Methanothermus fervidus (DSM 2088, ATCC 43054, JCM 10308)

Name: Methanothermus fervidus (DSM 2088, ATCC 43054, JCM 10308)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7137

Type strain

Strain Designation V24 S

Culture col. no. DSM 2088 ATCC 43054 JCM 10308 V24 S

NCBI tax ID(s) 523846 2180

Special Collections DSMZ JCM

History <- K. O. Stetter, Univ. Regensburg, Germany; V24 S <- K. O. Stetter {1980} DSM 2088 <-- K. O. Stetter V24S.

Links

Methanothermus fervidus V24 S is an anaerobe, hyperthermophilic prokaryote that was isolated from hot solfataric spring.

anaerobe hyperthermophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 47544

DSM 2088,ATCC 43054,JCM 10308

@ref 20215

Last LPSN update 2026-02-09 11:19:24

Domain Archaea

Phylum Methanobacteriota

Class Methanobacteria

Order Methanobacteriales

Family Methanothermaceae

Genus Methanothermus

Species Methanothermus fervidus

Full scientific name Methanothermus fervidus Stetter 1982

BacDive ID	Other strains from **Methanothermus fervidus** (2)	Type strain
7138	M. fervidus H9, DSM 3537
7139	M. fervidus KF1-St, DSM 3538

Morphology

Multimedia

@ref:	66793
multimedia content:	EM_DSM_2088_1.jpg
multimedia.multimedia content:	EM_DSM_2088_1.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
717	METHANOTHERMUS MEDIUM (DSMZ Medium 203)		Medium recipe at MediaDive	Name: METHANOTHERMUS MEDIUM (DSMZ Medium 203) Composition: Na2SO4 3.36967 g/l Trypticase peptone 1.98216 g/l Yeast extract 1.98216 g/l Na2CO3 0.99108 g/l L-Cysteine HCl x H2O 0.49554 g/l Na2S x 9 H2O 0.49554 g/l K2HPO4 0.222993 g/l (NH4)2SO4 0.222993 g/l KH2PO4 0.222993 g/l MgSO4 x 7 H2O 0.0297324 g/l Nitrilotriacetic acid 0.0148662 g/l NaCl 0.0099108 g/l MnSO4 x H2O 0.0049554 g/l CoSO4 x 7 H2O 0.00178394 g/l ZnSO4 x 7 H2O 0.00178394 g/l FeSO4 x 7 H2O 0.00099108 g/l CaCl2 x 2 H2O 0.00099108 g/l Sodium resazurin 0.00049554 g/l NiCl2 x 6 H2O 0.000297324 g/l AlK(SO4)2 x 12 H2O 0.000198216 g/l CuSO4 x 5 H2O 9.9108e-05 g/l H3BO3 9.9108e-05 g/l Na2MoO4 x 2 H2O 9.9108e-05 g/l Pyridoxine hydrochloride 9.9108e-05 g/l p-Aminobenzoic acid 4.9554e-05 g/l Calcium D-(+)-pantothenate 4.9554e-05 g/l Nicotinic acid 4.9554e-05 g/l Riboflavin 4.9554e-05 g/l Thiamine HCl 4.9554e-05 g/l (DL)-alpha-Lipoic acid 4.9554e-05 g/l Folic acid 1.98216e-05 g/l Biotin 1.98216e-05 g/l Na2WO4 x 2 H2O 3.96432e-06 g/l Na2SeO3 x 5 H2O 2.97324e-06 g/l Vitamin B12 9.9108e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
717	positive	growth	83	hyperthermophilic
67770	positive	growth	80	hyperthermophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
717	anaerobe
125438	anaerobe	90.127
125439	anaerobe	97

