Strain identifier
BacDive ID: 131457
Type strain: 
Species: Methanocalculus alkaliphilus
Strain Designation: AMF2
Strain history: <- D. Y. Sorokin, Dept. Biotechnol., Delft Univ. Technol., Netherlands; AMF2 <- D. Y. Sorokin {2010}
NCBI tax ID(s): 768730 (species)
version 9 (current version)
General
@ref: 22684
BacDive-ID: 131457
DSM-Number: 24457
keywords: genome sequence, 16S sequence, Archaea, anaerobe
description: Methanocalculus alkaliphilus AMF2 is an anaerobe archaeon that was isolated from anoxic sediments from hypersaline soda lakes.
NCBI tax id
- NCBI tax id: 768730
- Matching level: species
strain history
- @ref: 22684
- history: <- D. Y. Sorokin, Dept. Biotechnol., Delft Univ. Technol., Netherlands; AMF2 <- D. Y. Sorokin {2010}
doi: 10.13145/bacdive131457.20240510.9
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Methanomicrobia
- order: Methanomicrobiales
- family: Methanocalculaceae
- genus: Methanocalculus
- species: Methanocalculus alkaliphilus
- full scientific name: Methanocalculus alkaliphilus Sorokin et al. 2015
@ref: 22684
domain: Archaea
phylum: Euryarchaeota
class: Methanomicrobia
order: Methanomicrobiales
family: Methanocalculaceae
genus: Methanocalculus
species: Methanocalculus alkaliphilus
full scientific name: Methanocalculus alkaliphilus Sorokin et al. 2015
strain designation: AMF2
type strain: yes
Morphology
colony morphology
- @ref: 22684
- incubation period: 2-3 days
Culture and growth conditions
culture medium
- @ref: 22684
- name: METHANOCALCULUS ALKALIPHILUS MEDIUM (DSMZ Medium 1596)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1596
- composition: Name: METHANOCALCULUS ALKALIPHILUS MEDIUM (DSMZ Medium 1596) Composition: NaHCO3 19.9402 g/l Na2CO3 14.9551 g/l Na-formate 3.38983 g/l NaCl 2.99103 g/l K2HPO4 0.997009 g/l MgSO4 x 7 H2O 0.498504 g/l Na2S x 9 H2O 0.249252 g/l NH4Cl 0.199402 g/l Na-acetate 0.159521 g/l Yeast extract 0.0199402 g/l EDTA 0.00498504 g/l FeSO4 x 7 H2O 0.00219342 g/l NaOH 0.000498504 g/l CoCl2 x 6 H2O 0.000199402 g/l Pyridoxine hydrochloride 9.97009e-05 g/l ZnSO4 x 7 H2O 9.97009e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l MnCl2 x 4 H2O 2.99103e-05 g/l H3BO3 2.99103e-05 g/l CuCl2 x 2 H2O 2.99103e-05 g/l NiCl2 x 6 H2O 2.99103e-05 g/l Na2MoO4 x 2 H2O 2.99103e-05 g/l Folic acid 1.99402e-05 g/l Biotin 1.99402e-05 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water
culture temp
- @ref: 22684
- growth: positive
- type: growth
- temperature: 30
Physiology and metabolism
oxygen tolerance
- @ref: 22684
- oxygen tolerance: anaerobe
Isolation, sampling and environmental information
isolation
- @ref: 22684
- sample type: anoxic sediments from hypersaline soda lakes
- geographic location: South-East Siberia, Altai, Kulunda Steppe
- country: Russia
- origin.country: RUS
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Lake (large) |
| #Environmental | #Aquatic | #Sediment |
| #Condition | #Anoxic (anaerobic) | |
| #Condition | #Saline |
taxonmaps
- @ref: 69479
- File name: preview.99_191833.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17845;96_69179;97_92007;98_125034;99_191833&stattab=map
- Last taxonomy: Methanocalculus alkaliphilus subclade
- 16S sequence: HM053969
- Sequence Identity:
- Total samples: 28
- aquatic counts: 28
Safety information
risk assessment
- @ref: 22684
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22684
- description: Methanocalculus alkaliphilus strain AMF2 16S ribosomal RNA gene, partial sequence
- accession: HM053969
- length: 1433
- database: nuccore
- NCBI tax ID: 768730
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Methanocalculus alkaliphilus AMF2 | 2926682867 | draft | img | 768730 |
| 66792 | Methanocalculus alkaliphilus AMF2 | GCA_024170505 | contig | ncbi | 768730 |
GC content
- @ref: 22684
- GC-content: 51.1
- method: thermal denaturation, midpoint method (Tm)
External links
@ref: 22684
culture collection no.: DSM 24457, UNIQEM U859
straininfo link
- @ref: 89877
- straininfo: 399576
literature
- topic: Phylogeny
- Pubmed-ID: 26228570
- title: Methanosalsum natronophilum sp. nov., and Methanocalculus alkaliphilus sp. nov., haloalkaliphilic methanogens from hypersaline soda lakes.
- authors: Sorokin DY, Abbas B, Merkel AY, Rijpstra WIC, Damste JSS, Sukhacheva MV, van Loosdrecht MCM
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.000488
- year: 2015
- mesh: DNA, Archaeal/genetics, Geologic Sediments/microbiology, Lakes/*microbiology, Lipids/chemistry, Methanomicrobiales/*classification/genetics/isolation & purification, Methanosarcinaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Russia, *Salinity, Salt Tolerance, Sequence Analysis, DNA
- topic2: Enzymology
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 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 | |
| 22684 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24457 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24457) | |
| 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/ | |
| 89877 | 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-ID399576.1 |