Name: Hydrogenovibrio halophilus HL 5
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 11933

Type strain:

Species: Hydrogenovibrio halophilus

Strain Designation: HL 5

Culture col. no.: DSM 15072, CIP 109407, UNIQEM U 221

Strain history: <- D. Y. Sorokin, Russian Academy of Sciences, Inst. of Microbiology, Moscow, Russia; HL 5 <- D. Y. Sorokin {2002}

NCBI tax ID(s): 1123516 (strain), 373391 (species)

SI-ID 297379

DSM 15072, CIP 109407

Section

Hydrogenovibrio halophilus HL 5 is a microaerophile, chemolithoautotroph, mesophilic bacterium that was isolated from sediments hypersaline lake.

Gram-negative
motile
vibrio-shaped
chemolithoautotroph
mesophilic
microaerophile
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Beggiatoales*
	Family	*Piscirickettsiaceae*
	Genus	*Hydrogenovibrio*
	Species	**Hydrogenovibrio halophilus**
	Full Scientific Name (LPSN)	Hydrogenovibrio halophilus (Sorokin et al. 2006) Boden et al. 2017

Synonym

Thiomicrospira halophila

Information on morphological and physiological properties Morphology

[Ref.: #43182]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.998

[Ref.: #43182]	Cell length	1.0-2.0 µm

[Ref.: #43182]	Cell width	0.3-0.5 µm

[Ref.: #43182]	Cell shape	vibrio-shaped

[Ref.: #43182]	Motility	yes

[Ref.: #43182]	Flagellum arrangement	monotrichous

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5696]

Culture medium

THIOHALOPHILUS MEDIUM (DSMZ Medium 1058)

[Ref.: #5696]

Culture medium growth

[Ref.: #5696]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5696]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #5696]	growth	30 °C
[Ref.: #43182]	maximum	43 °C
[Ref.: #43182]	minimum	20 °C
[Ref.: #43182]	optimum	30 °C

[Ref.: #5696]	Temperature range	mesophilic
[Ref.: #43182]	Temperature range	thermophilic
[Ref.: #43182]	Temperature range	psychrophilic
[Ref.: #43182]	Temperature range	mesophilic

		pH
[Ref.: #43182]	maximum	8.5
[Ref.: #43182]	minimum	6.5
[Ref.: #43182]	optimum	7.5-7.8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #5696]

Oxygen tolerance

microaerophile

[Ref.: #43182]

Nutrition type

chemolithoautotroph

[Ref.: #43182]	Type of spore	endospore
[Ref.: #43182]	Ability of spore formation	no
[Ref.: #43182]	Type of spore	exospore (microbial cyst)
[Ref.: #43182]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.991

	Salt		Salt conc.
[Ref.: #43182]	NaCl	optimum	1.5	M
[Ref.: #43182]	NaCl	minimum	0.5	M
[Ref.: #43182]	NaCl	maximum	3.5	M

[Ref.: #43182]

Observation

produce carboxysomes

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43182]	ammonium ChEBI	+	nitrogen source
[Ref.: #43182]	dihydrogen ChEBI	-	electron donor
[Ref.: #43182]	dioxygen ChEBI	+	electron acceptor
[Ref.: #43182]	iron ChEBI	-	electron donor
[Ref.: #43182]	manganese ChEBI	-	electron donor
[Ref.: #43182]	nitrate ChEBI	-	nitrogen source
[Ref.: #43182]	nitrite ChEBI	-	nitrogen source
[Ref.: #43182]	sulfide ChEBI	+	electron donor
[Ref.: #43182]	sulfite ChEBI	-	electron donor
[Ref.: #43182]	tetrathionate ChEBI	-	electron donor
[Ref.: #43182]	thiocyanate ChEBI	-	electron donor
[Ref.: #43182]	thiosulfate ChEBI	+	electron donor
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #43182]		cobalamin ChEBI	yes

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #43182]		cytochrome oxidase	+	1.9.3.1
[Ref.: #43182]		NiFe-hydrogenase	+