Spore formation

@ref	Spore formation	Confidence
125438		91.342

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	hydrogen production	100	5 of 5
66794	ribulose monophosphate pathway	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	mannosylglycerate biosynthesis	100	2 of 2
66794	suberin monomers biosynthesis	100	2 of 2
66794	flavin biosynthesis	93.33	14 of 15
66794	coenzyme M biosynthesis	90	9 of 10
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	vitamin B12 metabolism	82.35	28 of 34
66794	factor 420 biosynthesis	80	4 of 5
66794	methanofuran biosynthesis	80	4 of 5
66794	palmitate biosynthesis	77.27	17 of 22
66794	sulfopterin metabolism	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	methanogenesis from CO2	75	9 of 12
66794	gluconeogenesis	75	6 of 8
66794	NAD metabolism	72.22	13 of 18
66794	photosynthesis	71.43	10 of 14
66794	pyrimidine metabolism	68.89	31 of 45
66794	valine metabolism	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	serine metabolism	66.67	6 of 9
66794	enterobactin biosynthesis	66.67	2 of 3
66794	molybdenum cofactor biosynthesis	66.67	6 of 9
66794	cyanate degradation	66.67	2 of 3
66794	purine metabolism	62.77	59 of 94
66794	C4 and CAM-carbon fixation	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	vitamin B1 metabolism	61.54	8 of 13
66794	glutamate and glutamine metabolism	60.71	17 of 28
66794	cellulose degradation	60	3 of 5
66794	threonine metabolism	60	6 of 10
66794	glycolysis	58.82	10 of 17
66794	citric acid cycle	57.14	8 of 14
66794	heme metabolism	57.14	8 of 14
66794	reductive acetyl coenzyme A pathway	57.14	4 of 7
66794	CO2 fixation in Crenarchaeota	55.56	5 of 9
66794	phenylalanine metabolism	53.85	7 of 13
66794	peptidoglycan biosynthesis	53.33	8 of 15
66794	glycogen biosynthesis	50	2 of 4
66794	CMP-KDO biosynthesis	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	CDP-diacylglycerol biosynthesis	50	1 of 2
66794	adipate degradation	50	1 of 2
66794	propionate fermentation	50	5 of 10
66794	phenylmercury acetate degradation	50	1 of 2
66794	biotin biosynthesis	50	2 of 4
66794	pantothenate biosynthesis	50	3 of 6
66794	selenocysteine biosynthesis	50	3 of 6
66794	ethanol fermentation	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	tyrosine metabolism	50	7 of 14
66794	histidine metabolism	48.28	14 of 29
66794	lysine metabolism	45.24	19 of 42
66794	nitrate assimilation	44.44	4 of 9
66794	methionine metabolism	42.31	11 of 26
66794	arginine metabolism	41.67	10 of 24
66794	gallate degradation	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	glycogen metabolism	40	2 of 5
66794	methylglyoxal degradation	40	2 of 5
66794	degradation of hexoses	38.89	7 of 18
66794	leucine metabolism	38.46	5 of 13
66794	oxidative phosphorylation	38.46	35 of 91
66794	ketogluconate metabolism	37.5	3 of 8
66794	tryptophan metabolism	36.84	14 of 38
66794	non-pathway related	36.84	14 of 38
66794	pentose phosphate pathway	36.36	4 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
66794	proline metabolism	36.36	4 of 11
66794	vitamin B6 metabolism	36.36	4 of 11
66794	tetrahydrofolate metabolism	35.71	5 of 14
66794	lipid metabolism	35.48	11 of 31
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	methane metabolism	33.33	1 of 3
66794	formaldehyde oxidation	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	acetoin degradation	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	urea cycle	30.77	4 of 13
66794	sulfate reduction	30.77	4 of 13
66794	isoprenoid biosynthesis	30.77	8 of 26
66794	Entner Doudoroff pathway	30	3 of 10
66794	mevalonate metabolism	28.57	2 of 7
66794	cardiolipin biosynthesis	28.57	2 of 7
66794	alanine metabolism	27.59	8 of 29
66794	toluene degradation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	acetate fermentation	25	1 of 4
66794	allantoin degradation	22.22	2 of 9
66794	polyamine pathway	21.74	5 of 23
66794	degradation of pentoses	21.43	6 of 28
66794	glutathione metabolism	21.43	3 of 14

