Strain identifier

BacDive ID: 13520

Type strain: Yes

Species: Psychromonas arctica

Strain Designation: Pull5.3

Strain history: CIP <- 2003, CECT <- T. Groudieva <- R. Grote

NCBI tax ID(s): 1123036 (strain), 168275 (species)

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General

@ref: 5300

BacDive-ID: 13520

DSM-Number: 14288

keywords: genome sequence, 16S sequence, Bacteria, Gram-negative

description: Psychromonas arctica Pull5.3 is a Gram-negative bacterium that was isolated from sea-ice.

NCBI tax id

NCBI tax idMatching level
1123036strain
168275species

strain history

@refhistory
5300<- G. Antranikian; Pull2 <- R. Grote
116475CIP <- 2003, CECT <- T. Groudieva <- R. Grote

doi: 10.13145/bacdive13520.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Alteromonadales
  • family: Psychromonadaceae
  • genus: Psychromonas
  • species: Psychromonas arctica
  • full scientific name: Psychromonas arctica Groudieva et al. 2003

@ref: 5300

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Psychromonadaceae

genus: Psychromonas

species: Psychromonas arctica

full scientific name: Psychromonas arctica Groudieva et al. 2003

strain designation: Pull5.3

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
116475negativerod-shapedyes
69480negative99

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5300BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
37412Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
116475CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperature
5300positivegrowth5-15
37412positivegrowth5
116475positivegrowth5-25
116475nogrowth30

Physiology and metabolism

spore formation

@refspore formationconfidence
69480no91.658
69481no100

halophily

@refsaltgrowthtested relationconcentration
116475NaClpositivegrowth2-4 %
116475NaClnogrowth0 %
116475NaClnogrowth6 %
116475NaClnogrowth8 %
116475NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1164754853esculin-hydrolysis
11647517632nitrate+reduction
11647516301nitrite-reduction

antibiotic resistance

  • @ref: 116475
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 116475
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
116475oxidase+
116475beta-galactosidase+3.2.1.23
116475alcohol dehydrogenase-1.1.1.1
116475gelatinase-
116475amylase-
116475caseinase-3.4.21.50
116475catalase+1.11.1.6
116475tween esterase-
116475lecithinase-
116475lipase-
116475lysine decarboxylase-4.1.1.18
116475ornithine decarboxylase-4.1.1.17
116475protease-
116475tryptophan deaminase-
116475urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116475-++--+----++-+------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116475+++++--+-++----+++-+--+--------+-+---------------+---------++--------------+---++-+-------++-+-----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5300sea-iceSpitzbergen
116475Environment, Sea-iceSpitzbergenNorwayNOREurope

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Ice
#Environmental#Aquatic#Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_2790.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_267;96_1074;97_1768;98_2162;99_2790&stattab=map
  • Last taxonomy: Psychromonas arctica
  • 16S sequence: AF374385
  • Sequence Identity:
  • Total samples: 3870
  • soil counts: 162
  • aquatic counts: 2886
  • animal counts: 792
  • plant counts: 30

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
53001Risk group (German classification)
1164751Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Psychromonas arctica 16S ribosomal RNA gene, complete sequence
  • accession: AF374385
  • length: 1507
  • database: nuccore
  • NCBI tax ID: 168275

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Psychromonas arctica DSM 14288GCA_000482725scaffoldncbi1123036
66792Psychromonas arctica DSM 142881123036.3wgspatric1123036
66792Psychromonas arctica DSM 142882528311092draftimg1123036

GC content

  • @ref: 5300
  • GC-content: 40.1

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno99no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no94.491no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no51.305no
69480spore-formingspore-formingAbility to form endo- or exosporesno91.658no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno98yes
69480flagellatedmotile2+Ability to perform flagellated movementyes86.085no

External links

@ref: 5300

culture collection no.: DSM 14288, Pull 2, CIP 108126, CECT 5674, KCTC 12111

straininfo link

  • @ref: 82711
  • straininfo: 100900

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12710624Psychromonas arctica sp. nov., a novel psychrotolerant, biofilm-forming bacterium isolated from Spitzbergen.Groudieva T, Grote R, Antranikian GInt J Syst Evol Microbiol10.1099/ijs.0.02182-02003Alteromonadaceae/*classification/genetics/isolation & purification/physiology, Arctic Regions, *Biofilms, DNA Fingerprinting, DNA, Bacterial/analysis/genetics, Gammaproteobacteria, Microscopy, Electron, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Seawater/*microbiology, Sequence Analysis, DNA, TemperatureGenetics
Phylogeny28109208Psychromonas aquatilis sp. nov., isolated from seawater samples obtained in the Chilean Antarctica.Kampfer P, Irgang R, Poblete-Morales M, Glaeser SP, Cortez-San Martin M, Avendano-Herrera RInt J Syst Evol Microbiol10.1099/ijsem.0.0018012017Antarctic Regions, Bacterial Typing Techniques, Base Composition, Chile, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5300Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14288)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14288
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
37412Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5714
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)
68382Automatically annotated from API zym
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
82711Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100900.1StrainInfo: A central database for resolving microbial strain identifiers
116475Curators of the CIPCollection of Institut Pasteur (CIP 108126)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108126