Methanofervidicoccus abyssi (DSM 105918, JCM 32161, HHB)

Name: Methanofervidicoccus abyssi (DSM 105918, JCM 32161, HHB)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 158497

Type strain

Strain Designation HHB

Culture col. no. DSM 105918 JCM 32161 HHB

NCBI tax ID(s) 2082189

Special Collections DSMZ JCM Literature strains

Links

Methanofervidicoccus abyssi HHB is an obligate anaerobe, thermophilic, coccus-shaped prokaryote that was isolated from a deep-sea hydrothermal vent chimney sample.

coccus-shaped obligate anaerobe thermophilic genome sequence

Name and taxonomic classification

SI-ID 396951

JCM 32161,DSM 105918

@ref 20215

Last LPSN update 2025-12-16 10:08:02

Domain Methanobacteriati

Phylum Methanobacteriota

Class Methanococci

Order Methanococcales

Family Methanococcaceae

Genus Methanofervidicoccus

Species Methanofervidicoccus abyssi

Full scientific name Methanofervidicoccus abyssi Sakai et al. 2019

Morphology

Cell morphology

@ref	Cell length	Cell shape	Motility
67852	0.8-2.3 µm	coccus-shaped

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
65173	METHANOCALDOCCUS LAUENSIS MEDIUM (DSMZ Medium 141a)		Medium recipe at MediaDive	Name: METHANOCALDOCCUS LAUENSIS MEDIUM (DSMZ Medium 141a) Composition: MgCl2 x 6 H2O 3.94867 g/l Na-acetate 0.987167 g/l L-Cysteine HCl x H2O 0.493583 g/l Na2S x 9 H2O 0.493583 g/l KCl 0.335637 g/l NH4Cl 0.246792 g/l K2HPO4 0.138203 g/l MgSO4 x 7 H2O 0.029615 g/l Nitrilotriacetic acid 0.0148075 g/l NaCl 0.00987167 g/l MnSO4 x H2O 0.00493583 g/l Fe(NH4)2(SO4)2 x 6 H2O 0.00197433 g/l ZnSO4 x 7 H2O 0.0017769 g/l CoSO4 x 7 H2O 0.0017769 g/l CaCl2 x 2 H2O 0.000987167 g/l FeSO4 x 7 H2O 0.000987167 g/l Sodium resazurin 0.000493583 g/l NiCl2 x 6 H2O 0.00029615 g/l AlK(SO4)2 x 12 H2O 0.000197433 g/l CuSO4 x 5 H2O 9.87167e-05 g/l H3BO3 9.87167e-05 g/l Na2MoO4 x 2 H2O 9.87167e-05 g/l Pyridoxine hydrochloride 9.87167e-05 g/l Nicotinic acid 4.93583e-05 g/l (DL)-alpha-Lipoic acid 4.93583e-05 g/l Riboflavin 4.93583e-05 g/l Thiamine HCl 4.93583e-05 g/l Calcium D-(+)-pantothenate 4.93583e-05 g/l p-Aminobenzoic acid 4.93583e-05 g/l Folic acid 1.97433e-05 g/l Biotin 1.97433e-05 g/l Na2WO4 x 2 H2O 3.94867e-06 g/l Na2SeO3 x 5 H2O 2.9615e-06 g/l Vitamin B12 9.87167e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
65173	positive	growth	70	thermophilic
67770	positive	growth	70	thermophilic
67852	positive	growth	60-80	hyperthermophilic
67852	positive	optimum	70	thermophilic

Culture pH

@ref	Ability	Type	PH
67852	positive	optimum	6-6.5
67852	positive	growth	5-7.4

Physiology and metabolism

Oxygen tolerance

67852

Oxygen toleranceobligate anaerobe

Halophily

@ref	Salt	Growth	Tested relation	Concentration
67852	NaCl	positive	growth	1-4 %(w/v)
67852	NaCl	positive	optimum	2-2.5 %(w/v)

Observation

@ref	Observation
67852	Cells are regular to irregular coccoid and occur singly and possess flagella.
67852	Methane is produced from H2 and CO2.
67852	Under the optimal condition (pH 6.5, 70°C with 2 % NaCl), the doubling time was approximately 2.3 h, as calculated from the methane production rate.

