Strain identifier

BacDive ID: 132578

Type strain: Yes

Species: Pyrococcus kukulkanii

Strain Designation: Souchothèque de Bretagne BG1337

Strain history: <- A. Godfroy, IFREMER; NCB100T <- C. Nolwenn {2010}

NCBI tax ID(s): 1609559 (species)

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General

@ref: 24367

BacDive-ID: 132578

DSM-Number: 101590

keywords: genome sequence, Archaea, obligate anaerobe, spore-forming, motile, coccus-shaped

description: Pyrococcus kukulkanii Souchothèque de Bretagne BG1337 is an obligate anaerobe, spore-forming, motile archaeon that was isolated from flange of an active deep-sea hydrothermal vent chimney at the depth of 1997 m.

NCBI tax id

  • NCBI tax id: 1609559
  • Matching level: species

strain history

  • @ref: 24367
  • history: <- A. Godfroy, IFREMER; NCB100T <- C. Nolwenn {2010}

doi: 10.13145/bacdive132578.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/archaea
  • keyword: phylum/methanobacteriota
  • domain: Archaea
  • phylum: Methanobacteriota
  • class: Thermococci
  • order: Thermococcales
  • family: Thermococcaceae
  • genus: Pyrococcus
  • species: Pyrococcus kukulkanii
  • full scientific name: Pyrococcus kukulkanii Callac et al. 2016

@ref: 24367

domain: Archaea

phylum: Euryarchaeota

class: Thermococci

order: Thermococcales

family: Thermococcaceae

genus: Pyrococcus

species: Pyrococcus kukulkanii

full scientific name: Pyrococcus kukulkanii Callac et al. 2016

strain designation: Souchothèque de Bretagne BG1337

type strain: yes

Morphology

cell morphology

  • @ref: 43080
  • cell width: 1 µm
  • cell shape: coccus-shaped
  • motility: yes

Culture and growth conditions

culture medium

  • @ref: 24367
  • name: PYROCOCCUS MEDIUM (DSMZ Medium 377)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/377
  • composition: Name: PYROCOCCUS MEDIUM (DSMZ Medium 377) Composition: Sulfur 30.0 g/l Peptone 5.0 g/l MgCl2 x 6 H2O 2.75 g/l Yeast extract 1.0 g/l KH2PO4 0.5 g/l Na2S x 9 H2O 0.5 g/l KCl 0.33 g/l NaBr 0.05 g/l MgSO4 x 7 H2O 0.03 g/l Nitrilotriacetic acid 0.015 g/l NaCl 0.01 g/l (NH4)2SO4 0.01 g/l SrCl2 x 6 H2O 0.007 g/l Citric acid 0.005 g/l MnSO4 x H2O 0.005 g/l CoSO4 x 7 H2O 0.0018 g/l ZnSO4 x 7 H2O 0.0018 g/l CaCl2 x 2 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Sodium resazurin 0.0005 g/l NiCl2 x 6 H2O 0.0003 g/l AlK(SO4)2 x 12 H2O 0.0002 g/l CuSO4 x 5 H2O 0.0001 g/l Na2MoO4 x 2 H2O 0.0001 g/l H3BO3 0.0001 g/l KI 5e-05 g/l Na2WO4 x 2 H2O 4e-06 g/l Na2SeO3 x 5 H2O 3e-06 g/l Distilled water

culture temp

@refgrowthtypetemperature
43080nogrowth70-112
43080positiveoptimum105
24367positivegrowth100

culture pH

@refabilitytypepHPH range
43080positiveoptimum7
43080positivegrowth3.5-8.5alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 43080
  • oxygen tolerance: obligate anaerobe

