Hydrogenovibrio marinus (DSM 11271, JCM 7688)

Name: Hydrogenovibrio marinus (DSM 11271, JCM 7688)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11902

Type strain

Culture col. no. DSM 11271 JCM 7688

NCBI tax ID(s) 1123513 28885

Special Collections DSMZ JCM

History DSMZ <- JCM <- T. Kodama, strain MH-110 JCM <-- T. Kodama MH-110.

Links

Hydrogenovibrio marinus DSM 11271 is a bacterium that was isolated from sea water.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 49062

JCM 7688,CECT 2870,CBS 620.72,DSM 11271

@ref 20215

Last LPSN update 2026-05-29 08:27:40

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Beggiatoales

Family Piscirickettsiaceae

Genus Hydrogenovibrio

Species Hydrogenovibrio marinus

Full scientific name Hydrogenovibrio marinus Nishihara et al. 1991

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	99.5

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
4273	MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81)		Medium recipe at MediaDive	Name: MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81; with strain-specific modifications) Composition: NaCl 30.0 g/l Agar 20.1005 g/l Na2HPO4 x 2 H2O 2.91457 g/l KH2PO4 2.31156 g/l NH4Cl 1.00503 g/l MgSO4 x 7 H2O 0.502512 g/l Ferric ammonium citrate 0.0502513 g/l CaCl2 x 2 H2O 0.0100503 g/l NaVO3 x H2O 0.00502512 g/l Thiamine-HCl x 2 H2O 0.00251256 g/l Nicotinic acid 0.00251256 g/l Pyridoxine hydrochloride 0.00251256 g/l Calcium pantothenate 0.00251256 g/l H3BO3 0.00150754 g/l CoCl2 x 6 H2O 0.00100503 g/l Riboflavin 0.000502513 g/l ZnSO4 x 7 H2O 0.000502513 g/l MnCl2 x 4 H2O 0.000150754 g/l Na2MoO4 x 2 H2O 0.000150754 g/l NiCl2 x 6 H2O 0.000100503 g/l CuCl2 x 2 H2O 5.02513e-05 g/l Vitamin B12 5.02513e-05 g/l Folic acid 1.00503e-05 g/l Biotin 5.02513e-06 g/l Distilled water
4273	HYDROGENOBACTER HALOPHILUS MEDIUM (DSMZ Medium 744)		Medium recipe at MediaDive	Name: HYDROGENOBACTER HALOPHILUS MEDIUM (DSMZ Medium 744) Composition: NaCl 29.3 g/l K2HPO4 2.5 g/l (NH4)2SO4 2.0 g/l KH2PO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l CaCl2 0.01 g/l FeSO4 x 7 H2O 0.01 g/l ZnSO4 x 7 H2O 1.4e-05 g/l CoCl2 x 6 H2O 2e-06 g/l MnSO4 x 5 H2O 2e-06 g/l MoO3 2e-06 g/l H3BO3 2e-06 g/l CuSO4 x 5 H2O 1e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
4273	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	91.421

