Archive BacDiveID:10.13145/bacdive7087.20230509.8.1

Strain identifier

BacDive ID: 7087

Type strain:

Species: Methanosarcina barkeri

Strain Designation: MS

Strain history: DSM 800 <-- M. P. Bryant MS.

NCBI tax ID(s): 1298606 (strain), 2208 (species)

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

General

@ref: 456

BacDive-ID: 7087

DSM-Number: 800

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

description: Methanosarcina barkeri MS is an anaerobe, mesophilic archaeon that was isolated from anaerobic sewage digester.

NCBI tax id

NCBI tax id	Matching level
1298606	strain
2208	species

strain history

@ref	history
456	<- M. P. Bryant, University of Illinois, Urbana, USA; MS <- M. P. Bryant {1968}
67770	DSM 800 <-- M. P. Bryant MS.

doi: 10.13145/bacdive7087.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/archaea
keyword: phylum/methanobacteriota
domain: Archaea
phylum: Methanobacteriota
class: Methanomicrobia
order: Methanosarcinales
family: Methanosarcinaceae
genus: Methanosarcina
species: Methanosarcina barkeri
full scientific name: Methanosarcina barkeri Schnellen 1947 (Approved Lists 1980)

@ref: 456

domain: Archaea

phylum: Euryarchaeota

class: Methanomicrobia

order: Methanosarcinales

family: Methanosarcinaceae

genus: Methanosarcina

species: Methanosarcina barkeri

full scientific name: Methanosarcina barkeri Schnellen 1947 emend. Bryant and Boone 1987 emend. Maestrojuán et al. 1992

strain designation: MS

type strain: yes

Culture and growth conditions

culture medium

@ref: 456
name: METHANOSARCINA MEDIUM (DSMZ Medium 120)
growth: yes
link: https://mediadive.dsmz.de/medium/120
composition: Name: METHANOSARCINA MEDIUM (DSMZ Medium 120) Composition: Methanol 15.4688 g/l Na-acetate 2.44141 g/l NaCl 2.19727 g/l NaHCO3 1.95312 g/l Casitone 1.95312 g/l Yeast extract 1.95312 g/l NH4Cl 0.488281 g/l MgSO4 x 7 H2O 0.488281 g/l K2HPO4 0.341797 g/l Na2S x 9 H2O 0.292969 g/l L-Cysteine HCl x H2O 0.292969 g/l CaCl2 x 2 H2O 0.244141 g/l KH2PO4 0.224609 g/l HCl 0.00244141 g/l FeSO4 x 7 H2O 0.00195312 g/l FeCl2 x 4 H2O 0.00146484 g/l Sodium resazurin 0.000488281 g/l CoCl2 x 6 H2O 0.000185547 g/l Pyridoxine hydrochloride 9.76563e-05 g/l MnCl2 x 4 H2O 9.76563e-05 g/l ZnCl2 6.83594e-05 g/l Riboflavin 4.88281e-05 g/l Calcium D-(+)-pantothenate 4.88281e-05 g/l Nicotinic acid 4.88281e-05 g/l (DL)-alpha-Lipoic acid 4.88281e-05 g/l Thiamine HCl 4.88281e-05 g/l p-Aminobenzoic acid 4.88281e-05 g/l Na2MoO4 x 2 H2O 3.51562e-05 g/l NiCl2 x 6 H2O 2.34375e-05 g/l Folic acid 1.95312e-05 g/l Biotin 1.95312e-05 g/l H3BO3 5.85938e-06 g/l CuCl2 x 2 H2O 1.95313e-06 g/l Vitamin B12 9.76563e-07 g/l H2SO4 Distilled water

culture temp

@ref	growth	type	temperature	range
456	positive	growth	35	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

oxygen tolerance

@ref: 456
oxygen tolerance: anaerobe

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
456	anaerobic sewage digester	Illinois, Urbana	USA	USA	North America
67770	Anaerobic sewage-sludge digester	Urbana, IL	USA	USA	North America

isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Biodegradation	#Anaerobic digestor
#Engineered	#Waste	#Wastewater
#Condition	#Anoxic (anaerobic)

Safety information

risk assessment

@ref: 456
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref	description	accession	length	database	NCBI tax ID
20218	Enterococcus faecalis clone OCM038 16S ribosomal RNA gene, partial sequence	GU417226	456	ena	1351
20218	Methanosarcina barkeri strain MS 16S ribosomal RNA gene, partial sequence	JQ346756	1268	ena	2208
456	Methanosarcina barkeri 16S rRNA gene, strain DSM 800 (T)	AJ012094	1411	ena	2208

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Methanosarcina barkeri MS	GCA_000970025	complete	ncbi	1434108
66792	Methanosarcina barkeri JCM 10043	GCA_001316305	contig	ncbi	1298606
66792	Methanosarcina barkeri MS	2630968729	complete	img	1434108
66792	Methanosarcina barkeri JCM 10043	2684622504	draft	img	1298606
66792	Methanosarcina barkeri MS	1434108.6	plasmid	patric	1434108
66792	Methanosarcina barkeri MS	1434108.4	complete	patric	1434108
66792	Methanosarcina barkeri JCM 10043	1298606.3	wgs	patric	1298606

