Strain identifier
BacDive ID: 6950
Type strain: 
Species: Methanobacterium arcticum
Strain Designation: M2
Strain history: <- V. Shcherbakova, Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Science, Pushchino, Russia; M2 <- V. A. Shcherbakova; {2005}
NCBI tax ID(s): 386456 (species)
version 9.3 (current version)
General
@ref: 8345
BacDive-ID: 6950
DSM-Number: 19844
keywords: genome sequence, 16S sequence, Archaea, anaerobe, mesophilic, Gram-negative, rod-shaped
description: Methanobacterium arcticum M2 is an anaerobe, mesophilic, Gram-negative archaeon that was isolated from Holocene permafrost sediments.
NCBI tax id
- NCBI tax id: 386456
- Matching level: species
strain history
- @ref: 8345
- history: <- V. Shcherbakova, Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Science, Pushchino, Russia; M2 <- V. A. Shcherbakova; {2005}
doi: 10.13145/bacdive6950.20250331.9.3
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 arcticum
- full scientific name: Methanobacterium arcticum Shcherbakova et al. 2011
@ref: 8345
domain: Archaea
phylum: Euryarchaeota
class: Methanobacteria
order: Methanobacteriales
family: Methanobacteriaceae
genus: Methanobacterium
species: Methanobacterium arcticum
full scientific name: Methanobacterium arcticum Shcherbakova et al. 2011
strain designation: M2
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 29798 | negative | 4.5 µm | 0.475 µm | rod-shaped | no | |
| 125439 | negative | 97.1 | ||||
| 125438 | no | 90.875 |
Culture and growth conditions
culture medium
- @ref: 8345
- name: METHANOGENIUM MEDIUM (H2/CO2) (DSMZ Medium 141)
- growth: yes
- link: https://mediadive.dsmz.de/medium/141
- composition: Name: METHANOGENIUM MEDIUM (H2/CO2) (DSMZ Medium 141) Composition: NaHCO3 4.89237 g/l MgCl2 x 6 H2O 3.91389 g/l Yeast extract 1.95695 g/l Trypticase peptone 1.95695 g/l Na-acetate 0.978474 g/l Na2S x 9 H2O 0.489237 g/l L-Cysteine HCl x H2O 0.489237 g/l KCl 0.332681 g/l NH4Cl 0.244618 g/l K2HPO4 0.136986 g/l MgSO4 x 7 H2O 0.0293542 g/l Nitrilotriacetic acid 0.0146771 g/l NaCl 0.00978474 g/l MnSO4 x H2O 0.00489237 g/l Fe(NH4)2(SO4)2 x 6 H2O 0.00195695 g/l CoSO4 x 7 H2O 0.00176125 g/l ZnSO4 x 7 H2O 0.00176125 g/l FeSO4 x 7 H2O 0.000978474 g/l CaCl2 x 2 H2O 0.000978474 g/l Sodium resazurin 0.000489237 g/l NiCl2 x 6 H2O 0.000293542 g/l AlK(SO4)2 x 12 H2O 0.000195695 g/l CuSO4 x 5 H2O 9.78474e-05 g/l Pyridoxine hydrochloride 9.78474e-05 g/l Na2MoO4 x 2 H2O 9.78474e-05 g/l H3BO3 9.78474e-05 g/l Nicotinic acid 4.89237e-05 g/l Riboflavin 4.89237e-05 g/l (DL)-alpha-Lipoic acid 4.89237e-05 g/l Thiamine HCl 4.89237e-05 g/l Calcium D-(+)-pantothenate 4.89237e-05 g/l p-Aminobenzoic acid 4.89237e-05 g/l Folic acid 1.95695e-05 g/l Biotin 1.95695e-05 g/l Na2WO4 x 2 H2O 3.91389e-06 g/l Na2SeO3 x 5 H2O 2.93542e-06 g/l Vitamin B12 9.78474e-07 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 8345 | positive | growth | 37 |
| 29798 | positive | growth | 15-45 |
| 29798 | positive | optimum | 37 |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 29798 | positive | growth | 5.5-8.5 | alkaliphile |
| 29798 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 8345 | anaerobe |
| 29798 | anaerobe |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 29798 | no | |
| 125439 | no | 95.4 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 29798 | NaCl | positive | growth | 0-1.74 % |
| 29798 | NaCl | positive | optimum | 0.58 % |
metabolite utilization
- @ref: 29798
- Chebi-ID: 15740
- metabolite: formate
- utilization activity: +
- kind of utilization tested: carbon source
metabolite production
- @ref: 29798
- Chebi-ID: 16183
- metabolite: methane
- production: yes
Isolation, sampling and environmental information
isolation
- @ref: 8345
- sample type: Holocene permafrost sediments
- geographic location: Kolyma Lowland, Russia (70° 06' N 154° 04' E)
- country: Russia
- origin.country: RUS
- continent: Asia
- latitude: 70.1
- longitude: 154.067
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Permafrost |
| #Environmental | #Terrestrial | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_187129.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17808;96_68811;97_89453;98_121726;99_187129&stattab=map
- Last taxonomy: Methanobacterium
- 16S sequence: DQ517520
- Sequence Identity:
- Total samples: 247
- soil counts: 80
- aquatic counts: 94
- animal counts: 15
- plant counts: 58
Safety information
risk assessment
- @ref: 8345
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 8345
- description: Methanobacterium arcticum 16S ribosomal RNA gene, partial sequence
- accession: DQ517520
- length: 1434
- database: nuccore
- NCBI tax ID: 386456
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Methanobacterium arcticum M2 | GCA_000746075 | scaffold | ncbi | 386456 |
| 66792 | Methanobacterium arcticum M2, DSM 19844 | 2574179771 | draft | img | 386456 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 8345 | 38.1 | thermal denaturation, midpoint method (Tm) |
| 29798 | 38.1 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 65.308 | yes |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 88.763 | yes |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 85.617 | yes |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 85.159 | yes |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 79.091 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 90.875 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 95.4 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | no | 73.8 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 97.1 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | anaerobe | 75.4 |
External links
@ref: 8345
culture collection no.: DSM 19844, VKM B-2371
straininfo link
- @ref: 76412
- straininfo: 401709
literature
- topic: Phylogeny
- Pubmed-ID: 20173003
- title: Methanobacterium arcticum sp. nov., a methanogenic archaeon from Holocene Arctic permafrost.
- authors: Shcherbakova V, Rivkina E, Pecheritsyna S, Laurinavichius K, Suzina N, Gilichinsky D
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.021311-0
- year: 2010
- mesh: Base Composition, Carbon Dioxide/metabolism, Cluster Analysis, DNA, Archaeal/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Hydrogen/metabolism, Hydrogen-Ion Concentration, Methanobacterium/*classification/genetics/*isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, Temperature
- topic2: Metabolism
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 8345 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19844) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19844 | |||
| 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 | |||
| 29798 | 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 | 26176 | 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) | |||
| 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 | |||
| 76412 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID401709.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |