Methanosarcina horonobensis (DSM 21571, JCM 15518, NBRC 102577)

Name: Methanosarcina horonobensis (DSM 21571, JCM 15518, NBRC 102577)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7131

Type strain

Strain Designation HB-1

Culture col. no. DSM 21571 JCM 15518 NBRC 102577 HB-1

NCBI tax ID(s) 1434110 418008

Special Collections DSMZ JCM

Links

Methanosarcina horonobensis HB-1 is an anaerobe, mesophilic prokaryote that was isolated from deep subsurface groundwater from a Miocene Wakkanai Formation aquifer consisting of siliceous mudstone.

anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 401545

JCM 15518,NBRC 102577,DSM 21571

@ref 20215

Last LPSN update 2025-12-16 09:48:30

Domain Methanobacteriati

Phylum Methanobacteriota

Class Methanosarcinia

Order Methanosarcinales

Family Methanosarcinaceae

Genus Methanosarcina

Species Methanosarcina horonobensis

Full scientific name Methanosarcina horonobensis Shimizu et al. 2011

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	99.2

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
15813	METHANOSARCINA MEDIUM (DSMZ Medium 120)		Medium recipe at MediaDive	Name: METHANOSARCINA MEDIUM (DSMZ Medium 120; with strain-specific modifications) Composition: Methanol 15.4688 g/l NaCl 5.85938 g/l Na-acetate 2.44141 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 (°C)	Range
15813	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

15813

Oxygen toleranceanaerobe

Spore formation

@ref	Spore formation	Confidence
125439		97.5

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
15813	deep subsurface groundwater from a Miocene Wakkanai Formation aquifer consisting of siliceous mudstone	Horonobe, Hokkaido	Japan	JPN	Asia
67770	Groundwater sampled from a subsurface Miocene formation located in Horonobe	Hokkaido	Japan	JPN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15813	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM97028v1 assembly for Methanosarcina horonobensis HB-1 = JCM 15518	complete	GCA_000970285	1434110.4	2627854269	1434110	95.98
66792	ASM131620v1 assembly for Methanosarcina horonobensis HB-1 = JCM 15518	contig	GCA_001316205	1434110.5	2684622506	1434110

Genome browser: GCA_000970285

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15813	Methanosarcina horonobensis gene for 16S rRNA, partial sequence	AB288262	1432		418008

GC content

@ref	GC-content (mol%)	Method
15813	41	high performance liquid chromatography (HPLC)
67770	41.4	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Methanosarcina horonobensis HB-1
IMG: 2627854269

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.50	no
125439	motility	BacteriaNetⓘ	no	81.70	no
125439	gram_stain	BacteriaNetⓘ	negative	99.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	76.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Methanosarcina horonobensis HB-1 = JCM 15518 HB-1
NCBI: GCA_000970285.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	66.99	no
125438	anaerobic	anaerobicⓘ	yes	82.92	yes
125438	aerobic	aerobicⓘ	no	87.37	yes
125438	spore-forming	spore-formingⓘ	no	81.16	no
125438	thermophilic	thermophileⓘ	no	85.70	yes
125438	flagellated	motile2+ⓘ	no	82.08	no