GC content

@ref	GC-content	method
456	38.8
67770	38.8	Buoyant density centrifugation (BD)
67770	39	thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
motile	no	91.43	no
flagellated	no	96.459	no
gram-positive	no	94.54	no
anaerobic	yes	97.783	yes
aerobic	no	94.068	no
halophile	no	87.398	no
spore-forming	no	94.499	no
thermophile	no	93.661	yes
glucose-util	yes	76.54	no
glucose-ferment	no	62.806	no

External links

@ref: 456

culture collection no.: DSM 800, ATCC 43569, JCM 10043, OCM 38, NBRC 100474, VKM B-1635

straininfo link

@ref: 76543
straininfo: 354032

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Metabolism	2924775	In vivo 31P- and 13C-NMR studies of ATP synthesis and methane formation by Methanosarcina barkeri.	Santos H, Fareleira P, Toci R, LeGall J, Peck HD Jr, Xavier AV	Eur J Biochem	10.1111/j.1432-1033.1989.tb14663.x	1989	Adenosine Diphosphate/metabolism, Adenosine Triphosphate/biosynthesis/metabolism, Carbon Isotopes, Euryarchaeota/metabolism, Magnetic Resonance Spectroscopy/methods, Methane/*metabolism, Phosphorus
Enzymology	3028382	Low-spin sulfite reductases: a new homologous group of non-heme iron-siroheme proteins in anaerobic bacteria.	Moura I, Lino AR, Moura JJ, Xavier AV, Fauque G, Peck HD Jr, LeGall J	Biochem Biophys Res Commun	10.1016/s0006-291x(86)80148-6	1986	Anaerobiosis, Bacteria/enzymology, Desulfovibrio/enzymology, Electron Spin Resonance Spectroscopy, Euryarchaeota/enzymology, Heme/analogs & derivatives/analysis, Iron/analysis, Molecular Weight, Oxidation-Reduction, Oxidoreductases/metabolism, Oxidoreductases Acting on Sulfur Group Donors/analysis/*metabolism, Spectrophotometry	Metabolism
Enzymology	6086341	Purification, characterization and redox properties of hydrogenase from Methanosarcina barkeri (DSM 800).	Fauque G, Teixeira M, Moura I, Lespinat PA, Xavier AV, Der Vartanian DV, Peck HD Jr, Le Gall J, Moura JG	Eur J Biochem	10.1111/j.1432-1033.1984.tb08245.x	1984	Allosteric Site, Electron Spin Resonance Spectroscopy, Euryarchaeota/enzymology, Hydrogenase, Molecular Weight, Oxidation-Reduction, Oxidoreductases/isolation & purification/metabolism, Spectrum Analysis	Phylogeny
Phylogeny	6754724	Amino acid sequence of a 3Fe:3S ferredoxin from the "archaebacterium" Methanosarcina barkeri (DSM 800).	Hausinger RP, Moura I, Moura JJ, Xavier AV, Santos MH, LeGall J, Howard JB	J Biol Chem	S0021-9258(19)45364-7	1982	Amino Acid Sequence, Endopeptidases, Euryarchaeota/analysis, Ferredoxins, Peptide Fragments/analysis, Species Specificity
Genetics	9425287	F0F1-ATPase genes from an archaebacterium, Methanosarcina barkeri.	Sumi M, Yohda M, Koga Y, Yoshida M	Biochem Biophys Res Commun	10.1006/bbrc.1997.7809	1997	Amino Acid Sequence, Base Composition, Genes, Archaeal, Methanosarcina barkeri/enzymology/genetics, Molecular Sequence Data, Multigene Family, Polymerase Chain Reaction, Protein Conformation, Proton-Translocating ATPases/genetics, Restriction Mapping, Sequence Analysis, DNA, Sequence Homology, Amino Acid	Transcriptome
Phylogeny	25052394	Methanosarcina spelaei sp. nov., a methanogenic archaeon isolated from a floating biofilm of a subsurface sulphurous lake.	Ganzert L, Schirmack J, Alawi M, Mangelsdorf K, Sand W, Hillebrand-Voiculescu A, Wagner D	Int J Syst Evol Microbiol	10.1099/ijs.0.064956-0	2014	Base Composition, Biofilms, Caves/microbiology, DNA, Archaeal/genetics, DNA, Bacterial/genetics, Lakes/microbiology, Lipids/chemistry, Methanosarcina/classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Romania, Sequence Analysis, DNA, Sulfur, Water Microbiology	Genetics
Transcriptome	28828628	Different substrate regimes determine transcriptional profiles and gene co-expression in Methanosarcina barkeri (DSM 800).	Lin Q, Fang X, Ho A, Li J, Yan X, Tu B, Li C, Li J, Yao M, Li X	Appl Microbiol Biotechnol	10.1007/s00253-017-8457-4	2017	Acetic Acid/chemistry, Carbon Dioxide/chemistry, Culture Media/chemistry, Euryarchaeota/genetics/metabolism, Gene Expression Regulation, Archaeal, Hydrogen/chemistry, Hydrogen-Ion Concentration, Methanol/chemistry, Methanosarcina barkeri/genetics/metabolism, RNA, Archaeal/genetics, Sequence Analysis, RNA, Substrate Specificity, Transcriptome	Metabolism

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
456	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 800)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-800
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
20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.		10.1016/j.syapm.2013.11.002	StrainInfo introduces electronic passports for microorganisms.	Syst Appl Microbiol. 37: 42-50 2014	24321274
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)
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
76543	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID354032.1	StrainInfo: A central database for resolving microbial strain identifiers