Strain identifier
BacDive ID: 6943
Type strain: 
Species: Methanobacterium subterraneum
Strain Designation: A8p
Strain history: <- S. Kotelnikova, Russian Academy of Sciences, Institute of Biochemistry and Physiology of Microorganisms, Moscow, Russia; A8p <- S. Kotelnikova {1995}
NCBI tax ID(s): 59277 (species)
version 8.1 (current version)
General
@ref: 4189
BacDive-ID: 6943
DSM-Number: 11074
keywords: genome sequence, 16S sequence, Archaea, anaerobe, mesophilic, Gram-negative
description: Methanobacterium subterraneum A8p is an anaerobe, mesophilic, Gram-negative archaeon that was isolated from groundwater of rock tunnel at 70 m depth..
NCBI tax id
- NCBI tax id: 59277
- Matching level: species
strain history
- @ref: 4189
- history: <- S. Kotelnikova, Russian Academy of Sciences, Institute of Biochemistry and Physiology of Microorganisms, Moscow, Russia; A8p <- S. Kotelnikova {1995}
doi: 10.13145/bacdive6943.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Methanobacteria
- order: Methanobacteriales
- family: Methanobacteriaceae
- genus: Methanobacterium
- species: Methanobacterium subterraneum
- full scientific name: Methanobacterium subterraneum Kotelnikova et al. 1998
@ref: 4189
domain: Archaea
phylum: Euryarchaeota
class: Methanobacteria
order: Methanobacteriales
family: Methanobacteriaceae
genus: Methanobacterium
species: Methanobacterium subterraneum
full scientific name: Methanobacterium subterraneum Kotelnikova et al. 1998
strain designation: A8p
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.914
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 4189 | METHANOBACTERIUM SUBTERRANEUM MEDIUM (DSMZ Medium 814) | yes | https://mediadive.dsmz.de/medium/814 | Name: METHANOBACTERIUM SUBTERRANEUM MEDIUM (DSMZ Medium 814) Composition: Na-formate 3.2 g/l Tryptone 1.0 g/l Na-acetate 1.0 g/l Na2CO3 1.0 g/l K2HPO4 0.5 g/l NH4Cl 0.4 g/l L-Cysteine HCl x H2O 0.25 g/l Na2S x 9 H2O 0.25 g/l MgCl2 x 6 H2O 0.03 g/l MgSO4 x 7 H2O 0.03 g/l Nitrilotriacetic acid 0.015 g/l NaCl 0.01 g/l MnSO4 x H2O 0.005 g/l ZnSO4 x 7 H2O 0.0018 g/l CoSO4 x 7 H2O 0.0018 g/l FeSO4 x 7 H2O 0.001 g/l CaCl2 x 2 H2O 0.001 g/l Sodium resazurin 0.0005 g/l NiCl2 x 6 H2O 0.0003 g/l Pyridoxine hydrochloride 0.0003 g/l Thiamine-HCl x 2 H2O 0.0002 g/l AlK(SO4)2 x 12 H2O 0.0002 g/l Nicotinic acid 0.0002 g/l CuSO4 x 5 H2O 0.0001 g/l Vitamin B12 0.0001 g/l Calcium pantothenate 0.0001 g/l Na2MoO4 x 2 H2O 0.0001 g/l H3BO3 0.0001 g/l p-Aminobenzoic acid 8e-05 g/l D-(+)-biotin 2e-05 g/l Na2WO4 x 2 H2O 4e-06 g/l Na2SeO3 x 5 H2O 3e-06 g/l Distilled water |
| 4189 | METHANOBACTERIUM MEDIUM (DSMZ Medium 119) | yes | https://mediadive.dsmz.de/medium/119 | 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: 4189
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 4189 | anaerobe | |
| 69480 | anaerobe | 99.312 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.246 |
Isolation, sampling and environmental information
isolation
- @ref: 4189
- sample type: groundwater of rock tunnel at 70 m depth.
- geographic location: Äspö Hard Rock Tunnel Laboratory
- country: Sweden
- origin.country: SWE
- continent: Europe
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Groundwater
taxonmaps
- @ref: 69479
- File name: preview.99_188779.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17808;96_68789;97_90296;98_122724;99_188779&stattab=map
- Last taxonomy: Methanobacterium subterraneum subclade
- 16S sequence: X99044
- Sequence Identity:
- Total samples: 287
- soil counts: 32
- aquatic counts: 222
- animal counts: 13
- plant counts: 20
Safety information
risk assessment
- @ref: 4189
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 4189
- description: Methanobacterium subterraneum 16S rRNA gene, strain A8p
- accession: X99044
- length: 1436
- database: ena
- NCBI tax ID: 59277
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Methanobacterium subterraneum A8p | GCA_002813695 | complete | ncbi | 59277 |
| 66792 | Methanobacterium subterraneum A8p | 2775506920 | complete | img | 59277 |
| 66792 | Methanobacterium subterraneum strain A8p | 59277.3 | complete | patric | 59277 |
GC content
- @ref: 4189
- GC-content: 54.5
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| flagellated | no | 96.647 | no |
| gram-positive | no | 96.84 | no |
| anaerobic | yes | 98.27 | yes |
| halophile | no | 78.45 | no |
| spore-forming | no | 94.638 | no |
| thermophile | no | 93.886 | yes |
| glucose-util | yes | 70.229 | no |
| aerobic | no | 95.122 | yes |
| motile | no | 88.806 | no |
| glucose-ferment | no | 67.794 | no |
External links
@ref: 4189
culture collection no.: DSM 11074, ATCC 700657, NBRC 105231
straininfo link
- @ref: 76405
- straininfo: 46247
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 9731274 | Methanobacterium subterraneum sp. nov., a new alkaliphilic, eurythermic and halotolerant methanogen isolated from deep granitic groundwater. | Kotelnikova S, Macario AJ, Pedersen K | Int J Syst Bacteriol | 10.1099/00207713-48-2-357 | 1998 | Anti-Bacterial Agents/pharmacology, Antigens, Bacterial/immunology, Base Composition, Base Sequence, DNA, Bacterial, Fresh Water/microbiology, Methanobacterium/*classification/genetics/isolation & purification/ultrastructure, Molecular Sequence Data, Phylogeny | Genetics |
| Phylogeny | 20639228 | Methanobacterium kanagiense sp. nov., a hydrogenotrophic methanogen, isolated from rice-field soil. | Kitamura K, Fujita T, Akada S, Tonouchi A | Int J Syst Evol Microbiol | 10.1099/ijs.0.026013-0 | 2010 | Anaerobiosis, Autotrophic Processes, Base Composition, Carbon Dioxide, Cell Wall/ultrastructure, Cluster Analysis, DNA, Archaeal/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Hydrogen/*metabolism, Hydrogen-Ion Concentration, Japan, Methane/metabolism, Methanobacterium/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Oryza/growth & development, Phylogeny, Propionates/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, Temperature | Metabolism |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 4189 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11074) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-11074 | |
| 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) | |
| 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 | |
| 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 | |
| 76405 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID46247.1 | StrainInfo: A central database for resolving microbial strain identifiers |