Spore formation

@ref	Spore formation	Confidence
125439		99.71
125438		93.703

Compound production

4273

Compoundribulose-1,5-bisphosphate carboxylase

Observation

67770

Observationquinones: Q-8

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	cyanate degradation	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	coenzyme A metabolism	100	4 of 4
66794	biotin biosynthesis	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	tetrahydrofolate metabolism	100	14 of 14
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CMP-KDO biosynthesis	100	4 of 4
66794	palmitate biosynthesis	95.45	21 of 22
66794	photosynthesis	92.86	13 of 14
66794	threonine metabolism	90	9 of 10
66794	lipid A biosynthesis	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	pentose phosphate pathway	81.82	9 of 11
66794	hydrogen production	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	heme metabolism	78.57	11 of 14
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	valine metabolism	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	glycogen biosynthesis	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	vitamin B6 metabolism	72.73	8 of 11
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glutathione metabolism	71.43	10 of 14
66794	vitamin B1 metabolism	69.23	9 of 13
66794	phenylalanine metabolism	69.23	9 of 13
66794	glutamate and glutamine metabolism	67.86	19 of 28
66794	flavin biosynthesis	66.67	10 of 15
66794	octane oxidation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	acetoin degradation	66.67	2 of 3
66794	serine metabolism	66.67	6 of 9
66794	formaldehyde oxidation	66.67	2 of 3
66794	NAD metabolism	66.67	12 of 18
66794	glycolysis	64.71	11 of 17
66794	purine metabolism	62.77	59 of 94
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	leucine metabolism	61.54	8 of 13
66794	sulfate reduction	61.54	8 of 13
66794	glycogen metabolism	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	pyrimidine metabolism	60	27 of 45
66794	starch degradation	60	6 of 10
66794	alanine metabolism	58.62	17 of 29
66794	cysteine metabolism	55.56	10 of 18
66794	non-pathway related	55.26	21 of 38
66794	methionine metabolism	53.85	14 of 26
66794	suberin monomers biosynthesis	50	1 of 2
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	tryptophan metabolism	50	19 of 38
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	gluconeogenesis	50	4 of 8
66794	C4 and CAM-carbon fixation	50	4 of 8
66794	tyrosine metabolism	50	7 of 14
66794	ketogluconate metabolism	50	4 of 8
66794	butanoate fermentation	50	2 of 4
66794	selenocysteine biosynthesis	50	3 of 6
66794	adipate degradation	50	1 of 2
66794	citric acid cycle	50	7 of 14
66794	glycine metabolism	50	5 of 10
66794	histidine metabolism	48.28	14 of 29
66794	lysine metabolism	47.62	20 of 42
66794	urea cycle	46.15	6 of 13
66794	proline metabolism	45.45	5 of 11
66794	metabolism of disaccharids	45.45	5 of 11
66794	CO2 fixation in Crenarchaeota	44.44	4 of 9
66794	degradation of sugar alcohols	43.75	7 of 16
66794	propanol degradation	42.86	3 of 7
66794	oxidative phosphorylation	41.76	38 of 91
66794	arginine metabolism	41.67	10 of 24
66794	glycine betaine biosynthesis	40	2 of 5
66794	propionate fermentation	40	4 of 10
66794	Entner Doudoroff pathway	40	4 of 10
66794	3-phenylpropionate degradation	40	6 of 15
66794	lipid metabolism	38.71	12 of 31
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	isoprenoid biosynthesis	34.62	9 of 26
66794	L-lactaldehyde degradation	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	nitrate assimilation	33.33	3 of 9
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	mevalonate metabolism	28.57	2 of 7
66794	degradation of hexoses	27.78	5 of 18
66794	ascorbate metabolism	27.27	6 of 22
66794	androgen and estrogen metabolism	25	4 of 16
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	phenol degradation	25	5 of 20
66794	degradation of pentoses	25	7 of 28
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	phenylpropanoid biosynthesis	23.08	3 of 13
66794	arachidonic acid metabolism	22.22	4 of 18
66794	polyamine pathway	21.74	5 of 23

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
4273	sea water	Shonan Coast, Kanagawa	Japan	JPN	Asia
67770	Seawater of the Shonan Coast	Kanagawa Pref.	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence D86374 (>99% sequence identity) for Hydrogenovibrio marinus subclade from Microbeatlas

Aquatic Samples	542
Soil Samples	84
Animal Samples	113
Plant Samples	14
Total Samples	753

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
4273	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	ASM1334084v1 assembly for Hydrogenovibrio marinus MH-110	complete	GCA_013340845	28885.6	8001990730	28885	99.27
67770	ASM71131v1 assembly for Hydrogenovibrio marinus DSM 11271	contig	GCA_000711315	1123513.6	2571042915	1123513	78.77
67770	HydMar1.0 assembly for Hydrogenovibrio marinus MH-110	scaffold	GCA_000696325	28885.5	2579778966	28885	55.57

