Strain identifier
BacDive ID: 6984
Type strain: 
Species: Methanocaldococcus fervens
Strain Designation: AG86
Strain history: DSM 4213 <-- H. Zhao and M. P. Bryant AG86.
NCBI tax ID(s): 573064 (strain), 83171 (species)
version 8.1 (current version)
General
@ref: 1616
BacDive-ID: 6984
DSM-Number: 4213
keywords: genome sequence, 16S sequence, Archaea, anaerobe, hyperthermophilic
description: Methanocaldococcus fervens AG86 is an anaerobe, hyperthermophilic archaeon that was isolated from core sample from a deep sea hydrothermal vent.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 573064 | strain |
| 83171 | species |
strain history
| @ref | history |
|---|---|
| 1616 | <- H. Zhao and M.P. Bryant, AG86 |
| 67770 | DSM 4213 <-- H. Zhao and M. P. Bryant AG86. |
doi: 10.13145/bacdive6984.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Methanococci
- order: Methanococcales
- family: Methanocaldococcaceae
- genus: Methanocaldococcus
- species: Methanocaldococcus fervens
- full scientific name: Methanocaldococcus fervens (Jeanthon et al. 1999) Whitman 2002
synonyms
- @ref: 20215
- synonym: Methanococcus fervens
@ref: 1616
domain: Archaea
phylum: Euryarchaeota
class: Methanococci
order: Methanococcales
family: Methanocaldococcaceae
genus: Methanocaldococcus
species: Methanocaldococcus fervens
full scientific name: Methanocaldococcus fervens (Jeanthon et al. 1999) Whitman 2002
strain designation: AG86
type strain: yes
Culture and growth conditions
culture medium
- @ref: 1616
- name: METHANOCALDOCOCCUS MEDIUM (DSMZ Medium 282)
- growth: yes
- link: https://mediadive.dsmz.de/medium/282
- composition: Name: METHANOCALDOCOCCUS MEDIUM (DSMZ Medium 282) Composition: MgCl2 x 6 H2O 4.05138 g/l NaHCO3 0.988142 g/l Na2S x 9 H2O 0.494071 g/l L-Cysteine HCl x H2O 0.494071 g/l KCl 0.326087 g/l NH4Cl 0.247036 g/l K2HPO4 0.13834 g/l MgSO4 x 7 H2O 0.0296443 g/l Nitrilotriacetic acid 0.0148221 g/l NaCl 0.00988142 g/l Fe(NH4)2(SO4)2 x 6 H2O 0.00988142 g/l MnSO4 x H2O 0.00494071 g/l ZnSO4 x 7 H2O 0.00177866 g/l CoSO4 x 7 H2O 0.00177866 g/l CaCl2 x 2 H2O 0.000988142 g/l FeSO4 x 7 H2O 0.000988142 g/l Sodium resazurin 0.000494071 g/l NiCl2 x 6 H2O 0.000296443 g/l AlK(SO4)2 x 12 H2O 0.000197628 g/l Na2MoO4 x 2 H2O 9.88142e-05 g/l CuSO4 x 5 H2O 9.88142e-05 g/l H3BO3 9.88142e-05 g/l Pyridoxine hydrochloride 9.88142e-05 g/l Thiamine HCl 4.94071e-05 g/l (DL)-alpha-Lipoic acid 4.94071e-05 g/l p-Aminobenzoic acid 4.94071e-05 g/l Riboflavin 4.94071e-05 g/l Nicotinic acid 4.94071e-05 g/l Calcium D-(+)-pantothenate 4.94071e-05 g/l Biotin 1.97628e-05 g/l Folic acid 1.97628e-05 g/l Na2WO4 x 2 H2O 3.95257e-06 g/l Na2SeO3 x 5 H2O 2.96443e-06 g/l Vitamin B12 9.88142e-07 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 1616 | positive | growth | 85 | hyperthermophilic |
| 67770 | positive | growth | 85 | hyperthermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 1616
- oxygen tolerance: anaerobe
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 1616 | core sample from a deep sea hydrothermal vent | Gulf of California, Guayamas Basin | USA | USA | North America |
| 67770 | Hydrothermal vent core sample from Guaymas Basin, at a depth of 2,003 m | Gulf of California | USA | USA | North America |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Hydrothermal vent |
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Terrestrial | #Core sample |
| #Condition | #Thermophilic (>45°C) |
Safety information
risk assessment
- @ref: 1616
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20218
- description: Methanococcus fervens 16S ribosomal RNA gene, partial sequence
- accession: AF056938
- length: 1398
- database: ena
- NCBI tax ID: 573064
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Methanocaldococcus fervens AG86 | GCA_000023985 | complete | ncbi | 573064 |
| 66792 | Methanocaldococcus fervens AG86 | 644736385 | complete | img | 573064 |
| 66792 | Methanocaldococcus fervens AG86 | 573064.13 | plasmid | patric | 573064 |
| 66792 | Methanocaldococcus fervens AG86 | 573064.11 | complete | patric | 573064 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 1616 | 33.0 | thermal denaturation, midpoint method (Tm) |
| 67770 | 33 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 81.808 | no |
| flagellated | no | 93.845 | no |
| gram-positive | no | 96.522 | no |
| anaerobic | yes | 99.143 | yes |
| aerobic | no | 97.15 | yes |
| halophile | no | 83.825 | no |
| spore-forming | no | 97.06 | no |
| thermophile | yes | 99.414 | yes |
| glucose-util | yes | 63.934 | no |
| glucose-ferment | no | 57.243 | no |
External links
@ref: 1616
culture collection no.: DSM 4213, JCM 15782
straininfo link
- @ref: 76445
- straininfo: 47812
literature
- topic: Phylogeny
- Pubmed-ID: 10319479
- title: Methanococcus vulcanius sp. nov., a novel hyperthermophilic methanogen isolated from East Pacific Rise, and identification of Methanococcus sp. DSM 4213T as Methanococcus fervens sp. nov.
- authors: Jeanthon C, L'Haridon S, Reysenbach AL, Corre E, Vernet M, Messner P, Sleytr UB, Prieur D
- journal: Int J Syst Bacteriol
- DOI: 10.1099/00207713-49-2-583
- year: 1999
- mesh: Base Composition, DNA, Archaeal/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Methanococcus/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Pacific Ocean, Phylogeny, RNA, Ribosomal, 16S/genetics, *Water Microbiology
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 1616 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4213) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-4213 | |||
| 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/ | ||||
| 76445 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID47812.1 | StrainInfo: A central database for resolving microbial strain identifiers |