Strain identifier

BacDive ID: 12678

Type strain: Yes

Species: Pseudoalteromonas denitrificans

Strain history: CIP <- 2002, DSMZ <- O. Enger <- 1977, I. Dundas, Nygaard

NCBI tax ID(s): 1123010 (strain), 43656 (species)

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General

@ref: 2422

BacDive-ID: 12678

DSM-Number: 6059

keywords: genome sequence, 16S sequence, Bacteria, psychrophilic, motile

description: Pseudoalteromonas denitrificans DSM 6059 is a psychrophilic, motile bacterium that was isolated from seawater.

NCBI tax id

NCBI tax idMatching level
1123010strain
43656species

strain history

@refhistory
2422<- I. Dundas, Nygaard 1977
67770IAM 14544 <-- ATCC 43337 <-- I. Dundasm strain Nygaard 1977.
118903CIP <- 2002, DSMZ <- O. Enger <- 1977, I. Dundas, Nygaard

doi: 10.13145/bacdive12678.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Alteromonadales
  • family: Pseudoalteromonadaceae
  • genus: Pseudoalteromonas
  • species: Pseudoalteromonas denitrificans
  • full scientific name: Pseudoalteromonas denitrificans (Enger et al. 1987) Gauthier et al. 1995

  • synonyms

    • @ref: 20215
    • synonym: Alteromonas denitrificans

@ref: 2422

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Pseudoalteromonadaceae

genus: Pseudoalteromonas

species: Pseudoalteromonas denitrificans

full scientific name: Pseudoalteromonas denitrificans (Enger et al. 1987) Gauthier et al. 1995

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes94
6948099.973negative

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2422BACTO 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
42024MEDIUM 104 - for Pseudoalteromonas denitrificansyesDistilled water make up to (200.000 ml);Agar (15.000 g);Yeast extract (0.500 g);Peptone (0.500 g);Tryptone (0.500 g);Synthetic sea solution - M0216 (800.000 ml)
118903CIP Medium 99yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=99

culture temp

@refgrowthtypetemperaturerange
2422positivegrowth10psychrophilic
42024positivegrowth15psychrophilic
67770positivegrowth10psychrophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.911

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
2422seawaterNorwayNOREurope
67770SeawaterNorwayNOREurope
118903Environment, SeawaterNorwayNOREurope

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_144030.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_57;96_1125;97_1320;98_1593;99_144030&stattab=map
  • Last taxonomy: Pseudoalteromonas sp.
  • 16S sequence: X82138
  • Sequence Identity:
  • Total samples: 121
  • aquatic counts: 113
  • animal counts: 8

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
24221Risk group (German classification)
1189031Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: A.denitrificans 16S rRNA gene (ATCC 43337T)
  • accession: X82138
  • length: 1424
  • database: ena
  • NCBI tax ID: 43656

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudoalteromonas denitrificans DSM 60591123010.3wgspatric1123010
66792Pseudoalteromonas denitrificans DSM 60592599185267draftimg1123010
67770Pseudoalteromonas denitrificans DSM 6059GCA_900112265scaffoldncbi1123010

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes87.5no
flagellatedyes80.954no
gram-positiveno98.933no
anaerobicno98no
aerobicyes76.39no
halophileyes64.854no
spore-formingno94.535no
glucose-utilyes91.636no
thermophileno99.634yes
glucose-fermentno69.131no

External links

@ref: 2422

culture collection no.: DSM 6059, ATCC 43337, CIP 104108, IAM 14445, Nygaard 1977, JCM 21248, IAM 14544, LMG 8808, NCIMB 13179

straininfo link

  • @ref: 81889
  • straininfo: 10034

literature

  • topic: Phylogeny
  • Pubmed-ID: 24096356
  • title: Pseudoalteromonas xiamenensis sp. nov., a marine bacterium isolated from coastal surface seawater.
  • authors: Zhao CH, Luo JJ, Gong T, Huang XL, Ye DZ, Luo ZH
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.050229-0
  • year: 2013
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, *Phylogeny, Pseudoalteromonas/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2422Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6059)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6059
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
42024Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15981
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
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
81889Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10034.1StrainInfo: A central database for resolving microbial strain identifiers
118903Curators of the CIPCollection of Institut Pasteur (CIP 104108)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104108