spore formation

  • @ref: 69481
  • spore formation: yes
  • confidence: 99

halophily

@refsaltgrowthtested relationconcentration
43080NaClpositivegrowth1.5-7 %(w/v)
43080NaClpositiveoptimum2.5-3 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4308033403elemental sulfur+required for growth
4308033403elemental sulfur+reduction
43080yeast extract+carbon source
43080peptone+carbon source
43080tryptone+carbon source
4308028087glycogen+carbon source
4308028017starch+carbon source
4308017306maltose-carbon source
4308017234glucose-carbon source
4308017992sucrose-carbon source
4308028260galactose-carbon source
4308017057cellobiose-carbon source
4308030089acetate-carbon source
4308015740formate-carbon source
4308015361pyruvate-carbon source
4308030031succinate-carbon source
43080casein-carbon source
43080casamino acids-carbon source
4308017029chitin-carbon source
4308016236ethanol-carbon source
4308017754glycerol-carbon source
4308016189sulfate-electron acceptor
4308016094thiosulfate-electron acceptor
4308017359sulfite-electron acceptor
4308017632nitrate-electron acceptor
4308016283L-cystine-electron acceptor
4308029034ferric iron-electron acceptor
4308017632nitrate+nitrogen source
4308016199urea+nitrogen source
430805291gelatin+nitrogen source
43080yeast extract+nitrogen source
43080peptone+nitrogen source
43080tryptone+nitrogen source

metabolite production

@refChebi-IDmetaboliteproduction
4308016136hydrogen sulfideyes
4308016526carbon dioxideyes
4308018276dihydrogenyes

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
24367flange of an active deep-sea hydrothermal vent chimney at the depth of 1997 mGulf of California, Guaymas Basin at the Rebecca's Roost siteMexicoMEXNorth America27.0106-111.407
43080flange of an active deep-sea hydrothermal chimney at the depth of 1997 mRebecca's Roost, Guaymas Basin, Gulf of California, MexicoMexicoMEXNorth America27-111

isolation source categories

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

Safety information

risk assessment

  • @ref: 24367
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pyrococcus kukulkanii NCB100GCA_001577775completencbi1609559
66792Pyrococcus kukulkanii NCB1002687453501completeimg1609559
66792Pyrococcus sp. NCB1001609559.3completepatric1609559

GC content

  • @ref: 24367
  • GC-content: 41.3
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesyes99no
69480gram-positivegram-positivePositive reaction to Gram-stainingno64.961no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes86.785yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no87.934yes
69480spore-formingspore-formingAbility to form endo- or exosporesno89.456no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cyes87.637yes
69480flagellatedmotile2+Ability to perform flagellated movementno74.958no

External links

@ref: 24367

culture collection no.: DSM 101590, NCB 100

straininfo link

  • @ref: 90895
  • straininfo: 406939

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27189596Pyrococcus kukulkanii sp. nov., a hyperthermophilic, piezophilic archaeon isolated from a deep-sea hydrothermal vent.Callac N, Oger P, Lesongeur F, Rattray JE, Vannier P, Michoud G, Beauverger M, Gayet N, Rouxel O, Jebbar M, Godfroy AInt J Syst Evol Microbiol10.1099/ijsem.0.0011602016Base Composition, DNA, Archaeal/genetics, Hot Temperature, Hydrostatic Pressure, Hydrothermal Vents/*microbiology, *Phylogeny, Pyrococcus/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNAStress
Genetics28209839Complete Genome Sequence of the Hyperthermophilic Piezophilic Archaeon Pyrococcus kukulkanii NCB100 Isolated from the Rebecca's Roost Hydrothermal Vent in the Guaymas Basin.Oger PM, Callac N, Oger-Desfeux C, Hughes S, Gillet B, Jebbar M, Godfroy AGenome Announc10.1128/genomeA.01667-162017Phylogeny

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
24367Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-101590Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 101590)
43080Nolwenn Callac, Philippe Oger, Françoise Lesongeur, Jayne E. Rattray, Pauline Vannier, Grégoire Michoud, Mickael Beauverger, Nicolas Gayet, Olivier Rouxel, Mohamed Jebbar and Anne GodfroyPyrococcus kukulkanii sp. nov., a hyperthermophilic, piezophilic archaeon isolated from a deep-sea hydrothermal vent10.1099/ijsem.0.001160IJSEM 66: 3142-3149 201627189596
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
90895Reimer, 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 identifiers10.60712/SI-ID406939.1