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Hydrogenovibrio marinus gene for 16S rRNA, partial sequence	D86374	1409		28885

GC content

@ref	GC-content (mol%)	Method
4273	44.1
67770	44.1	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: ASM1334084v1 assembly for Hydrogenovibrio marinus MH-110
BV-BRC: 28885.6

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	91.42	no
125439	motility	BacteriaNetⓘ	yes	44.60	no
125439	gram_stain	BacteriaNetⓘ	negative	89.94	no
125439	spore_formation	BacteriaNetⓘ	no	99.71	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Hydrogenovibrio marinus strain MH-110
PATRIC: 28885.6

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.50	no
125438	anaerobic	anaerobicⓘ	no	75.99	no
125438	spore-forming	spore-formingⓘ	no	93.70	no
125438	aerobic	aerobicⓘ	no	51.83	no
125438	thermophilic	thermophileⓘ	no	94.73	yes
125438	flagellated	motile2+ⓘ	yes	76.78	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Continuous Valorization of Carbon Dioxide into the Fine Chemical Ectoine by Hydrogenovibrio marinus: A New Strategy for Pharmaceutical Production.	Huang-Lin E, Lebrero R, Cantera S.	Environ Sci Technol	10.1021/acs.est.4c12259	2025
	Complete Genome Sequence of a Mesophilic Obligately Chemolithoautotrophic Hydrogen-Oxidizing Bacterium, Hydrogenovibrio marinus MH-110.	Arai H, Ishii M.	Microbiol Resour Announc	10.1128/mra.01132-19	2019
Metabolism	Activation of formate hydrogen-lyase via expression of uptake [NiFe]-hydrogenase in Escherichia coli BL21(DE3).	Jo BH, Cha HJ.	Microb Cell Fact	10.1186/s12934-015-0343-0	2015
Enzymology	Distribution of Hydrogenases in Cyanobacteria: A Phylum-Wide Genomic Survey.	Puggioni V, Tempel S, Latifi A.	Front Genet	10.3389/fgene.2016.00223	2016
Phylogeny	A Genus Definition for Bacteria and Archaea Based on a Standard Genome Relatedness Index.	Barco RA, Garrity GM, Scott JJ, Amend JP, Nealson KH, Emerson D.	mBio	10.1128/mbio.02475-19	2020
Metabolism	Diversity in CO₂-Concentrating Mechanisms among Chemolithoautotrophs from the Genera Hydrogenovibrio, Thiomicrorhabdus, and Thiomicrospira, Ubiquitous in Sulfidic Habitats Worldwide.	Scott KM, Leonard JM, Boden R, Chaput D, Dennison C, Haller E, Harmer TL, Anderson A, Arnold T, Budenstein S, Brown R, Brand J, Byers J, Calarco J, Campbell T, Carter E, Chase M, Cole M, Dwyer D, Grasham J, Hanni C, Hazle A, Johnson C, Johnson R, Kirby B, Lewis K, Neumann B, Nguyen T, Nino Charari J, Morakinyo O, Olsson B, Roundtree S, Skjerve E, Ubaldini A, Whittaker R.	Appl Environ Microbiol	10.1128/aem.02096-18	2019
Enzymology	Applications of Marine-Derived Microorganisms and Their Enzymes in Biocatalysis and Biotransformation, the Underexplored Potentials.	Birolli WG, Lima RN, Porto ALM.	Front Microbiol	10.3389/fmicb.2019.01453	2019
Phylogeny	Jeotgalibacillus soli sp. nov., a Gram-stain-positive bacterium isolated from soil.	Cunha S, Tiago I, Paiva G, Nobre F, da Costa MS, Verissimo A.	Int J Syst Evol Microbiol	10.1099/ijs.0.028878-0	2012

References

#4273	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 11271
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#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) .
#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;
#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 )

Content

About us

Hydrogenovibrio marinus (DSM 11271, JCM 7688)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Compound production

Observation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_013340845

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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