Methanosarcina subterranea (DSM 22503, JCM 15540, NBRC 102578)

Name: Methanosarcina subterranea (DSM 22503, JCM 15540, NBRC 102578)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24167

Type strain

Strain Designation HC-2

Culture col. no. DSM 22503 JCM 15540 NBRC 102578 HC-2

NCBI tax ID(s) 418010

Special Collections DSMZ JCM

History <- S. Shimizu, Horonobe Research Institute for the Subsurface Environment, Horonobe-cho, Hokkaido, Japan.; HC-2 <- S. Shimizu; {2006} S. Shimizu; H-RISE, Japan; HC-2.

Links

Methanosarcina subterranea HC-2 is an anaerobe archaeon that was isolated from deep subsurface groundwater within a diatomaceous shale formation.

anaerobe 16S sequence Archaea

Name and taxonomic classification

SI-ID 403909

NBRC 102578,JCM 15540,DSM 22503

@ref 20215

Last LPSN update 2026-02-09 11:23:54

Domain Archaea

Phylum Methanobacteriota

Class Methanosarcinia

Order Methanosarcinales

Family Methanosarcinaceae

Genus Methanosarcina

Species Methanosarcina subterranea

Full scientific name Methanosarcina subterranea Shimizu et al. 2015

Morphology

Colony morphology

21020

Incubation period3-7 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
21020	METHANOMICROCOCCUS MEDIUM (DSMZ Medium 120b)		Medium recipe at MediaDive	Name: METHANOMICROCOCCUS MEDIUM (DSMZ Medium 120b; with strain-specific modifications) Composition: Methanol 15.4688 g/l NaCl 5.85938 g/l NaHCO3 2.44141 g/l Na-acetate 2.44141 g/l Yeast extract 1.95312 g/l Casitone 1.95312 g/l NH4Cl 0.488281 g/l MgSO4 x 7 H2O 0.488281 g/l Na2S x 9 H2O 0.351562 g/l L-Cysteine HCl x H2O 0.351562 g/l K2HPO4 0.341797 g/l CaCl2 x 2 H2O 0.244141 g/l KH2PO4 0.224609 g/l 2-Mercaptoethanesulfonate 0.136719 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 p-Aminobenzoic acid 4.88281e-05 g/l (DL)-alpha-Lipoic acid 4.88281e-05 g/l Calcium D-(+)-pantothenate 4.88281e-05 g/l Nicotinic acid 4.88281e-05 g/l Riboflavin 4.88281e-05 g/l Thiamine HCl 4.88281e-05 g/l Na2MoO4 x 2 H2O 3.51562e-05 g/l NiCl2 x 6 H2O 2.34375e-05 g/l Biotin 1.95312e-05 g/l Folic acid 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 (°C)
21020	positive	growth	30
67770	positive	growth	35

Physiology and metabolism

Oxygen tolerance

21020

Oxygen toleranceanaerobe

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Groundwater
#Environmental	#Terrestrial	#Geologic

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
21020	deep subsurface groundwater within a diatomaceous shale formation	Hokkaido, Horonobe-cho	Japan	JPN	Asia
67770	Deep-subsurface groundwater within a diatomaceous shale in Horonobe		Japan	JPN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
21020	1	Risk group (German classification)

Sequence information

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
21020	Methanosarcina subterranea gene for 16S rRNA, partial sequence	AB288264	1445		418010

GC content

@ref	GC-content (mol%)	Method
21020	41.5	high performance liquid chromatography (HPLC)

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Methanosarcina subterranea sp. nov., a methanogenic archaeon isolated from a deep subsurface diatomaceous shale formation.	Shimizu S, Ueno A, Naganuma T, Kaneko K	Int J Syst Evol Microbiol	10.1099/ijs.0.000072	2015

References

#20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#21020	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22503
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Methanosarcina subterranea (DSM 22503, JCM 15540, NBRC 102578)

Name and taxonomic classification

Morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

16S sequences

GC content

Genome-based predictions

Literature

Literature

References

BacDive

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