Strain identifier
BacDive ID: 23082
Type strain: 
Species: Methanothermobacter tenebrarum
Strain Designation: RMAS
Strain history: K. Nakamura strain RMAS.
NCBI tax ID(s): 680118 (species)
version 8.1 (current version)
General
@ref: 19215
BacDive-ID: 23082
DSM-Number: 23052
keywords: genome sequence, 16S sequence, Archaea, anaerobe, thermophilic, Gram-positive, rod-shaped
description: Methanothermobacter tenebrarum RMAS is an anaerobe, thermophilic, Gram-positive archaeon that was isolated from gas-associated formation water from a well of natural gas field.
NCBI tax id
- NCBI tax id: 680118
- Matching level: species
strain history
| @ref | history |
|---|---|
| 19215 | <- K. Nakamura, Faculty Applied Biological Sci., Gifu Univ., Japan; RMAS <- A. Takahashi {2008} |
| 67770 | K. Nakamura strain RMAS. |
doi: 10.13145/bacdive23082.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Methanobacteria
- order: Methanobacteriales
- family: Methanobacteriaceae
- genus: Methanothermobacter
- species: Methanothermobacter tenebrarum
- full scientific name: Methanothermobacter tenebrarum Nakamura et al. 2013
@ref: 19215
domain: Archaea
phylum: Euryarchaeota
class: Methanobacteria
order: Methanobacteriales
family: Methanobacteriaceae
genus: Methanothermobacter
species: Methanothermobacter tenebrarum
full scientific name: Methanothermobacter tenebrarum Nakamura et al. 2013
strain designation: RMAS
type strain: yes
Morphology
cell morphology
- @ref: 30672
- gram stain: positive
- cell length: 7 µm
- cell width: 0.5 µm
- cell shape: rod-shaped
- motility: no
colony morphology
- @ref: 19215
- incubation period: 2-3 days
Culture and growth conditions
culture medium
- @ref: 19215
- name: METHANOBACTERIUM MEDIUM (DSMZ Medium 119)
- growth: yes
- link: https://mediadive.dsmz.de/medium/119
- composition: Name: METHANOBACTERIUM MEDIUM (DSMZ Medium 119) Composition: NaHCO3 3.98804 g/l Na-formate 1.99402 g/l Na-acetate 0.997009 g/l Na2S x 9 H2O 0.498504 g/l L-Cysteine HCl x H2O 0.498504 g/l KH2PO4 0.498504 g/l NH4Cl 0.398804 g/l NaCl 0.398804 g/l MgSO4 x 7 H2O 0.398804 g/l Yeast extract 0.199402 g/l CaCl2 x 2 H2O 0.0498504 g/l HCl 0.00249252 g/l FeSO4 x 7 H2O 0.00199402 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l H3BO3 5.98205e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Isobutyric acid DL-2-Methylbutyric acid Valeric acid Isovaleric acid H2SO4 Sludge Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 19215 | positive | growth | 70 | thermophilic |
| 30672 | positive | growth | 45-80 | hyperthermophilic |
| 30672 | positive | optimum | 70 | thermophilic |
| 67770 | positive | growth | 65 | thermophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 30672 | positive | growth | 5.8-8.7 | alkaliphile |
| 30672 | positive | optimum | 7.3 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 19215 | anaerobe |
| 30672 | anaerobe |
halophily
- @ref: 30672
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-2 %
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 19215 | gas-associated formation water from a well of natural gas field | Niigata | Japan | JPN | Asia |
| 67770 | Gas-associated formation water of a gas-producing well in a natural gas field | Japan | JPN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | |
| #Environmental | #Terrestrial | #Geologic |
taxonmaps
- @ref: 69479
- File name: preview.99_187752.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17808;96_69194;97_89887;98_122215;99_187752&stattab=map
- Last taxonomy: Methanothermobacter tenebrarum subclade
- 16S sequence: AB523785
- Sequence Identity:
- Total samples: 46
- soil counts: 3
- aquatic counts: 42
- plant counts: 1
Safety information
risk assessment
- @ref: 19215
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 19215
- description: Methanothermobacter tenebrarum gene for 16S rRNA, partial sequence
- accession: AB523785
- length: 1414
- database: ena
- NCBI tax ID: 680118
Genome sequences
- @ref: 66792
- description: Methanothermobacter tenebrarum RMAS
- accession: GCA_023167465
- assembly level: complete
- database: ncbi
- NCBI tax ID: 680118
GC content
| @ref | GC-content | method |
|---|---|---|
| 19215 | 41.5 | high performance liquid chromatography (HPLC) |
| 30672 | 41.5 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| flagellated | no | 96.543 | yes |
| gram-positive | no | 96.43 | yes |
| anaerobic | yes | 98.929 | yes |
| aerobic | no | 97.384 | yes |
| halophile | no | 80.844 | no |
| spore-forming | no | 96.764 | no |
| motile | no | 87.108 | no |
| glucose-ferment | no | 63.002 | no |
| thermophile | yes | 96.407 | yes |
| glucose-util | yes | 73.526 | no |
External links
@ref: 19215
culture collection no.: DSM 23052, JCM 16532, NBRC 106236
straininfo link
- @ref: 87320
- straininfo: 398257
literature
- topic: Phylogeny
- Pubmed-ID: 22561588
- title: Methanothermobacter tenebrarum sp. nov., a hydrogenotrophic, thermophilic methanogen isolated from gas-associated formation water of a natural gas field.
- authors: Nakamura K, Takahashi A, Mori C, Tamaki H, Mochimaru H, Nakamura K, Takamizawa K, Kamagata Y
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.041681-0
- year: 2012
- mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Japan, Lipids/analysis, Methane/metabolism, Methanobacteriaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Natural Gas/microbiology, Oil and Gas Fields/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Water Microbiology
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 19215 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23052) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23052 | |||
| 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 | |||
| 30672 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 27003 | 28776041 | |
| 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/ | ||||
| 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 | |||
| 87320 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID398257.1 | StrainInfo: A central database for resolving microbial strain identifiers |