Strain identifier

BacDive ID: 16852

Type strain: Yes

Species: Palaeococcus ferrophilus

Strain Designation: DMJ

Strain history: K. Takai strain DMJ.

NCBI tax ID(s): 588319 (strain), 83868 (species)

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General

@ref: 5059

BacDive-ID: 16852

DSM-Number: 13482

keywords: genome sequence, 16S sequence, Archaea, anaerobe, hyperthermophilic

description: Palaeococcus ferrophilus DMJ is an anaerobe, hyperthermophilic archaeon that was isolated from deep-sea hydrothermal vent chimney, 1338 m depth.

NCBI tax id

NCBI tax idMatching level
83868species
588319strain

strain history

@refhistory
5059<- JCM <- K. Takai, Japan Agency for Marine-Earth Sci. and Technol. (JAMSTEC), Yokosuka; DMJ
67770K. Takai strain DMJ.

doi: 10.13145/bacdive16852.20230509.8.1

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 ferrophilus
  • full scientific name: Palaeococcus ferrophilus Takai et al. 2000

@ref: 5059

domain: Archaea

phylum: Euryarchaeota

class: Thermococci

order: Thermococcales

family: Thermococcaceae

genus: Palaeococcus

species: Palaeococcus ferrophilus

full scientific name: Palaeococcus ferrophilus Takai et al. 2000

strain designation: DMJ

type strain: yes

Culture and growth conditions

culture medium

  • @ref: 5059
  • 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

@refgrowthtypetemperaturerange
5059positivegrowth80hyperthermophilic
67770positivegrowth80hyperthermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 5059
  • oxygen tolerance: anaerobe

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5059deep-sea hydrothermal vent chimney, 1338 m depthOgasawara-Bonin ArcJapanJPNAsia
67770Deep-sea hydrothermal vent chimneyMyojin Knoll, Okinawa TroughJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Hydrothermal vent
#Environmental#Aquatic#Marine
#Condition#Thermophilic (>45°C)

taxonmaps

  • @ref: 69479
  • File name: preview.99_187232.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17827;96_68882;97_89530;98_121811;99_187232&stattab=map
  • Last taxonomy: Palaeococcus ferrophilus subclade
  • 16S sequence: AB019239
  • Sequence Identity:
  • Total samples: 12
  • aquatic counts: 12

Safety information

risk assessment

  • @ref: 5059
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 5059
  • description: Palaeococcus ferriphilus gene for small subunit rRNA, partial sequence
  • accession: AB019239
  • length: 1409
  • database: ena
  • NCBI tax ID: 588319

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Palaeococcus ferrophilus DMJ, DSM 134822501025505draftimg588319
67770Palaeococcus ferrophilus DSM 13482GCA_000966265contigncbi588319
66792Palaeococcus ferrophilus DSM 13482588319.9wgspatric588319

GC content

  • @ref: 5059
  • GC-content: 53.5
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 5059

culture collection no.: DSM 13482, JCM 10417, ATCC BAA 128

straininfo link

  • @ref: 85861
  • straininfo: 49475

literature

  • topic: Phylogeny
  • Pubmed-ID: 10758851
  • title: Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney.
  • authors: Takai K, Sugai A, Itoh T, Horikoshi K
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-50-2-489
  • year: 2000
  • mesh: Anti-Bacterial Agents/pharmacology, Base Composition, Culture Media/chemistry, DNA, Archaeal/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Hydrogen-Ion Concentration, Lipids/analysis, Microbial Sensitivity Tests, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Temperature, Thermococcales/*classification/cytology/isolation & purification/physiology, Water Microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitle
5059Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13482)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13482
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69479João 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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
85861Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49475.1StrainInfo: A central database for resolving microbial strain identifiers