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

[Ref.: #5696]	Sample type/isolated from	sediments hypersaline lake
[Ref.: #5696]	Geographic location (country and/or sea, region)	south-western Siberia
[Ref.: #5696]	Country	Russia
[Ref.: #5696]	Country ISO 3 Code	RUS
[Ref.: #5696]	Continent	Asia

[Ref.: #43182]	Sample type/isolated from	Sediment from hypersaline lake
[Ref.: #43182]	Geographic location (country and/or sea, region)	Kulunda Steppe, Russia
[Ref.: #43182]	Country	Russia
[Ref.: #43182]	Country ISO 3 Code	RUS
[Ref.: #43182]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Lake (large)
#Environmental	#Aquatic	#Sediment
#Condition	#Saline	-

What are isolation sources categories?

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

[Ref.: #5696]

Biosafety level

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.: #5696]	Thiomicrospira halophila DSM 15072 genomic scaffold A377DRAFT_scaffold1.1, whole genome shotgun sequence	KB913033	2356686	ENA	1123516 tax ID
[Ref.: #43182]	16S rRNA gene sequences	DQ390450	1420	ENA	373391 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Hydrogenovibrio halophilus DSM 15072	GCA_000384235	scaffold	GenBank	1123516 tax ID	*
[Ref.: #66792]	Thiomicrospira halophila DSM 15072	1123516.3	wgs	PATRIC	1123516 tax ID	*
[Ref.: #66792]	Hydrogenovibrio halophilus DSM 15072	2517572244	draft	JGI IMG/M	1123516 tax ID	*

[Ref.: #43182]	GC-content	54.9 mol%
[Ref.: #5696]	GC-content	54.9 mol%	sequence analysis

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Hydrogenovibrio halophilus DSM 15072 DSM 15072 NCBI: GCA_000384235.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Hydrogenovibrio halophilus DSM 15072 DSM 15072 NCBI: GCA_000384235.1
[Ref.: #69480]	motile	yes	90.547	no
[Ref.: #69480]	flagellated	yes	91.719	yes
[Ref.: #69480]	gram-positive	no	99.207	yes
[Ref.: #69480]	anaerobic	no	95.122	yes
[Ref.: #69480]	aerobic	no	86.099	yes
[Ref.: #69480]	halophile	yes	58.923	yes
[Ref.: #69480]	spore-forming	no	95.704	no
[Ref.: #69480]	thermophile	no	81.305	no
[Ref.: #69480]	glucose-util	yes	52.741	no
[Ref.: #69480]	glucose-ferment	no	88.191	no

Availability in culture collections External links

[Ref.: #5696]

Culture collection no.

DSM 15072, CIP 109407, UNIQEM U 221

[Ref.: #81147]

SI-ID 297379

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Thiomicrospira halophila sp. nov., a moderately halophilic, obligately chemolithoautotrophic, sulfur-oxidizing bacterium from hypersaline lakes.	Sorokin DY, Tourova TP, Kolganova TV, Spiridonova EM, Berg IA, Muyzer G	Int J Syst Evol Microbiol	10.1099/ijs.0.64445-0	2006	*

References

#5696

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15072

#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 )

#43182

Rich Boden, Kathleen M. Scott, John Williams, Sydney Russel, Kirsten Antonen, Alex W. Rae and Lee P. Hutt: An evaluation of Thiomicrospira, Hydrogenovibrio and Thioalkalimicrobium: reclassification of four species of Thiomicrospira to each Thiomicrorhabdus gen. nov. and Hydrogenovibrio, and reclassification of all four species of Thioalkalimicrobium to Thiomicrospira. IJSEM 67: 1140 - 1151 2017 ( DOI 10.1099/ijsem.0.001855 , PubMed 28581925 )

#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) .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#81147

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-ID297379.1 )

* These data were automatically processed and therefore are not curated

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Hydrogenovibrio halophilus DSM 15072 DSM 15072

Hydrogenovibrio halophilus DSM 15072 DSM 15072

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