Name: Phorcysia thermohydrogeniphila EPRHB-8
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17648

Type strain:

Species: Phorcysia thermohydrogeniphila

Strain Designation: EPRHB-8, HB-8

Culture col. no.: DSM 24425, JCM 17384

Strain history: C. Vetriani HB-8.

NCBI tax ID(s): 936138 (species)

SI-ID 397221

DSM 24425

Section

Phorcysia thermohydrogeniphila EPRHB-8 is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from biofilm-covered tube of Alvinella pompejana from a colonization device on the wall of an active chimney vent, 2621 m depth.

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	*Phorcysia*
	Species	**Phorcysia thermohydrogeniphila**
	Full Scientific Name (LPSN)	Phorcysia thermohydrogeniphila Pérez-Rodríguez et al. 2012

Information on morphological and physiological properties Morphology

[Ref.: #30419]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.999

[Ref.: #30419]	Cell length	1.25 µm

[Ref.: #30419]	Cell width	0.5 µm

[Ref.: #30419]	Cell shape	rod-shaped

[Ref.: #30419]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %92.851

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17675]

Culture medium

THERMOVIBRIO AMMONIFICANS MEDIUM (DSMZ Medium 792a)

[Ref.: #17675]

Culture medium growth

[Ref.: #17675]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17675]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #17675]	growth	75 °C
[Ref.: #30419]	growth	65-80 °C
[Ref.: #30419]	optimum	75 °C
[Ref.: #67770]	growth	75 °C

[Ref.: #17675]	Temperature range	thermophilic
[Ref.: #30419]	Temperature range	hyperthermophilic
[Ref.: #30419]	Temperature range	thermophilic
[Ref.: #67770]	Temperature range	thermophilic
[Ref.: #69480]	Temperature range	thermophilic Confidence in %99.999

	pH	Kind of pH		pH
[Ref.: #30419]			optimum	6
[Ref.: #30419]			growth	4.5-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #17675]	Oxygen tolerance	anaerobe
[Ref.: #30419]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.999

[Ref.: #30419]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.931

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

[Ref.: #17675]	Sample type/isolated from	biofilm-covered tube of Alvinella pompejana from a colonization device on the wall of an active chimney vent, 2621 m depth
[Ref.: #17675]	Host species	Alvinella pompejana
[Ref.: #17675]	Geographic location (country and/or sea, region)	East Pacific Rise, 'Jumeaux' site
[Ref.: #17675]	Country	International waters
[Ref.: #17675]	Geographic location	12.8000°/-103.9330°

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

Isolation sources categories

#Environmental	#Aquatic	#Hydrothermal vent
#Environmental	#Biofilm	-
#Host	#Invertebrates (Other)	#Annelida
#Condition	#Thermophilic (>45°C)	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence HQ336972 (>99% sequence identity) for Phorcysia thermohydrogeniphila subclade from Microbeatlas

Aquatic Samples	92
Soil Samples
Animal Samples	3
Plant Samples
Total Samples	95

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

[Ref.: #17675]

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.: #17675]	Phorcysia thermohydrogeniphila strain HB-8 16S ribosomal RNA gene, partial sequence	HQ336972	1349	ENA	936138 tax ID
[Ref.: #67770]	Phorcysia thermohydrogeniphila strain HB-8 ATP citrate lyase alpha subunit (aclA) gene, partial cds	JN118840	907	ENA	936138 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Phorcysia thermohydrogeniphila DSM 24425	GCA_004339575	scaffold	GenBank	936138 tax ID
[Ref.: #66792]	Phorcysia thermohydrogeniphila strain DSM 24425	936138.7	wgs	PATRIC	936138 tax ID	*
[Ref.: #66792]	Phorcysia thermohydrogeniphila DSM 24425	2728369737	draft	JGI IMG/M	936138 tax ID	*

[Ref.: #17675]	GC-content	47.8 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30419]	GC-content	47.8 mol%

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: Phorcysia thermohydrogeniphila DSM 24425 NCBI: GCA_004339575.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Phorcysia thermohydrogeniphila strain DSM 24425 PATRIC: 936138.7
[Ref.: #69480]	motile	yes	85.795	yes
[Ref.: #69480]	flagellated	no	92.335	no
[Ref.: #69480]	gram-positive	no	99.29	yes
[Ref.: #69480]	anaerobic	yes	98.949	yes
[Ref.: #69480]	halophile	no	84.913	no
[Ref.: #69480]	spore-forming	no	95.597	yes
[Ref.: #69480]	glucose-util	no	52.87	no
[Ref.: #69480]	aerobic	no	98.89	yes
[Ref.: #69480]	thermophile	yes	100	yes
[Ref.: #69480]	glucose-ferment	no	79.159	no

Availability in culture collections External links

[Ref.: #17675]

Culture collection no.

DSM 24425, JCM 17384

[Ref.: #86639]

SI-ID 397221

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Phorcysia thermohydrogeniphila gen. nov., sp. nov., a thermophilic, chemolithoautotrophic, nitrate-ammonifying bacterium from a deep-sea hydrothermal vent.	Perez-Rodriguez I, Grosche A, Massenburg L, Starovoytov V, Lutz RA, Vetriani C	Int J Syst Evol Microbiol	10.1099/ijs.0.035642-0	2011	*

References

#17675

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24425

#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 )

#30419

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 #26755 (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;

#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 .

#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 )

#86639

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-ID397221.1 )

#26755

IJSEM 2388 2012 ( DOI 10.1099/ijs.0.035642-0 , PubMed 22140151 )

* These data were automatically processed and therefore are not curated

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Phorcysia thermohydrogeniphila DSM 24425

Phorcysia thermohydrogeniphila strain DSM 24425

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