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Thermal spring
#Condition	#Sulfuric	-
#Condition	#Thermophilic (>45°C)	-

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
717	hot solfataric spring	Iceland	ISL	Europe
67770	Hot spring	Iceland	ISL	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
717	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	ASM16609v1 assembly for Methanothermus fervidus DSM 2088	complete	GCA_000166095	523846.9	649633067	523846	74.4

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
717	Methanothermus fervidus 16S ribosomal RNA	M59145	1479		2180

GC content

@ref	GC-content (mol%)	Method
717	33.0
67770	33	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Methanothermus fervidus V24S, DSM 2088
IMG: 649633067

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	52.80	no
125439	motility	BacteriaNetⓘ	yes	66.00	no
125439	gram_stain	BacteriaNetⓘ	variable	71.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	97.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Methanothermus fervidus DSM 2088 DSM 2088
NCBI: GCA_000166095.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	51.74	no
125438	anaerobic	anaerobicⓘ	yes	90.13	no
125438	aerobic	aerobicⓘ	no	89.34	no
125438	spore-forming	spore-formingⓘ	no	91.34	no
125438	thermophilic	thermophileⓘ	yes	70.13	yes
125438	flagellated	motile2+ⓘ	no	79.46	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Identification of enriched hyperthermophilic microbial communities from a deep-sea hydrothermal vent chimney under electrolithoautotrophic culture conditions.	Pillot G, Amin Ali O, Davidson S, Shintu L, Godfroy A, Combet-Blanc Y, Bonin P, Liebgott PP.	Sci Rep	10.1038/s41598-021-94135-2	2021
	Complete genome sequence of Methanothermus fervidus type strain (V24S).	Anderson I, Djao OD, Misra M, Chertkov O, Nolan M, Lucas S, Lapidus A, Del Rio TG, Tice H, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Brambilla E, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Sikorski J, Spring S, Rohde M, Eichinger K, Huber H, Wirth R, Goker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC.	Stand Genomic Sci	10.4056/sigs.1283367	2010
Enzymology	Isolation of an Obligate Mixotrophic Methanogen That Represents the Major Population in Thermophilic Fixed-Bed Anaerobic Digesters.	Nagoya M, Kouzuma A, Ueno Y, Watanabe K.	Microorganisms	10.3390/microorganisms8020217	2020
Enzymology	A Reduced F₄₂₀-Dependent Nitrite Reductase in an Anaerobic Methanotrophic Archaeon.	Heryakusuma C, Susanti D, Yu H, Li Z, Purwantini E, Hettich RL, Orphan VJ, Mukhopadhyay B.	J Bacteriol	10.1128/jb.00078-22	2022
Genetics	Archaea Microbiome Dysregulated Genes and Pathways as Molecular Targets for Lung Adenocarcinoma and Squamous Cell Carcinoma.	Uzelac M, Li Y, Chakladar J, Li WT, Ongkeko WM.	Int J Mol Sci	10.3390/ijms231911566	2022
	Genome-resolved metagenomics and metatranscriptomics reveal niche differentiation in functionally redundant microbial communities at deep-sea hydrothermal vents.	Galambos D, Anderson RE, Reveillaud J, Huber JA.	Environ Microbiol	10.1111/1462-2920.14806	2019
	Veillonella, Firmicutes: Microbes disguised as Gram negatives.	Vesth T, Ozen A, Andersen SC, Kaas RS, Lukjancenko O, Bohlin J, Nookaew I, Wassenaar TM, Ussery DW.	Stand Genomic Sci	10.4056/sigs.2981345	2013
