Strain identifier
BacDive ID: 158352
Type strain: 
Species: Methanolobus psychrotolerans
Strain Designation: YSF-03
Strain history: <- M.-C. Lai, National Chung Hsing Univ., Dept. of Life Scs., Taiwan; YSF-03 <- S.-L. Tang and A. G. Degermendzhy, Siberian Federal University, Krasnoyarsk, Russia {2014}
NCBI tax ID(s): 1874706 (species)
version 8.1 (current version)
General
@ref: 65028
BacDive-ID: 158352
DSM-Number: 104044
keywords: genome sequence, 16S sequence, Archaea, obligate anaerobe, mesophilic, Gram-negative, coccus-shaped
description: Methanolobus psychrotolerans YSF-03 is an obligate anaerobe, mesophilic, Gram-negative archaeon that was isolated from sediment of saline lake.
NCBI tax id
- NCBI tax id: 1874706
- Matching level: species
strain history
- @ref: 65028
- history: <- M.-C. Lai, National Chung Hsing Univ., Dept. of Life Scs., Taiwan; YSF-03 <- S.-L. Tang and A. G. Degermendzhy, Siberian Federal University, Krasnoyarsk, Russia {2014}
doi: 10.13145/bacdive158352.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Methanomicrobia
- order: Methanosarcinales
- family: Methanosarcinaceae
- genus: Methanolobus
- species: Methanolobus psychrotolerans
- full scientific name: Methanolobus psychrotolerans Chen et al. 2018
@ref: 65028
domain: Archaea
phylum: Euryarchaeota
class: Methanomicrobia
order: Methanosarcinales
family: Methanosarcinaceae
genus: Methanolobus
species: Methanolobus psychrotolerans
full scientific name: Methanolobus psychrotolerans Chen et al. 2018
strain designation: YSF-03
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell shape | motility | confidence |
|---|---|---|---|---|---|
| 65460 | negative | 0.8-1.2 µm | coccus-shaped | no | |
| 69480 | negative | 99.97 |
Culture and growth conditions
culture medium
- @ref: 65028
- name: METHANOCOCCOIDES MEDIUM (DSMZ Medium 141c)
- growth: yes
- link: https://mediadive.dsmz.de/medium/141c
- composition: Name: METHANOCOCCOIDES MEDIUM (DSMZ Medium 141c; with strain-specific modifications) Composition: NaHCO3 4.89237 g/l MgCl2 x 6 H2O 3.91389 g/l Methanol 3.87476 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 CaCl2 x 2 H2O 0.000978474 g/l FeSO4 x 7 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 (DL)-alpha-Lipoic acid 4.89237e-05 g/l Thiamine HCl 4.89237e-05 g/l Riboflavin 4.89237e-05 g/l Nicotinic acid 4.89237e-05 g/l Calcium D-(+)-pantothenate 4.89237e-05 g/l p-Aminobenzoic acid 4.89237e-05 g/l Biotin 1.95695e-05 g/l Folic acid 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 | range |
|---|---|---|---|---|
| 65028 | positive | growth | 35 | mesophilic |
| 65460 | positive | growth | 0-37 | |
| 65460 | positive | optimum | 30-37 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 65460 | positive | growth | 6-8.9 | alkaliphile |
| 65460 | positive | optimum | 7-7.4 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 65460 | obligate anaerobe | |
| 69480 | anaerobe | 99.431 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69480 | no | 99.049 |
| 69481 | no | 100 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 65460 | NaCl | positive | growth | 0-0.85 M |
| 65460 | NaCl | positive | optimum | 0.17 M |
observation
| @ref | observation |
|---|---|
| 65460 | occur singly, in pairs, in tetra-cocci and in aggregates |
| 65460 | cell growth is completely inhibited by chloramphenicol and tetracycline, but not by ampicillin, kanamycin, penicillin, spectinomycin or vancomycin |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 65460 | 16526 | carbon dioxide | - | assimilation |
| 65460 | 18276 | dihydrogen | - | assimilation |
| 65460 | 17437 | dimethyl sulfide | - | assimilation |
| 65460 | 17170 | dimethylamine | - | assimilation |
| 65460 | 17790 | methanol | + | assimilation |