Literature

Title	Authors	Journal	DOI	Year
Correlation of Key Physiological Properties of Methanosarcina Isolates with Environment of Origin.	Zhou J, Holmes DE, Tang HY, Lovley DR.	Appl Environ Microbiol	10.1128/aem.00731-21	2021
Posttranslational Methylation of Arginine in Methyl Coenzyme M Reductase Has a Profound Impact on both Methanogenesis and Growth of Methanococcus maripaludis.	Lyu Z, Shao N, Chou CW, Shi H, Patel R, Duin EC, Whitman WB.	J Bacteriol	10.1128/jb.00654-19	2020
Convergent Evolution of Coenzyme Metabolism in Methanosarcina mazei: Insights Into Primitive Life and Metabolic Adaptations.	Saranya SV, Chellapandi P.	J Basic Microbiol	10.1002/jobm.70015	2025
Improved methane mitigation potential and modulated methane cycling microbial communities in arable soil by compost addition.	van den Bergh SG, Chardon I, Meima-Franke M, Perez G, Rocha GS, Brenzinger K, Korthals GW, Mayer J, Cougnon M, Reheul D, de Boer W, Bodelier PLE.	ISME Commun	10.1093/ismeco/ycaf139	2025
Superior resolution characterisation of microbial diversity in anaerobic digesters using full-length 16S rRNA gene amplicon sequencing.	Lam TYC, Mei R, Wu Z, Lee PKH, Liu WT, Lee PH.	Water Res	10.1016/j.watres.2020.115815	2020
Putative Extracellular Electron Transfer in Methanogenic Archaea.	Gao K, Lu Y.	Front Microbiol	10.3389/fmicb.2021.611739	2021
Response of soil microbial compositional and functional heterogeneity to grazing exclusion in alpine shrub and meadows in the Qinghai-Tibet Plateau.	Wang S, Abalori TA, Wang W, Deng X, Liu W, Wang J, Cao W.	Front Microbiol	10.3389/fmicb.2022.1038805	2022
Bacillus subtilis and Macleaya cordata extract regulate the rumen microbiota associated with enteric methane emission in dairy cows.	Jia P, Dong LF, Tu Y, Diao QY.	Microbiome	10.1186/s40168-023-01654-3	2023
Time-shifted expression of acetoclastic and methylotrophic methanogenesis by a single Methanosarcina genomospecies predominates the methanogen dynamics in Philippine rice field soil.	Li X, Bei Q, Rabiei Nematabad M, Peng J, Liesack W.	Microbiome	10.1186/s40168-023-01739-z	2024
Extracellular electron uptake in Methanosarcinales is independent of multiheme c-type cytochromes.	Yee MO, Rotaru AE.	Sci Rep	10.1038/s41598-019-57206-z	2020
Mechanisms for Electron Uptake by Methanosarcina acetivorans during Direct Interspecies Electron Transfer.	Holmes DE, Zhou J, Ueki T, Woodard T, Lovley DR.	mBio	10.1128/mbio.02344-21	2021
Early response of methanogenic archaea to H₂ as evaluated by metagenomics and metatranscriptomics.	Kakuk B, Wirth R, Maroti G, Szuhaj M, Rakhely G, Laczi K, Kovacs KL, Bagi Z.	Microb Cell Fact	10.1186/s12934-021-01618-y	2021
Stratified active archaeal communities in the sediments of Jiulong River estuary, China.	Li Q, Wang F, Chen Z, Yin X, Xiao X.	Front Microbiol	10.3389/fmicb.2012.00311	2012
Microbial methane formation in deep aquifers of a coal-bearing sedimentary basin, Germany.	Grundger F, Jimenez N, Thielemann T, Straaten N, Luders T, Richnow HH, Kruger M.	Front Microbiol	10.3389/fmicb.2015.00200	2015
Structural and Phylogenetic Diversity of Anaerobic Carbon-Monoxide Dehydrogenases.	Inoue M, Nakamoto I, Omae K, Oguro T, Ogata H, Yoshida T, Sako Y.	Front Microbiol	10.3389/fmicb.2018.03353	2018
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
Methanosarcina soligelidi sp. nov., a desiccation- and freeze-thaw-resistant methanogenic archaeon from a Siberian permafrost-affected soil.	Wagner D, Schirmack J, Ganzert L, Morozova D, Mangelsdorf K	Int J Syst Evol Microbiol	10.1099/ijs.0.046565-0	2013
Methanosarcina horonobensis sp. nov., a methanogenic archaeon isolated from a deep subsurface Miocene formation.	Shimizu S, Upadhye R, Ishijima Y, Naganuma T	Int J Syst Evol Microbiol	10.1099/ijs.0.028548-0	2010

References

#15813	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21571
#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 )
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#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 horonobensis (DSM 21571, JCM 15518, NBRC 102577)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000970285

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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