Metabolism	An intertwined evolutionary history of methanogenic archaea and sulfate reduction.	Susanti D, Mukhopadhyay B.	PLoS One	10.1371/journal.pone.0045313	2012
	Phylogeny and Taxonomy of Archaea: A Comparison of the Whole-Genome-Based CVTree Approach with 16S rRNA Sequence Analysis.	Zuo G, Xu Z, Hao B.	Life (Basel)	10.3390/life5010949	2015
	Peptidoglycan: a post-genomic analysis.	Cayrou C, Henrissat B, Gouret P, Pontarotti P, Drancourt M.	BMC Microbiol	10.1186/1471-2180-12-294	2012
	Protein signature-based estimation of metagenomic abundances including all domains of life and viruses.	Klingenberg H, Asshauer KP, Lingner T, Meinicke P.	Bioinformatics	10.1093/bioinformatics/btt077	2013
Metabolism	An uncharacterized member of the ribokinase family in Thermococcus kodakarensis exhibits myo-inositol kinase activity.	Sato T, Fujihashi M, Miyamoto Y, Kuwata K, Kusaka E, Fujita H, Miki K, Atomi H.	J Biol Chem	10.1074/jbc.m113.457259	2013
Enzymology	Cloning, sequencing, and expression of the gene encoding cyclic 2, 3-diphosphoglycerate synthetase, the key enzyme of cyclic 2, 3-diphosphoglycerate metabolism in Methanothermus fervidus.	Matussek K, Moritz P, Brunner N, Eckerskorn C, Hensel R.	J Bacteriol	10.1128/jb.180.22.5997-6004.1998	1998
	Organic solutes in hyperthermophilic archaea.	Martins LO, Huber R, Huber H, Stetter KO, Da Costa MS, Santos H.	Appl Environ Microbiol	10.1128/aem.63.3.896-902.1997	1997
Metabolism	Phylogenomic reconstruction of archaeal fatty acid metabolism.	Dibrova DV, Galperin MY, Mulkidjanian AY.	Environ Microbiol	10.1111/1462-2920.12359	2014
Enzymology	Reverse gyrase, a hallmark of the hyperthermophilic archaebacteria.	Bouthier de la Tour C, Portemer C, Nadal M, Stetter KO, Forterre P, Duguet M.	J Bacteriol	10.1128/jb.172.12.6803-6808.1990	1990
	S-Layer proteins.	Sara M, Sleytr UB.	J Bacteriol	10.1128/jb.182.4.859-868.2000	2000
Metabolism	Posttranscriptional modification of tRNA in thermophilic archaea (Archaebacteria).	Edmonds CG, Crain PF, Gupta R, Hashizume T, Hocart CH, Kowalak JA, Pomerantz SC, Stetter KO, McCloskey JA.	J Bacteriol	10.1128/jb.173.10.3138-3148.1991	1991
	S-layer nanoglycobiology of bacteria.	Messner P, Steiner K, Zarschler K, Schaffer C.	Carbohydr Res	10.1016/j.carres.2007.12.025	2008
Enzymology	ADP-dependent phosphofructokinases in mesophilic and thermophilic methanogenic archaea.	Verhees CH, Tuininga JE, Kengen SW, Stams AJ, van der Oost J, de Vos WM.	J Bacteriol	10.1128/jb.183.24.7145-7153.2001	2001
Phylogeny	Discontinuous occurrence of the hsp70 (dnaK) gene among Archaea and sequence features of HSP70 suggest a novel outlook on phylogenies inferred from this protein.	Gribaldo S, Lumia V, Creti R, Conway de Macario E, Sanangelantoni A, Cammarano P.	J Bacteriol	10.1128/jb.181.2.434-443.1999	1999

References

#717	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 2088
#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) .
#66793	Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#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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Methanothermus fervidus (DSM 2088, ATCC 43054, JCM 10308)

Name and taxonomic classification

Morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000166095

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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