| 65460 | 16830 | methylamine | - | assimilation |
| 65460 | 32954 | sodium acetate | - | assimilation |
| 65460 | 62965 | sodium formate | - | assimilation |
| 65460 | 18139 | trimethylamine | + | assimilation |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude | sampling date | isolation procedure |
|---|---|---|---|---|---|---|---|---|---|
| 65028 | sediment of saline lake | East Siberia, Republic of Khakassia, Lake Shira | Russia | RUS | Europe | 54.5167 | 90.2 | ||
| 65460 | sediment samples of the saline meromictic Lake Shira | Republic of Khakassia, Siberia | Russia | RUS | Asia | 54.5097 | 90.1922 | July 2010 | one to two ml of the sediment samples were immediately inoculated into 20 ml MB/W enrichment medium with acetate (50 mM), formate (100 mM) or methanol (50 mM) as catabolic substrates in 60 ml serum bottles sealed with butyl rubber stoppers and aluminium caps. These samples were incubated at room temperature in the laboratory |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Lake (large) |
| #Environmental | #Aquatic | #Sediment |
| #Condition | #Saline |
taxonmaps
- @ref: 69479
- File name: preview.99_191985.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17802;96_69178;97_89866;98_122191;99_191985&stattab=map
- Last taxonomy: Methanolobus psychrotolerans subclade
- 16S sequence: KX573102
- Sequence Identity:
- Total samples: 13
- soil counts: 1
- aquatic counts: 8
- plant counts: 4
Sequence information
16S sequences
- @ref: 65028
- description: Methanolobus psychrotolerans strain YSF-03 16S ribosomal RNA gene, partial sequence
- accession: KX573102
- length: 1404
- database: ena
- NCBI tax ID: 1874706
Genome sequences
- @ref: 66792
- description: Methanolobus psychrotolerans YSF-03
- accession: GCA_002243045
- assembly level: contig
- database: ncbi
- NCBI tax ID: 1874706
GC content
- @ref: 65028
- GC-content: 41.3
- method: sequence analysis
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| flagellated | no | 96.252 | yes |
| gram-positive | no | 97.807 | no |
| anaerobic | yes | 98.488 | no |
| aerobic | no | 94.327 | yes |
| halophile | no | 85.245 | no |
| spore-forming | no | 93.897 | no |
| glucose-util | yes | 71.695 | no |
| thermophile | no | 93.135 | yes |
| motile | no | 89.302 | yes |
| glucose-ferment | no | 69.666 | no |
External links
@ref: 65028
culture collection no.: DSM 104044, BCRC AR10049, NBRC 112514
straininfo link
- @ref: 111157
- straininfo: 400903
literature
- topic: Phylogeny
- Pubmed-ID: 29509131
- title: Methanolobus psychrotolerans sp. nov., a psychrotolerant methanoarchaeon isolated from a saline meromictic lake in Siberia.
- authors: Chen SC, Huang HH, Lai MC, Weng CY, Chiu HH, Tang SL, Rogozin DY, Degermendzhy AG
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.002685
- year: 2018
- mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Lakes/*microbiology, Methanosarcinaceae/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Salinity, Sequence Analysis, DNA, Siberia
- topic2: Transcriptome
Reference
| @id | authors | title | doi/url | catalogue | journal | 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 | |||
| 65028 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-104044 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104044) | |||
| 65460 | Sheng-Chung Chen, Hsing-Hua Huang, Mei-Chin Lai, Chieh-Yin Weng, Hsiu-Hui Chiu, Sen-Lin Tang, Denis Yu Rogozin, Andrey G. Degermendzhy | Methanolobus psychrotolerans sp. nov., a psychrotolerant methanoarchaeon isolated from a saline meromictic lake in Siberia | 10.1099/ijsem.0.002685 | IJSEM 68: 1378-1383 2018 | 29509131 | |
| 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 | |||
| 111157 | 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-ID400903.1 |