Palaeococcus pacificus (DSM 24777, JCM 17873, DY20341)

Name: Palaeococcus pacificus (DSM 24777, JCM 17873, DY20341)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 23332

Type strain

Strain Designation DY20341

Culture col. no. DSM 24777 JCM 17873 DY20341

NCBI tax ID(s) 971279

Special Collections DSMZ JCM Literature strains

History <- X. Zeng, Third Inst. Oceanography, State Oceanic Admin., China; DY20341 <- X. Zeng {2009} X. Zeng DY20341.

Links

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

motile coccus-shaped anaerobe genome sequence 16S sequence Archaea

Name and taxonomic classification

SI-ID 407005

JCM 17873,DSM 24777

@ref 20215

Last LPSN update 2026-02-09 11:23:43

Domain Archaea

Phylum Methanobacteriota

Class Thermococci

Order Thermococcales

Family Thermococcaceae

Genus Palaeococcus

Species Palaeococcus pacificus

Full scientific name Palaeococcus pacificus Zeng et al. 2013

Morphology

Cell morphology

@ref	Cell length	Cell width	Cell shape	Motility
30795	1.15 µm	1.15 µm	coccus-shaped

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
19335	PALAEOCOCCUS MEDIUM (DSMZ Medium 377a)		Medium recipe at MediaDive	Name: PALAEOCOCCUS MEDIUM (DSMZ Medium 377a) Composition: Sulfur 29.2398 g/l Peptone 4.87329 g/l MgCl2 x 6 H2O 2.68031 g/l Yeast extract 0.974659 g/l KH2PO4 0.487329 g/l Na2S x 9 H2O 0.487329 g/l KCl 0.321637 g/l NaBr 0.0487329 g/l MgSO4 x 7 H2O 0.0292398 g/l Nitrilotriacetic acid 0.0146199 g/l (NH4)2SO4 0.00974659 g/l NaCl 0.00974659 g/l SrCl2 x 6 H2O 0.00682261 g/l Citric acid 0.00487329 g/l MnSO4 x H2O 0.00487329 g/l ZnSO4 x 7 H2O 0.00175439 g/l CoSO4 x 7 H2O 0.00175439 g/l FeSO4 x 7 H2O 0.000974659 g/l CaCl2 x 2 H2O 0.000974659 g/l Sodium resazurin 0.000487329 g/l NiCl2 x 6 H2O 0.000292398 g/l AlK(SO4)2 x 12 H2O 0.000194932 g/l H3BO3 9.74659e-05 g/l CuSO4 x 5 H2O 9.74659e-05 g/l Pyridoxine hydrochloride 9.74659e-05 g/l Na2MoO4 x 2 H2O 9.74659e-05 g/l (DL)-alpha-Lipoic acid 4.87329e-05 g/l p-Aminobenzoic acid 4.87329e-05 g/l Calcium D-(+)-pantothenate 4.87329e-05 g/l Nicotinic acid 4.87329e-05 g/l Riboflavin 4.87329e-05 g/l Thiamine HCl 4.87329e-05 g/l KI 4.87329e-05 g/l Folic acid 1.94932e-05 g/l Biotin 1.94932e-05 g/l Na2WO4 x 2 H2O 3.89864e-06 g/l Na2SeO3 x 5 H2O 2.92398e-06 g/l Vitamin B12 9.74659e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
19335	positive	growth	80
30795	positive	growth	50-90
30795	positive	optimum	80
67770	positive	growth	80

Culture pH

@ref	Ability	Type	PH
30795	positive	optimum	7
30795	positive	growth	05-08

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
19335	anaerobe
30795	anaerobe
125439	anaerobe	98.9

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30795	NaCl	positive	growth	01-04 %
30795	NaCl	positive	optimum	3 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30795	30089 ChEBI	acetate	+	carbon source
30795	16947 ChEBI	citrate	+	carbon source
30795	24996 ChEBI	lactate	+	carbon source
30795	15361 ChEBI	pyruvate	+	carbon source

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Latitude	Longitude
19335	deep sea sediment, 2737 m depth	East Pacific Ocean hydrothermal field	International waters	-1.6167	-102.75 -1.6167/-102.75
67770	Sediment collected from an East Pacific Ocean hydrothermal field at a depth of 2,737 m

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
19335	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM72542v1 assembly for Palaeococcus pacificus DY20341	complete	GCA_000725425	1343739.3	2588253738	1343739	99.39

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
19335	Palaeococcus pacificus strain DY20341 16S ribosomal RNA gene, partial sequence	HQ696462	1446		1343739

GC content

@ref	GC-content (mol%)	Method
19335	43.6	high performance liquid chromatography (HPLC)
30795	43.6

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Palaeococcus pacificus DY20341
IMG: 2588253738

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	60.60	no
125439	motility	BacteriaNetⓘ	yes	53.40	no
125439	gram_stain	BacteriaNetⓘ	variable	84.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	98.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Palaeococcus pacificus DY20341 DY20341
NCBI: GCA_000725425.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	70.03	no
125438	anaerobic	anaerobicⓘ	yes	89.55	yes
125438	aerobic	aerobicⓘ	no	88.44	yes
125438	spore-forming	spore-formingⓘ	no	88.16	no
125438	thermophilic	thermophileⓘ	yes	77.25	yes
125438	flagellated	motile2+ⓘ	no	75.46	no

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 )
#27126	IJSEM 2155 2013 ( DOI 10.1099/ijs.0.044487-0 , PubMed 23104364 )
#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
#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;
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Palaeococcus pacificus (DSM 24777, JCM 17873, DY20341)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Halophily

Metabolite utilization

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000725425

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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