Strain identifier
BacDive ID: 7001
Type strain:
Species: Methanococcus aeolicus
Strain Designation: Nankai-3
Strain history: <- M. Kendall, Portland State Univ., USA; Nankai-3 <- Y. Liu
NCBI tax ID(s): 42879 (species)
General
@ref: 7030
BacDive-ID: 7001
DSM-Number: 17508
keywords: genome sequence, 16S sequence, Archaea, anaerobe, thermophilic, motile, coccus-shaped
description: Methanococcus aeolicus Nankai-3 is an anaerobe, thermophilic, motile archaeon that was isolated from deep marine sediment.
NCBI tax id
- NCBI tax id: 42879
- Matching level: species
strain history
- @ref: 7030
- history: <- M. Kendall, Portland State Univ., USA; Nankai-3 <- Y. Liu
doi: 10.13145/bacdive7001.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Methanococci
- order: Methanococcales
- family: Methanococcaceae
- genus: Methanococcus
- species: Methanococcus aeolicus
- full scientific name: Methanococcus aeolicus Kendall et al. 2006
@ref: 7030
domain: Archaea
phylum: Euryarchaeota
class: Methanococci
order: Methanococcales
family: Methanococcaceae
genus: Methanococcus
species: Methanococcus aeolicus
full scientific name: Methanococcus aeolicus Kendall et al. 2006
strain designation: Nankai-3
type strain: yes
Morphology
cell morphology
- @ref: 31762
- cell width: 1.5-2 µm
- cell shape: coccus-shaped
- motility: yes
pigmentation
- @ref: 31762
- production: yes
Culture and growth conditions
culture medium
- @ref: 7030
- 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 | range |
---|---|---|---|---|
7030 | positive | growth | 40 | thermophilic |
31762 | positive | growth | 20-55 | |
31762 | positive | optimum | 40-50 | thermophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
31762 | positive | growth | 5.5-7.5 |
31762 | positive | optimum | 6.5-7.5 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
7030 | anaerobe |
31762 | anaerobe |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31762 | NaCl | positive | growth | 0.29-5.8 % |
31762 | NaCl | positive | optimum | 0.29-5.8 % |
observation
- @ref: 31762
- observation: aggregates in chains
metabolite utilization
- @ref: 31762
- Chebi-ID: 15740
- metabolite: formate
- utilization activity: +
- kind of utilization tested: carbon source
Isolation, sampling and environmental information
isolation
- @ref: 7030
- sample type: deep marine sediment
- 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_190190.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17939;96_70207;97_91176;98_123904;99_190190&stattab=map
- Last taxonomy: Methanococcus
- 16S sequence: DQ195164
- Sequence Identity:
- Total samples: 15
- aquatic counts: 8
- animal counts: 7
Safety information
risk assessment
- @ref: 7030
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 7030
- description: Methanococcus aeolicus Nankai-3 16S ribosomal RNA gene, partial sequence
- accession: DQ195164
- length: 1394
- database: ena
- NCBI tax ID: 419665
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Methanococcus aeolicus Nankai-3 | GCA_000017185 | complete | ncbi | 419665 |
66792 | Methanococcus aeolicus Nankai-3 | 640753034 | complete | img | 419665 |
66792 | Methanococcus aeolicus Nankai-3 | 419665.15 | complete | patric | 419665 |
GC content
- @ref: 31762
- GC-content: 32
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 91.215 | no |
flagellated | no | 95.677 | no |
gram-positive | no | 97.011 | no |
anaerobic | yes | 98.542 | yes |
halophile | no | 86.661 | no |
spore-forming | no | 96.758 | no |
thermophile | yes | 97.846 | yes |
glucose-util | yes | 68.946 | no |
aerobic | no | 95.897 | yes |
glucose-ferment | no | 64.914 | no |
External links
@ref: 7030
culture collection no.: DSM 17508, OCM 812
straininfo link
- @ref: 76462
- straininfo: 297267
literature
- topic: Phylogeny
- Pubmed-ID: 16825624
- title: Methanococcus aeolicus sp. nov., a mesophilic, methanogenic archaeon from shallow and deep marine sediments.
- authors: Kendall MM, Liu Y, Sieprawska-Lupa M, Stetter KO, Whitman WB, Boone DR
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.64216-0
- year: 2006
- mesh: Archaeal Proteins/analysis, Base Composition, DNA, Archaeal/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Genes, rRNA, Geologic Sediments/*microbiology, Mediterranean Sea, Methanococcus/chemistry/*classification/*isolation & purification/physiology, Molecular Sequence Data, Pacific Ocean, Phylogeny, Proteome/analysis, RNA, Archaeal/genetics, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Temperature, Water Microbiology
- topic2: Enzymology
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
7030 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17508) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17508 | |||
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 | |||
31762 | 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 | 28035 | 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 | |||
76462 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID297267.1 | StrainInfo: A central database for resolving microbial strain identifiers |