Strain identifier
BacDive ID: 24171
Type strain: 
Species: Methanospirillum stamsii
Strain Designation: ps, Pt1
Strain history: <- S. N. Parshina, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; Pt1 <- S. N. Parshina; ps {2011}
NCBI tax ID(s): 1277351 (species)
version 8.1 (current version)
General
@ref: 21024
BacDive-ID: 24171
DSM-Number: 26304
keywords: genome sequence, 16S sequence, Archaea, anaerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Methanospirillum stamsii ps is an anaerobe, mesophilic, Gram-negative archaeon that was isolated from granulated biomass of an anaerobic expanded granular sludge bed bioreactor operated at low temperature.
NCBI tax id
- NCBI tax id: 1277351
- Matching level: species
strain history
- @ref: 21024
- history: <- S. N. Parshina, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; Pt1 <- S. N. Parshina; ps {2011}
doi: 10.13145/bacdive24171.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Methanomicrobia
- order: Methanomicrobiales
- family: Methanospirillaceae
- genus: Methanospirillum
- species: Methanospirillum stamsii
- full scientific name: Methanospirillum stamsii Parshina et al. 2014
@ref: 21024
domain: Archaea
phylum: Euryarchaeota
class: Methanomicrobia
order: Methanomicrobiales
family: Methanospirillaceae
genus: Methanospirillum
species: Methanospirillum stamsii
full scientific name: Methanospirillum stamsii Parshina et al. 2014
strain designation: ps, Pt1
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 31177 | negative | 7-25 µm | 0.4-0.5 µm | rod-shaped | yes | |
| 69480 | negative | 99.969 |
colony morphology
- @ref: 21024
- incubation period: 2-3 days
Culture and growth conditions
culture medium
- @ref: 21024
- 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 |
|---|---|---|---|---|
| 21024 | positive | growth | 30 | mesophilic |
| 31177 | positive | growth | 05-37 | |
| 31177 | positive | optimum | 20-30 |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 31177 | positive | growth | 6.0-10.0 | alkaliphile |
| 31177 | positive | optimum | 7.0-7.5 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 21024 | anaerobe | |
| 31177 | anaerobe | |
| 69480 | anaerobe | 100 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 31177 | no | |
| 69481 | no | 100 |
| 69480 | no | 99.91 |
halophily
- @ref: 31177
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-0.3 %
metabolite utilization
- @ref: 31177
- Chebi-ID: 30089
- metabolite: acetate
- utilization activity: +
- kind of utilization tested: carbon source
metabolite production
- @ref: 31177
- Chebi-ID: 16183
- metabolite: methane
- production: yes
Isolation, sampling and environmental information
isolation
- @ref: 21024
- sample type: granulated biomass of an anaerobic expanded granular sludge bed bioreactor operated at low temperature
- geographic location: Wageningen
- country: Netherlands
- origin.country: NLD
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Bioreactor | |
| #Engineered | #Waste | #Activated sludge |
| #Condition | #Anoxic (anaerobic) |
taxonmaps
- @ref: 69479
- File name: preview.99_187524.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17807;96_68777;97_89727;98_122033;99_187524&stattab=map
- Last taxonomy: Methanospirillum stamsii subclade
- 16S sequence: HF569045
- Sequence Identity:
- Total samples: 567
- soil counts: 17
- aquatic counts: 450
- animal counts: 25
- plant counts: 75
Safety information
risk assessment
- @ref: 21024
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 21024
- description: Methanospirillum stamsii partial 16S rRNA gene, strain DSM 26304
- accession: HF569045
- length: 1408
- database: ena
- NCBI tax ID: 1277351
Genome sequences
- @ref: 66792
- description: Methanospirillum stamsii Pt1
- accession: GCA_003173335
- assembly level: contig
- database: ncbi
- NCBI tax ID: 1277351
GC content
| @ref | GC-content | method |
|---|---|---|
| 21024 | 40 | thermal denaturation, midpoint method (Tm) |
| 31177 | 40 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| flagellated | no | 95.316 | no |
| gram-positive | no | 97.601 | yes |
| anaerobic | yes | 99.234 | yes |
| halophile | no | 93.961 | no |
| spore-forming | no | 95.214 | yes |
| glucose-util | yes | 68.481 | no |
| aerobic | no | 96.644 | no |
| thermophile | no | 98.373 | yes |
| motile | no | 84.303 | yes |
| glucose-ferment | no | 57.843 | no |
External links
@ref: 21024
culture collection no.: DSM 26304, VKM B-2808
straininfo link
- @ref: 88126
- straininfo: 398829
literature
- topic: Phylogeny
- Pubmed-ID: 24048867
- title: Methanospirillum stamsii sp. nov., a psychrotolerant, hydrogenotrophic, methanogenic archaeon isolated from an anaerobic expanded granular sludge bed bioreactor operated at low temperature.
- authors: Parshina SN, Ermakova AV, Bomberg M, Detkova EN
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.056218-0
- year: 2013
- mesh: Base Composition, Bioreactors/*microbiology, Cold Temperature, DNA, Archaeal/genetics, Methanospirillum/*classification/genetics/growth & development/isolation & purification, Molecular Sequence Data, Netherlands, Nucleic Acid Hybridization, Oxidoreductases/genetics, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Temperature
- topic2: Enzymology
Reference
| @id | authors | title | doi/url | catalogue | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |||
| 21024 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-26304 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26304) | |||
| 31177 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 27504 | 28776041 | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
| 88126 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID398829.1 |