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
67852	30089 ChEBI	acetate	-	assimilation
67852	28938 ChEBI	ammonium	+	required for growth
67852	17045 ChEBI	dinitrogen oxide	-	nitrogen source
67852	15740 ChEBI	formate	-	assimilation
67852	17632 ChEBI	nitrate	-	nitrogen source
67852	26710 ChEBI	sodium chloride	+	required for growth

Antibiotic resistance

@ref	ChEBI	Metabolite	Resistance conc.	Sensitivity conc.
67852	28971	ampicillin	100 µg/mL
67852	17698	chloramphenicol		25 µg/mL
67852	6104	kanamycin	100 µg/mL
67852	28077	rifampicin		25 µg/mL
67852	17076	streptomycin	100 µg/mL
67852	27902	tetracycline	100 µg/mL
67852	28001	vancomycin	100 µg/mL

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Hydrothermal vent
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Latitude	Longitude	Enrichment culture	Enrichment culture temperature	Isolation procedure	Country ISO 3 Code	Continent
65173	a deep-sea hydrothermal vent chimney sample		Cayman Islands Exclusive Economic Zone	United Kingdom	18.5459	-81.7182 18.5459/-81.7182				GBR	Europe
67770	Deep-sea hydrothermal vent chimney sample from Beebe Vent Field at the Mid Cayman Spreading Center		Caribbean Sea
67852	deep-sea hydrothermal vent chimney at a water depth of 4963 m	2013-06	Beebe Vent Field in the Mid-Cayman Spreading Center, the Caribbean Sea	International waters	18.5459	-81.7181 18.5459/-81.7181	basal medium	70	Prior to cultivation, approximately 10 g of stored chimney samples were suspended in 10 ml of basal medium, which was slightly modified MJ synthetic seawater [19]; the concentrations of the following compounds were changed; NaCl, 20 gl-1; NH4Cl, 0.5 gl-1 and Na2NO3 was omitted. Then 0.5 ml suspended sample was inoculated into 5 ml basal medium under a gas phase of H2/CO2 [80:20 (v/v), 200 kPa], and serial dilution (1:5 dilution series) was performed at 70°C to evaluate the abundance of cultivable microorganisms. One of the grown cultures was isolated by using the dilution-to-extinction technique at 70°C and a pure culture was obtained.

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67852	ASM431039v1 assembly for Methanofervidicoccus abyssi HHB	contig	GCA_004310395	2082189.3	2993744746	2082189	78.38

GC content

@ref	GC-content (mol%)	Method
65173	35.2	sequence analysis
67852	35.3	genome sequence analysis
67852	35.9	high performance liquid chromatography (HPLC)
67770	35.9	genome sequence analysis

Genome-based predictions

Predictions

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Methanofervidicoccus abyssi HHB
NCBI: GCA_004310395.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	63.46	no
125438	anaerobic	anaerobicⓘ	yes	89.38	no
125438	aerobic	aerobicⓘ	no	89.06	no
125438	spore-forming	spore-formingⓘ	no	88.87	no
125438	thermophilic	thermophileⓘ	yes	69.27	yes
125438	flagellated	motile2+ⓘ	no	84.71	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Methanofervidicoccus abyssi gen. nov., sp. nov., a hydrogenotrophic methanogen, isolated from a hydrothermal vent chimney in the Mid-Cayman Spreading Center, the Caribbean Sea.	Sakai S, Takaki Y, Miyazaki M, Ogawara M, Yanagawa K, Miyazaki J, Takai K	Int J Syst Evol Microbiol	10.1099/ijsem.0.003297	2019

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 )
#65173	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 105918
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67852	Sanae Sakai, Yoshihiro Takaki, Masayuki Miyazaki, Miyuki Ogawara, Katsunori Yanagawa, Junichi Miyazaki, Ken Takai: Methanofervidicoccus abyssi gen. nov., sp. nov., a hydrogenotrophic methanogen, isolated from a hydrothermal vent chimney in the Mid-Cayman Spreading Center, the Caribbean Sea. IJSEM 69: 1225 - 1230 2019 ( DOI 10.1099/ijsem.0.003297 )
#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 )
#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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Methanofervidicoccus abyssi (DSM 105918, JCM 32161, HHB)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Halophily

Observation

Metabolite utilization

Antibiotic resistance

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_004310395

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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