Archive BacDiveID:10.13145/bacdive23332.20240916.9.1

Strain identifier

BacDive ID: 23332

Type strain:

Species: Palaeococcus pacificus

Strain Designation: DY20341

Strain history: X. Zeng DY20341.

NCBI tax ID(s): 971279 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 19335

BacDive-ID: 23332

DSM-Number: 24777

keywords: genome sequence, 16S sequence, Archaea, anaerobe, motile, coccus-shaped

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

NCBI tax id

NCBI tax id: 971279
Matching level: species

strain history

@ref	history
19335	<- X. Zeng, Third Inst. Oceanography, State Oceanic Admin., China; DY20341 <- X. Zeng {2009}
67770	X. Zeng DY20341.

doi: 10.13145/bacdive23332.20240916.9.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/archaea
keyword: phylum/methanobacteriota
domain: Archaea
phylum: Methanobacteriota
class: Thermococci
order: Thermococcales
family: Thermococcaceae
genus: Palaeococcus
species: Palaeococcus pacificus
full scientific name: Palaeococcus pacificus Zeng et al. 2013

@ref: 19335

domain: Archaea

phylum: Euryarchaeota

class: Thermococci

order: Thermococcales

family: Thermococcaceae

genus: Palaeococcus

species: Palaeococcus pacificus

full scientific name: Palaeococcus pacificus Zeng et al. 2013

strain designation: DY20341

type strain: yes

Morphology

cell morphology

@ref: 30795
cell length: 1.15 µm
cell width: 1.15 µm
cell shape: coccus-shaped
motility: yes

Culture and growth conditions

culture medium

@ref: 19335
name: PALAEOCOCCUS MEDIUM (DSMZ Medium 377a)
growth: yes
link: https://mediadive.dsmz.de/medium/377a
composition: 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
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	growth	05-08
30795	positive	optimum	7

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance
19335	anaerobe
30795	anaerobe

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	acetate	+	carbon source
30795	16947	citrate	+	carbon source
30795	24996	lactate	+	carbon source
30795	15361	pyruvate	+	carbon source

Isolation, sampling and environmental information

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
67770	Sediment collected from an East Pacific Ocean hydrothermal field at a depth of 2,737 m

isolation source categories

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

Safety information

risk assessment

@ref: 19335
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 19335
description: Palaeococcus pacificus strain DY20341 16S ribosomal RNA gene, partial sequence
accession: HQ696462
length: 1446
database: nuccore
NCBI tax ID: 1343739

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Palaeococcus pacificus DY20341	GCA_000725425	complete	ncbi	1343739
66792	Palaeococcus pacificus DY20341	2588253738	complete	img	1343739
66792	Palaeococcus pacificus DY20341	1343739.3	complete	patric	1343739

GC content

@ref	GC-content	method
19335	43.6	high performance liquid chromatography (HPLC)
30795	43.6

Genome-based predictions

predictions

@ref	trait	model	description	prediction	confidence	training_data
69480	gram-positive	gram-positive	Positive reaction to Gram-staining	no	70.028	no
69480	anaerobic	anaerobic	Ability to grow under anoxygenic conditions (including facultative anaerobes)	yes	89.546	yes
69480	aerobic	aerobic	Ability to grow under oxygenic conditions (including facultative aerobes)	no	88.436	yes
69480	spore-forming	spore-forming	Ability to form endo- or exospores	no	88.164	no
69480	thermophilic	thermophile	Ability to grow at temperatures above or equal to 45°C	yes	77.246	yes
69480	flagellated	motile2+	Ability to perform flagellated movement	no	75.458	no

External links

@ref: 19335

culture collection no.: DSM 24777, JCM 17873

straininfo link

@ref: 87549
straininfo: 407005

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	23104364	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	Base Composition, DNA, Archaeal/genetics, Geologic Sediments/microbiology, Hydrothermal Vents/microbiology, Molecular Sequence Data, Pacific Ocean, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Thermococcaceae/classification/genetics/isolation & purification	Genetics
Genetics	26383653	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
Metabolism	31935923	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	Adaptation, Physiological, Bacterial Proteins/genetics/metabolism, Hydrogenase/genetics/metabolism, Hydrothermal Vents/microbiology, Iron-Sulfur Proteins/genetics/metabolism, Oceans and Seas, Sulfur/metabolism, Thermococcaceae/genetics/metabolism, *Transcriptome	Transcriptome

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed
19335	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24777)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-24777
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
30795	Barberan A, Caceres Velazquez H, Jones S, Fierer N.		10.1128/mSphere.00237-17	Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information	27126	28776041
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
69480	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	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.		10.60712/SI-ID407005.1	StrainInfo: A central database for resolving microbial strain identifiers