Strain identifier

BacDive ID: 7061

Type strain: Yes

Species: Methanococcoides alaskense

Strain Designation: AK-5

Strain history: <- M. Kendall, Portland State Univ., USA; AK-5 <- Y. Liu {1999}

NCBI tax ID(s): 325778 (species)

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General

@ref: 6865

BacDive-ID: 7061

DSM-Number: 17273

keywords: genome sequence, 16S sequence, Archaea, anaerobe, psychrophilic

description: Methanococcoides alaskense AK-5 is an anaerobe, psychrophilic archaeon that was isolated from marine sediment.

NCBI tax id

  • NCBI tax id: 325778
  • Matching level: species

strain history

  • @ref: 6865
  • history: <- M. Kendall, Portland State Univ., USA; AK-5 <- Y. Liu {1999}

doi: 10.13145/bacdive7061.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/archaea
  • keyword: phylum/methanobacteriota
  • domain: Archaea
  • phylum: Methanobacteriota
  • class: Methanomicrobia
  • order: Methanosarcinales
  • family: Methanosarcinaceae
  • genus: Methanococcoides
  • species: Methanococcoides alaskense
  • full scientific name: Methanococcoides alaskense Singh et al. 2005

@ref: 6865

domain: Archaea

phylum: Euryarchaeota

class: Methanomicrobia

order: Methanosarcinales

family: Methanosarcinaceae

genus: Methanococcoides

species: Methanococcoides alaskense

full scientific name: Methanococcoides alaskense Singh et al. 2005

strain designation: AK-5

type strain: yes

Morphology

colony morphology

  • @ref: 6865
  • incubation period: 3-7 days

Culture and growth conditions

culture medium

  • @ref: 6865
  • name: METHANOCOCCOIDES MEDIUM (DSMZ Medium 141c)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/141c
  • composition: Name: METHANOCOCCOIDES MEDIUM (DSMZ Medium 141c) Composition: NaHCO3 4.89237 g/l Trimethylammonium chloride 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 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 H3BO3 9.78474e-05 g/l Na2MoO4 x 2 H2O 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: 6865
  • growth: positive
  • type: growth
  • temperature: 20
  • range: psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 6865
  • oxygen tolerance: anaerobe

Isolation, sampling and environmental information

isolation

  • @ref: 6865
  • sample type: marine sediment
  • geographic location: Alaska, Skan Bay
  • country: USA
  • origin.country: USA
  • continent: North America

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_189632.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17802;96_69061;97_89733;98_122956;99_189632&stattab=map
  • Last taxonomy: Methanococcoides
  • 16S sequence: AY941801
  • Sequence Identity:
  • Total samples: 2
  • aquatic counts: 2

Safety information

risk assessment

  • @ref: 6865
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6865
  • description: Methanococcoides alaskense strain AK-5 16S ribosomal RNA gene, partial sequence
  • accession: AY941801
  • length: 1369
  • database: ena
  • NCBI tax ID: 325778

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Methanococcoides alaskense DSM 172732913378003draftimg325778
66792Methanococcoides alaskense DSM 17273GCA_027594145contigncbi325778

GC content

  • @ref: 6865
  • GC-content: 39.5

External links

@ref: 6865

culture collection no.: DSM 17273, NBRC 107632, OCM 775

straininfo link

  • @ref: 76518
  • straininfo: 281457

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16280522Isolation and characterization of methylotrophic methanogens from anoxic marine sediments in Skan Bay, Alaska: description of Methanococcoides alaskense sp. nov., and emended description of Methanosarcina baltica.Singh N, Kendall MM, Liu Y, Boone DRInt J Syst Evol Microbiol10.1099/ijs.0.63886-02005Alaska, Cold Temperature, Culture Media, DNA, Ribosomal/analysis, Geologic Sediments/microbiology, Hydrogen/*metabolism, Kinetics, Methane/*metabolism, Methanomicrobiaceae/classification/genetics/growth & development/*isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, RNA, Ribosomal, 16S/analysis/genetics, Seawater/*microbiologyEnzymology
Phylogeny24614846Methanococcoides vulcani sp. nov., a marine methylotrophic methanogen that uses betaine, choline and N,N-dimethylethanolamine for methanogenesis, isolated from a mud volcano, and emended description of the genus Methanococcoides.L'Haridon S, Chalopin M, Colombo D, Toffin LInt J Syst Evol Microbiol10.1099/ijs.0.058289-02014Base Composition, Betaine/metabolism, Choline/metabolism, DNA, Bacterial/genetics, Deanol/metabolism, Hydrothermal Vents/*microbiology, Mediterranean Sea, Methanosarcinaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAMetabolism
Phylogeny35583432Methanococcoides orientis sp. nov., a methylotrophic methanogen isolated from sediment of the East China Sea.Liang L, Sun Y, Dong Y, Ahmad T, Chen Y, Wang J, Wang FInt J Syst Evol Microbiol10.1099/ijsem.0.0053842022Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, *Fatty Acids/chemistry, *Methanosarcinaceae, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitle
6865Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17273)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17273
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
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
76518Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID281457.1StrainInfo: A central database for resolving microbial strain identifiers