Methanobacterium arcticum (DSM 19844, VKM B-2371, M2)

Name: Methanobacterium arcticum (DSM 19844, VKM B-2371, M2)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6950

Type strain

Strain Designation M2

Culture col. no. DSM 19844 VKM B-2371 M2

NCBI tax ID(s) 386456

Special Collections DSMZ Literature strains

Links

Methanobacterium arcticum M2 is an anaerobe, mesophilic, Gram-negative prokaryote that was isolated from Holocene permafrost sediments.

Gram-negative rod-shaped anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 401709

VKM B-2371,DSM 19844

@ref 20215

Last LPSN update 2025-12-16 09:48:27

Domain Methanobacteriati

Phylum Methanobacteriota

Class Methanobacteria

Order Methanobacteriales

Family Methanobacteriaceae

Genus Methanobacterium

Species Methanobacterium arcticum

Full scientific name Methanobacterium arcticum Shcherbakova et al. 2011

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29798	negative	4.5 µm	0.475 µm	rod-shaped
125439	negative				97.1
125438					90.875

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
8345	METHANOGENIUM MEDIUM (H2/CO2) (DSMZ Medium 141)		Medium recipe at MediaDive	Name: METHANOGENIUM MEDIUM (H2/CO2) (DSMZ Medium 141) Composition: NaHCO3 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 FeSO4 x 7 H2O 0.000978474 g/l CaCl2 x 2 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 Na2MoO4 x 2 H2O 9.78474e-05 g/l H3BO3 9.78474e-05 g/l Nicotinic acid 4.89237e-05 g/l Riboflavin 4.89237e-05 g/l (DL)-alpha-Lipoic acid 4.89237e-05 g/l Thiamine HCl 4.89237e-05 g/l Calcium D-(+)-pantothenate 4.89237e-05 g/l p-Aminobenzoic acid 4.89237e-05 g/l Folic acid 1.95695e-05 g/l Biotin 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	Growth	Type	Temperature (°C)	Range
8345	positive	growth	37	mesophilic
29798	positive	growth	15-45
29798	positive	optimum	37	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
29798	positive	optimum	7
29798	positive	growth	5.5-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
8345	anaerobe
29798	anaerobe

Spore formation

@ref	Spore formation	Confidence
29798
125439		95.4

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29798	NaCl	positive	growth	0-1.74 %
29798	NaCl	positive	optimum	0.58 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29798	15740 ChEBI	formate	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
29798	16183 ChEBI	methane

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Permafrost
#Environmental	#Terrestrial	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
8345	Holocene permafrost sediments	Kolyma Lowland, Russia (70° 06' N 154° 04' E)	Russia	RUS	Asia	70.1	154.067 70.1/154.067

Taxonmaps

69479

Global distribution of 16S sequence DQ517520 (>99% sequence identity) for Methanobacterium from Microbeatlas

Aquatic Samples	94
Soil Samples	80
Animal Samples	15
Plant Samples	58
Total Samples	247

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8345	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	ASM74607v1 assembly for Methanobacterium arcticum M2	scaffold	GCA_000746075	386456.3	2574179771	386456	67.52

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
8345	Methanobacterium arcticum 16S ribosomal RNA gene, partial sequence	DQ517520	1434		386456

GC content

@ref	GC-content (mol%)	Method
8345	38.1	thermal denaturation, midpoint method (Tm)
29798	38.1

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Methanobacterium arcticum M2
NCBI: GCA_000746075

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.40	no
125439	motility	BacteriaNetⓘ	no	73.80	no
125439	gram_stain	BacteriaNetⓘ	negative	97.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	75.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Methanobacterium arcticum M2
NCBI: GCA_000746075.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	65.31	yes
125438	anaerobic	anaerobicⓘ	yes	88.76	yes
125438	aerobic	aerobicⓘ	no	85.62	yes
125438	spore-forming	spore-formingⓘ	no	85.16	yes
125438	thermophilic	thermophileⓘ	no	79.09	yes
125438	flagellated	motile2+ⓘ	no	90.88	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Proteiniphilum and Methanothrix harundinacea became dominant acetate utilizers in a methanogenic reactor operated under strong ammonia stress.	Feng G, Zeng Y, Wang HZ, Chen YT, Tang YQ.	Front Microbiol	10.3389/fmicb.2022.1098814	2022
	High Tolerance of Hydrogenothermus marinus to Sodium Perchlorate.	Beblo-Vranesevic K, Huber H, Rettberg P.	Front Microbiol	10.3389/fmicb.2017.01369	2017
Phylogeny	Methanobacterium arcticum sp. nov., a methanogenic archaeon from Holocene Arctic permafrost.	Shcherbakova V, Rivkina E, Pecheritsyna S, Laurinavichius K, Suzina N, Gilichinsky D	Int J Syst Evol Microbiol	10.1099/ijs.0.021311-0	2010

References

#8345	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19844
#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 )
#26176	IJSEM 144 2013 ( DOI 10.1099/ijs.0.021311-0 , PubMed 20173003 )
#29798	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26176
#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) .
#69479	João 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.: MicrobeAtlas 1.0 beta .
#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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Methanobacterium arcticum (DSM 19844, VKM B-2371, M2)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000746075

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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