Strain identifier

BacDive ID: 7001

Type strain: Yes

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)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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

@refgrowthtypetemperaturerange
7030positivegrowth40thermophilic
31762positivegrowth20-55
31762positiveoptimum40-50thermophilic

culture pH

@refabilitytypepH
31762positivegrowth5.5-7.5
31762positiveoptimum6.5-7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
7030anaerobe
31762anaerobe

halophily

@refsaltgrowthtested relationconcentration
31762NaClpositivegrowth0.29-5.8 %
31762NaClpositiveoptimum0.29-5.8 %

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

Cat1Cat2Cat3
#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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Methanococcus aeolicus Nankai-3GCA_000017185completencbi419665
66792Methanococcus aeolicus Nankai-3640753034completeimg419665
66792Methanococcus aeolicus Nankai-3419665.15completepatric419665

GC content

  • @ref: 31762
  • GC-content: 32

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno91.215no
flagellatedno95.677no
gram-positiveno97.011no
anaerobicyes98.542yes
halophileno86.661no
spore-formingno96.758no
thermophileyes97.846yes
glucose-utilyes68.946no
aerobicno95.897yes
glucose-fermentno64.914no

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

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7030Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17508)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17508
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
31762Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2803528776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69479João 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
76462Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297267.1StrainInfo: A central database for resolving microbial strain identifiers