Hydrogenivirga okinawensis 12-2, LS12-2 | Type strain | DSM 17378, JCM 13302 | BacDiveID:510

Strain identifier

BacDive ID: 510

Type strain:

Species: Hydrogenivirga okinawensis

Strain Designation: 12-2, LS12-2

Culture col. no.: DSM 17378, JCM 13302

Strain history: T. Nunoura LS12-2.

NCBI tax ID(s): 345592 (species)

SI-ID 343446

JCM 13302, DSM 17378

Section

Hydrogenivirga okinawensis 12-2 is an aerobe, thermophilic, motile bacterium that was isolated from sulfide chimney structure at the Yonaguni Knoll IV hydrothermal field.

motile
rod-shaped
aerobe
thermophilic
16S sequence
Bacteria

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Aquificota*
	Class	*Aquificia*
	Order	*Aquificales*
	Family	*Aquificaceae*
	Genus	*Hydrogenivirga*
	Species	**Hydrogenivirga okinawensis**
	Full Scientific Name (LPSN)	Hydrogenivirga okinawensis Nunoura et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #31898]	Cell length	2.75 µm

[Ref.: #31898]	Cell width	0.45 µm

[Ref.: #31898]	Cell shape	rod-shaped

[Ref.: #31898]	Motility	yes

Multimedia content

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Information on culture and growth conditions Culture and growth conditions

Culture medium

HYDROGENIVIRGA OKINAWENSIS MEDIUM (DSMZ Medium 1131)

Culture medium growth

Culture medium link

Medium recipe at MediaDive

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #6935]			growth	72 °C
[Ref.: #31898]			growth	65-85 °C
[Ref.: #31898]			optimum	72.5 °C
[Ref.: #67770]			growth	70 °C

[Ref.: #6935]	Temperature range	thermophilic
[Ref.: #31898]	Temperature range	hyperthermophilic
[Ref.: #31898]	Temperature range	thermophilic
[Ref.: #67770]	Temperature range	thermophilic

	pH	Kind of pH		pH
[Ref.: #31898]			optimum	7.2
[Ref.: #31898]			growth	5.8-8.3

Information on physiology and metabolism Physiology and metabolism

Oxygen tolerance

aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31898]		NaCl		growth	01-04	%
[Ref.: #31898]		NaCl		optimum	2.5	%

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #6935]	Sample type/isolated from	sulfide chimney structure at the Yonaguni Knoll IV hydrothermal field
[Ref.: #6935]	Geographic location (country and/or sea, region)	Southern Okinawa Trough
[Ref.: #6935]	Country	Japan
[Ref.: #6935]	Country ISO 3 Code	JPN
[Ref.: #6935]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Deep-sea hydrothermal field at the Yonaguni Knoll IV
[Ref.: #67770]	Geographic location (country and/or sea, region)	Southern Okinawa Trough
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Hydrothermal vent
#Condition	#Sulfuric	-
#Condition	#Thermophilic (>45°C)	-

What are isolation sources categories?

Global distribution of 16S sequence AB235314 (>99% sequence identity) for Hydrogenivirga okinawensis subclade from Microbeatlas

Aquatic Samples	72
Soil Samples	2
Animal Samples	1
Plant Samples
Total Samples	75

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

Biosafety level

1

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #6935]	Hydrogenivirga okinawensis gene for 16S rRNA, partial sequence	AB235314	1461	ENA	345592 tax ID

[Ref.: #6935]	GC-content	51.3 mol%	high performance liquid chromatography (HPLC)
[Ref.: #31898]	GC-content	51.3 mol%

Availability in culture collections External links

Culture collection no.

DSM 17378, JCM 13302

SI-ID 343446

*

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Hydrogenivirga okinawensis sp. nov., a thermophilic sulfur-oxidizing chemolithoautotroph isolated from a deep-sea hydrothermal field, Southern Okinawa Trough.	Nunoura T, Miyazaki M, Suzuki Y, Takai K, Horikoshi K	Int J Syst Evol Microbiol	10.1099/ijs.0.64615-0	2008	*

References

#6935

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17378

#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 )

#31898

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 #28156 (see below)

#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 )

#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 .

#70189

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID343446.1 )

#28156

IJSEM 676 2008 ( DOI 10.1099/ijs.0.64615-0 , PubMed 18319477 )

* These data were automatically processed and therefore are not curated

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