Strain identifier

BacDive ID: 7058

Type strain: Yes

Species: Methanococcoides methylutens

Strain Designation: TMA-10

Strain history: <- K.R. Sowers and J.G. Ferry, TMA-10

NCBI tax ID(s): 2226 (species)

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General

@ref: 1191

BacDive-ID: 7058

DSM-Number: 2657

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

description: Methanococcoides methylutens TMA-10 is an anaerobe, mesophilic archaeon that was isolated from marine sediment.

NCBI tax id

  • NCBI tax id: 2226
  • Matching level: species

strain history

  • @ref: 1191
  • history: <- K.R. Sowers and J.G. Ferry, TMA-10

doi: 10.13145/bacdive7058.20230509.8.1

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 methylutens
  • full scientific name: Methanococcoides methylutens Sowers and Ferry 1985

@ref: 1191

domain: Archaea

phylum: Euryarchaeota

class: Methanomicrobia

order: Methanosarcinales

family: Methanosarcinaceae

genus: Methanococcoides

species: Methanococcoides methylutens

full scientific name: Methanococcoides methylutens Sowers and Ferry 1985

strain designation: TMA-10

type strain: yes

Culture and growth conditions

culture medium

  • @ref: 1191
  • 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: 1191
  • growth: positive
  • type: growth
  • temperature: 30
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 1191
  • oxygen tolerance: anaerobe

Isolation, sampling and environmental information

isolation

  • @ref: 1191
  • sample type: marine sediment
  • geographic location: California, Scripps Canyon near La Jolla
  • 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_187331.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17802;96_68841;97_89486;98_121882;99_187331&stattab=map
  • Last taxonomy: Methanococcoides
  • 16S sequence: FR733669
  • Sequence Identity:
  • Total samples: 55
  • soil counts: 2
  • aquatic counts: 53

Safety information

risk assessment

  • @ref: 1191
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Methylcoccoides methylutans 16S ribosomal RNAM591271477ena2226
1191Methanococcoides methylutens partial 16S rRNA gene, type strain DSM2657TFR7336691468ena2226

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Methanococcoides methylutens DSM 2657GCA_000765475contigncbi2226
66792Methanococcoides methylutens DSM2657GCA_900773915contigncbi2226
66792Methanococcoides methylutens DSM 26572630968972draftimg2226
66792Methanococcoides methylutens strain DSM26572226.10wgspatric2226
66792Methanococcoides methylutens strain DSM 26572226.9wgspatric2226

GC content

  • @ref: 1191
  • GC-content: 42.0

External links

@ref: 1191

culture collection no.: DSM 2657, ATCC 33938, OCM 158

straininfo link

  • @ref: 76515
  • straininfo: 40773

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16346215Isolation and Characterization of a Methylotrophic Marine Methanogen, Methanococcoides methylutens gen. nov., sp. nov.Sowers KR, Ferry JGAppl Environ Microbiol10.1128/aem.45.2.684-690.19831983
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
Metabolism35581283Mineralogical control on methylotrophic methanogenesis and implications for cryptic methane cycling in marine surface sediment.Xiao KQ, Moore OW, Babakhani P, Curti L, Peacock CLNat Commun10.1038/s41467-022-30422-42022Carbon/metabolism, Clay, *Geologic Sediments/chemistry, *Methane/metabolism, Methylamines
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/urltitlejournalpubmed
1191Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2657)https://www.dsmz.de/collection/catalogue/details/culture/DSM-2657
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
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
76515Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID40773.1StrainInfo: A central database for resolving microbial strain identifiers