermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 1209
- oxygen tolerance: anaerobe
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 1209 | submarine solfataric field | Vulcano island, Porto di Levante | Italy | ITA | Europe |
| 67770 | Submarine solfataric field off Vulcano | Italy | ITA | Europe |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Condition | #Sulfuric |
taxonmaps
- @ref: 69479
- File name: preview.99_187295.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_18189;96_68916;97_89566;98_121857;99_187295&stattab=map
- Last taxonomy: Pyrodictium occultum
- 16S sequence: M21087
- Sequence Identity:
- Total samples: 44
- aquatic counts: 44
Safety information
risk assessment
- @ref: 1209
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 1209
- description: Pyrodictium occultum 16S ribosomal RNA gene
- accession: M21087
- length: 1497
- database: ena
- NCBI tax ID: 2309
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 67770 | Pyrodictium occultum PL-19 | GCA_001462395 | contig | ncbi | 2309 |
| 66792 | Pyrodictium occultum strain PL-19 | 2309.8 | wgs | patric | 2309 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 1209 | 61.3 | |
| 67770 | 62.2 | high performance liquid chromatography (HPLC) |
| 67770 | 61.3 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 70.159 | no |
| gram-positive | no | 96.825 | no |
| anaerobic | yes | 98.783 | no |
| aerobic | no | 95.776 | yes |
| halophile | no | 79.392 | no |
| spore-forming | no | 96.331 | no |
| glucose-util | yes | 75.739 | no |
| flagellated | no | 93.277 | no |
| thermophile | yes | 100 | yes |
| glucose-ferment | no | 65.993 | no |
External links
@ref: 1209
culture collection no.: DSM 2709, JCM 9393, NBRC 100438
straininfo link
- @ref: 82717
- straininfo: 47660
literature
- topic: Phylogeny
- Pubmed-ID: 27260263
- title: Pyrodictium delaneyi sp. nov., a hyperthermophilic autotrophic archaeon that reduces Fe(III) oxide and nitrate.
- authors: Lin TJ, El Sebae G, Jung JH, Jung DH, Park CS, Holden JF
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.001201
- year: 2016
- mesh: Base Composition, DNA, Archaeal/genetics, Ferric Compounds/*metabolism, Ferrosoferric Oxide/metabolism, Hydrothermal Vents/*microbiology, Iron/metabolism, Nitrates/metabolism, Pacific Ocean, *Phylogeny, Pyrodictiaceae/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA
- topic2: Metabolism
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 1209 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2709) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-2709 | |||
| 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/ | ||||
| 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 | |||
| 82717 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID47660.1 | StrainInfo: A central database for resolving microbial strain identifiers |