Name: Pyrodictium delaneyi Su06
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 132610

Type strain:

Species: Pyrodictium delaneyi

Strain Designation: Su06

Culture col. no.: DSM 28599, ATCC BAA-2559

Strain history: <- J. Holden, University of Massachusetts, Department of Microbiology, USA; Su06 <- H.C. Ver Eecke {2009}

NCBI tax ID(s): 1273541 (species)

SI-ID 401599

DSM 28599

Section

Pyrodictium delaneyi Su06 is an obligate anaerobe, autotroph, hyperthermophilic archaeon that was isolated from actively venting deep-sea hydrothermal chimney, depth 2197 m.

coccus-shaped
motile
autotroph
hyperthermophilic
obligate anaerobe
16S sequence
Archaea
genome sequence

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Archaea"
	Phylum	*Thermoproteota*
	Class	*Thermoprotei*
	Order	*Desulfurococcales*
	Family	*Pyrodictiaceae*
	Genus	*Pyrodictium*
	Species	**Pyrodictium delaneyi**
	Full Scientific Name (LPSN)	Pyrodictium delaneyi Lin et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.987

[Ref.: #43115]	Cell length	0.8 µm

[Ref.: #43115]	Cell width	0.8 µm

[Ref.: #43115]	Cell shape	coccus-shaped

[Ref.: #43115]	Motility	yes

[Ref.: #43115]	Flagellum arrangement	lophotrichous

Information on culture and growth conditions Culture and growth conditions

[Ref.: #24399]

Culture medium

PYRODICTIUM DELANEYI MEDIUM (DSMZ Medium 1210b)

[Ref.: #24399]

Culture medium growth

[Ref.: #24399]

Culture medium link

Medium recipe at MediaDive

[Ref.: #24399]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #24399]	growth	90 °C
[Ref.: #43115]	growth	82-97 °C
[Ref.: #43115]	optimum	90-92 °C

[Ref.: #24399]	Temperature range	hyperthermophilic
[Ref.: #43115]	Temperature range	hyperthermophilic
[Ref.: #69480]	Temperature range	thermophilic Confidence in %100

	pH	Kind of pH		pH
[Ref.: #43115]			optimum	5
[Ref.: #43115]			growth	5.0-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43115]	Oxygen tolerance	obligate anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %98.074

[Ref.: #43115]

Nutrition type

autotroph

[Ref.: #69480]

Ability of spore formation

no Confidence in %99.856

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43115]		NaCl		growth	0.9-3.6	%
[Ref.: #43115]		NaCl		optimum	1.9	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43115]	butyrate ChEBI	-	electron donor
[Ref.: #43115]	dioxygen ChEBI	-	electron acceptor
[Ref.: #43115]	elemental sulfur ChEBI	-	electron acceptor
[Ref.: #43115]	ferric oxide ChEBI	+	electron acceptor
[Ref.: #43115]	goethite	-	growth
[Ref.: #43115]	malate ChEBI	-	electron donor
[Ref.: #43115]	nitrate ChEBI	+	electron acceptor
[Ref.: #43115]	succinate ChEBI	-	electron donor
[Ref.: #43115]	thiosulfate ChEBI	-	electron acceptor

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #43115]		nitrate reductase	+	1.7.99.4

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

[Ref.: #24399]	Sample type/isolated from	actively venting deep-sea hydrothermal chimney, depth 2197 m
[Ref.: #24399]	Geographic location (country and/or sea, region)	North-eastern Pacific, Juan de Fuca Ridge, Endeavour Segment hydrothermal vent field
[Ref.: #24399]	Country	Canada
[Ref.: #24399]	Country ISO 3 Code	CAN
[Ref.: #24399]	Continent	North America
[Ref.: #24399]	Geographic location	47.9500°/-129.1000°

[Ref.: #43115]	Sample type/isolated from	active hydrothermal vent sulfide chimney at a depth of 2197 m
[Ref.: #43115]	Geographic location (country and/or sea, region)	Endeavour Segment, Juan de Fuca Ridge, north-eastern Pacific Ocean
[Ref.: #43115]	Geographic location	47.0000°/-129.0000°
* marker position based on {}

Isolation sources categories

#Condition

#Sulfuric

What are isolation sources categories?

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

[Ref.: #24399]

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.: #24399]	Pyrodictium delaneyi strain Su06 16S ribosomal RNA gene, partial sequence	KC145154	1290	ENA	1273541 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pyrodictium delaneyi Su06	GCA_001412615	complete	GenBank	1273541 tax ID	*
[Ref.: #66792]	Pyrodictium delaneyi Su06	2773858058	complete	JGI IMG/M	1273541 tax ID	*

[Ref.: #43115]	GC-content	53.9 mol%	genome sequence analysis
[Ref.: #24399]	GC-content	53.9 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: Pyrodictium delaneyi Su06 NCBI: GCA_001412615.1
[Ref.: #69481]	spore-forming	yes	89	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pyrodictium delaneyi Su06 NCBI: GCA_001412615.1
[Ref.: #69480]	flagellated	no	92.52	yes
[Ref.: #69480]	gram-positive	no	97.496	no
[Ref.: #69480]	anaerobic	yes	97.928	yes
[Ref.: #69480]	aerobic	no	93.971	no
[Ref.: #69480]	halophile	no	81.976	no
[Ref.: #69480]	spore-forming	no	95.559	no
[Ref.: #69480]	glucose-util	yes	76.083	no
[Ref.: #69480]	thermophile	yes	100	yes
[Ref.: #69480]	motile	no	65.084	yes
[Ref.: #69480]	glucose-ferment	no	70.021	no

Availability in culture collections External links

[Ref.: #24399]

Culture collection no.

DSM 28599, ATCC BAA-2559

[Ref.: #90924]

SI-ID 401599

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pyrodictium delaneyi sp. nov., a hyperthermophilic autotrophic archaeon that reduces Fe(III) oxide and nitrate.	Lin TJ, El Sebae G, Jung JH, Jung DH, Park CS, Holden JF	Int J Syst Evol Microbiol	10.1099/ijsem.0.001201	2016	*

References

#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 )

#24399

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28599

#43115

T. Jennifer Lin, Gabriel El Sebae, Jong-Hyun Jung, Dong-Hyun Jung, Cheon-Seok Park, James F. Holden: Pyrodictium delaneyi sp. nov., a hyperthermophilic autotrophic archaeon that reduces Fe(III) oxide and nitrate. IJSEM 66: 3372 - 3376 2016 ( DOI 10.1099/ijsem.0.001201 , PubMed 27260263 )

#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 )

#90924

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-ID401599.1 )

* These data were automatically processed and therefore are not curated

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