Name: Thermovibrio ammonificans HB-1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17646

Type strain:

Species: Thermovibrio ammonificans

Strain Designation: HB-1

Culture col. no.: DSM 15698, JCM 12110

Strain history: C. Vetriani HB-1.

NCBI tax ID(s): 648996 (strain), 228745 (species)

SI-ID 130854

DSM 15698, JCM 12110

Section

Thermovibrio ammonificans HB-1 is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from wall of black smoker chimney.

Gram-negative
motile
rod-shaped
anaerobe
thermophilic
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	*Aquificota*
	Class	*Aquificia*
	Order	*Desulfurobacteriales*
	Family	*Desulfurobacteriaceae*
	Genus	*Thermovibrio*
	Species	**Thermovibrio ammonificans**
	Full Scientific Name (LPSN)	Thermovibrio ammonificans Vetriani et al. 2004

Information on morphological and physiological properties Morphology

[Ref.: #29981]	Gram stain	negative

[Ref.: #29981]	Cell length	1 µm

[Ref.: #29981]	Cell width	0.6 µm

[Ref.: #29981]	Cell shape	rod-shaped

[Ref.: #29981]	Motility	yes

[Ref.: #29981]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6064]

Culture medium

THERMOVIBRIO AMMONIFICANS MEDIUM (DSMZ Medium 792a)

[Ref.: #6064]

Culture medium growth

[Ref.: #6064]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6064]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #6064]	growth	75 °C
[Ref.: #29981]	growth	60-80 °C
[Ref.: #29981]	optimum	75 °C
[Ref.: #67770]	growth	75 °C

[Ref.: #6064]	Temperature range	thermophilic
[Ref.: #29981]	Temperature range	hyperthermophilic
[Ref.: #29981]	Temperature range	thermophilic
[Ref.: #67770]	Temperature range	thermophilic

	pH	Kind of pH		pH
[Ref.: #29981]			optimum	5.5
[Ref.: #29981]			growth	05-07

Information on physiology and metabolism Physiology and metabolism

[Ref.: #6064]	Oxygen tolerance	anaerobe
[Ref.: #29981]	Oxygen tolerance	anaerobe

[Ref.: #29981]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29981]		NaCl		growth	0.5-4.5	%
[Ref.: #29981]		NaCl		optimum	2	%

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #29981]		catalase	+	1.11.1.6

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

[Ref.: #6064]	Sample type/isolated from	wall of black smoker chimney
[Ref.: #6064]	Geographic location (country and/or sea, region)	Deep-Sea hydrothermal vent
[Ref.: #6064]	Geographic location	9.8333°/-104.3000°

[Ref.: #67770]	Sample type/isolated from	Walls of an active deep-sea hydrothermal vent chimney on the East Pacific Rise
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Hydrothermal vent

What are isolation sources categories?

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

[Ref.: #6064]

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.: #6064]	Thermovibrio ammoniificans strain HB-1 16S ribosomal RNA gene, partial sequence	AY263403	1472	ENA	648996 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Thermovibrio ammonificans HB-1	GCA_000185805	complete	GenBank	648996 tax ID	*
[Ref.: #66792]	Thermovibrio ammonificans HB-1	648996.25	plasmid	PATRIC	648996 tax ID	*
[Ref.: #66792]	Thermovibrio ammonificans HB-1	648996.5	complete	PATRIC	648996 tax ID	*
[Ref.: #66792]	Thermovibrio ammonificans HB-1	649633104	complete	JGI IMG/M	648996 tax ID	*

[Ref.: #6064]	GC-content	54.6 mol%
[Ref.: #67770]	GC-content	54.6 mol%	high performance liquid chromatography (HPLC)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Thermovibrio ammonificans HB-1 HB-1 NCBI: GCA_000185805.1
[Ref.: #69480]	motile	yes	83.81	yes
[Ref.: #69480]	flagellated	no	92.318	no
[Ref.: #69480]	gram-positive	no	99.473	yes
[Ref.: #69480]	anaerobic	yes	98.366	no
[Ref.: #69480]	aerobic	no	98.946	yes
[Ref.: #69480]	halophile	no	81.184	no
[Ref.: #69480]	spore-forming	no	95.326	yes
[Ref.: #69480]	glucose-util	no	51.953	no
[Ref.: #69480]	thermophile	yes	100	yes
[Ref.: #69480]	glucose-ferment	no	84.352	no

Availability in culture collections External links

[Ref.: #6064]

Culture collection no.

DSM 15698, JCM 12110

[Ref.: #86637]

SI-ID 130854

Literature:

	Title	Authors	Journal	DOI	Year
Genetics	Complete genome sequence of Thermovibrio ammonificans HB-1(T), a thermophilic, chemolithoautotrophic bacterium isolated from a deep-sea hydrothermal vent.	Giovannelli D, Ricci J, Perez-Rodriguez I, Hugler M, O'Brien C, Keddis R, Grosche A, Goodwin L, Bruce D, Davenport KW, Detter C, Han J, Han S, Ivanova N, Land ML, Mikhailova N, Nolan M, Pitluck S, Tapia R, Woyke T, Vetriani C	Stand Genomic Sci	10.4056/sigs.2856770	2012	*
Phylogeny	Thermovibrio ammonificans sp. nov., a thermophilic, chemolithotrophic, nitrate-ammonifying bacterium from deep-sea hydrothermal vents.	Vetriani C, Speck MD, Ellor SV, Lutz RA, Starovoytov V	Int J Syst Evol Microbiol	10.1099/ijs.0.02781-0	2004	*
	Genomic analyses of bacterial porin-cytochrome gene clusters.	Shi L, Fredrickson JK, Zachara JM	Front Microbiol	10.3389/fmicb.2014.00657	2014	*

References

#6064

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15698

#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 )

#29981

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 #26349 (see below)

#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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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) .

#86637

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-ID130854.1 )

#26349

IJSEM 175 2004 ( DOI 10.1099/ijs.0.02781-0 , PubMed 14742477 )

* These data were automatically processed and therefore are not curated

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Thermovibrio ammonificans HB-1 HB-1

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