Name: Palaeococcus pacificus DY20341
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 23332

Type strain:

Species: Palaeococcus pacificus

Strain Designation: DY20341

Culture col. no.: DSM 24777, JCM 17873

Strain history: X. Zeng DY20341.

NCBI tax ID(s): 971279 (species)

SI-ID 407005

DSM 24777

Special Collections

Section

Palaeococcus pacificus DY20341 is an anaerobe, motile, coccus-shaped archaeon that was isolated from deep sea sediment, 2737 m depth.

coccus-shaped
motile
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	*Methanobacteriota*
	Class	*Thermococci*
	Order	*Thermococcales*
	Family	*Thermococcaceae*
	Genus	*Palaeococcus*
	Species	**Palaeococcus pacificus**
	Full Scientific Name (LPSN)	Palaeococcus pacificus Zeng et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #30795]	Cell length	1.15 µm

[Ref.: #30795]	Cell width	1.15 µm

[Ref.: #30795]	Cell shape	coccus-shaped

[Ref.: #30795]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #19335]

Culture medium

PALAEOCOCCUS MEDIUM (DSMZ Medium 377a)

[Ref.: #19335]

Culture medium growth

[Ref.: #19335]

Culture medium link

Medium recipe at MediaDive

[Ref.: #19335]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #19335]	growth	80 °C
[Ref.: #30795]	growth	50-90 °C
[Ref.: #30795]	optimum	80 °C
[Ref.: #67770]	growth	80 °C

	pH	Kind of pH		pH
[Ref.: #30795]			optimum	7
[Ref.: #30795]			growth	05-08

Information on physiology and metabolism Physiology and metabolism

[Ref.: #19335]	Oxygen tolerance	anaerobe
[Ref.: #30795]	Oxygen tolerance	anaerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30795]		NaCl		growth	01-04	%
[Ref.: #30795]		NaCl		optimum	3	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30795]	acetate ChEBI	+	carbon source
[Ref.: #30795]	citrate ChEBI	+	carbon source
[Ref.: #30795]	lactate ChEBI	+	carbon source
[Ref.: #30795]	pyruvate ChEBI	+	carbon source

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

[Ref.: #19335]	Sample type/isolated from	deep sea sediment, 2737 m depth
[Ref.: #19335]	Geographic location (country and/or sea, region)	East Pacific Ocean hydrothermal field
[Ref.: #19335]	Country	International waters
[Ref.: #19335]	Geographic location	-1.6167°/-102.7500°

[Ref.: #67770]	Sample type/isolated from	Sediment collected from an East Pacific Ocean hydrothermal field at a depth of 2,737 m
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

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

[Ref.: #19335]

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.: #19335]	Palaeococcus pacificus strain DY20341 16S ribosomal RNA gene, partial sequence	HQ696462	1446	GenBank ENA	1343739 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Palaeococcus pacificus DY20341	GCA_000725425	complete	GenBank ENA	1343739 tax ID	*
[Ref.: #66792]	Palaeococcus pacificus DY20341	2588253738	complete	JGI IMG/M	1343739 tax ID	*
[Ref.: #66792]	Palaeococcus pacificus DY20341	1343739.3	complete	PATRIC	1343739 tax ID	*

[Ref.: #19335]	GC-content	43.6 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30795]	GC-content	43.6 mol%

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Palaeococcus pacificus DY20341 DY20341 NCBI: GCA_000725425.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	70.028	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	89.546	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	88.436	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	88.164	no
[Ref.: #69480]	thermophilic	thermophileⓘ	yes	77.246	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	75.458	no

Availability in culture collections External links

[Ref.: #19335]

Culture collection no.

DSM 24777, JCM 17873

[Ref.: #87549]

SI-ID 407005

Literature:

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Metabolic Adaptation to Sulfur of Hyperthermophilic Palaeococcus pacificus DY20341(T) from Deep-Sea Hydrothermal Sediments.	Zeng X, Zhang X, Shao Z	Int J Mol Sci	10.3390/ijms21010368	2020	*
Genetics	Complete Genome Sequence of Hyperthermophilic Piezophilic Archaeon Palaeococcus pacificus DY20341T, Isolated from Deep-Sea Hydrothermal Sediments.	Zeng X, Jebbar M, Shao Z	Genome Announc	10.1128/genomeA.01080-15	2015	*
Phylogeny	Palaeococcus pacificus sp. nov., an archaeon from deep-sea hydrothermal sediment.	Zeng X, Zhang X, Jiang L, Alain K, Jebbar M, Shao Z	Int J Syst Evol Microbiol	10.1099/ijs.0.044487-0	2012	*

References

#19335

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24777

#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 )

#30795

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 #27126 (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) .

#87549

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-ID407005.1 )

#27126

IJSEM 2155 2013 ( DOI 10.1099/ijs.0.044487-0 , PubMed 23104364 )

* These data were automatically processed and therefore are not curated

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Palaeococcus pacificus DY20341 DY20341

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