Strain identifier
BacDive ID: 7030
Type strain: 
Species: Methanoculleus submarinus
Strain Designation: Nankai-1
Strain history: <- D. R. Boone, Portland State Univ., USA; Nankai-1 <- Y. Liu {1999}
NCBI tax ID(s): 204050 (species)
version 8.1 (current version)
General
@ref: 5621
BacDive-ID: 7030
DSM-Number: 15122
keywords: genome sequence, 16S sequence, Archaea, anaerobe, mesophilic
description: Methanoculleus submarinus Nankai-1 is an anaerobe, mesophilic archaeon that was isolated from deep marine sediments where methane hydrates were present, 250 m below seafloor.
NCBI tax id
- NCBI tax id: 204050
- Matching level: species
strain history
- @ref: 5621
- history: <- D. R. Boone, Portland State Univ., USA; Nankai-1 <- Y. Liu {1999}
doi: 10.13145/bacdive7030.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Methanomicrobia
- order: Methanomicrobiales
- family: Methanomicrobiaceae
- genus: Methanoculleus
- species: Methanoculleus submarinus
- full scientific name: Methanoculleus submarinus Mikucki et al. 2003
@ref: 5621
domain: Archaea
phylum: Euryarchaeota
class: Methanomicrobia
order: Methanomicrobiales
family: Methanomicrobiaceae
genus: Methanoculleus
species: Methanoculleus submarinus
full scientific name: Methanoculleus submarinus Mikucki et al. 2003
strain designation: Nankai-1
type strain: yes
Culture and growth conditions
culture medium
- @ref: 5621
- 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: 5621
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
oxygen tolerance
- @ref: 5621
- oxygen tolerance: anaerobe
Isolation, sampling and environmental information
isolation
- @ref: 5621
- sample type: deep marine sediments where methane hydrates were present, 250 m below seafloor
- geographic location: Nankai Trough
- country: Japan
- origin.country: JPN
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Aquatic | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_188231.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17869;96_69167;97_90152;98_122545;99_188231&stattab=map
- Last taxonomy: Methanoculleus
- 16S sequence: AF531178
- Sequence Identity:
- Total samples: 20
- soil counts: 1
- aquatic counts: 16
- animal counts: 2
- plant counts: 1
Safety information
risk assessment
- @ref: 5621
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 5621
- description: Methanoculleus submarinus strain Nankai-1 16S ribosomal RNA gene, partial sequence
- accession: AF531178
- length: 1395
- database: ena
- NCBI tax ID: 204050
Genome sequences
- @ref: 66792
- description: Methanoculleus submarinus DSM 15122
- accession: GCA_025914035
- assembly level: complete
- database: ncbi
- NCBI tax ID: 204050
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 90.378 | no |
| flagellated | no | 97.485 | no |
| gram-positive | no | 97.038 | no |
| anaerobic | yes | 98.702 | no |
| aerobic | no | 96.427 | yes |
| halophile | no | 85.185 | no |
| spore-forming | no | 95.357 | no |
| glucose-ferment | no | 62.646 | no |
| thermophile | no | 88.04 | yes |
| glucose-util | yes | 76.731 | no |
External links
@ref: 5621
culture collection no.: DSM 15122, OCM 780, SMCC 780W
straininfo link
- @ref: 76490
- straininfo: 128000
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 12788731 | Isolation of a methanogen from deep marine sediments that contain methane hydrates, and description of Methanoculleus submarinus sp. nov. | Mikucki JA, Liu Y, Delwiche M, Colwell FS, Boone DR | Appl Environ Microbiol | 10.1128/AEM.69.6.3311-3316.2003 | 2003 | Culture Media, DNA, Archaeal/analysis, DNA, Ribosomal/analysis, Euryarchaeota/*classification/*genetics/growth & development/isolation & purification, Geologic Sediments/*microbiology, Methane/metabolism, Methanomicrobiaceae/*classification/*genetics/growth & development/isolation & purification, Microscopy, Electron, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA | Cultivation |
| Genetics | 30935830 | Comparative genomic analyses reveal trehalose synthase genes as the signature in genus Methanoculleus. | Chen SC, Weng CY, Lai MC, Tamaki H, Narihiro T | Mar Genomics | 10.1016/j.margen.2019.03.008 | 2019 | *Genome, Archaeal, Glucosyltransferases/*genetics/metabolism, Methanomicrobiaceae/enzymology/*genetics, RNA, Archaeal/analysis, RNA, Ribosomal, 16S/analysis | Metabolism |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 5621 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15122) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-15122 | |
| 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 | |
| 76490 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID128000.1 | StrainInfo: A central database for resolving microbial strain identifiers |