Strain identifier

BacDive ID: 8186

Type strain: Yes

Species: Psychrobacter submarinus

Strain history: CIP <- 2002, DSMZ <- P. Schumann <- L.A. Romanenko, KMM

NCBI tax ID(s): 154108 (species)

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

@ref: 5237

BacDive-ID: 8186

DSM-Number: 14161

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Psychrobacter submarinus DSM 14161 is a mesophilic bacterium that was isolated from seawater at a depth of 300 m.

NCBI tax id

  • NCBI tax id: 154108
  • Matching level: species

strain history

@refhistory
5237<- P. Schumann <- L. A. Romanenko, KMM
123347CIP <- 2002, DSMZ <- P. Schumann <- L.A. Romanenko, KMM

doi: 10.13145/bacdive8186.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pseudomonadales
  • family: Moraxellaceae
  • genus: Psychrobacter
  • species: Psychrobacter submarinus
  • full scientific name: Psychrobacter submarinus Romanenko et al. 2002

@ref: 5237

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Moraxellaceae

genus: Psychrobacter

species: Psychrobacter submarinus

full scientific name: Psychrobacter submarinus Romanenko et al. 2002

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no93.051
6948099.998negative
123347nonegativeoval-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5237BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514; with strain-specific modifications) Composition: NaCl 30.0 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
33154Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
123347CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
5237positivegrowth25mesophilic
33154positivegrowth25mesophilic
123347positivegrowth15-25psychrophilic
123347nogrowth5psychrophilic
123347nogrowth30mesophilic
123347nogrowth37mesophilic
123347nogrowth41thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
123347NaClpositivegrowth2-8 %
123347NaClnogrowth0 %
123347NaClnogrowth10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
123347citrate-carbon source16947
123347esculin-hydrolysis4853
123347nitrate-reduction17632
123347nitrite-reduction16301
123347nitrate-respiration17632

antibiotic resistance

  • @ref: 123347
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 123347
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12334715688acetoin-
12334717234glucose-

enzymes

@refvalueactivityec
123347oxidase+
123347beta-galactosidase-3.2.1.23
123347alcohol dehydrogenase-1.1.1.1
123347gelatinase-
123347amylase-
123347DNase-
123347caseinase-3.4.21.50
123347catalase+1.11.1.6
123347tween esterase+
123347lecithinase-
123347lipase-
123347lysine decarboxylase-4.1.1.18
123347ornithine decarboxylase-4.1.1.17
123347phenylalanine ammonia-lyase-4.3.1.24
123347tryptophan deaminase-
123347urease-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
123347-+++-+----++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123347---------------------------+/----------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationlatitudelongitudecountryisolation date
5237seawater at a depth of 300 mPacific Ocean 12°41'N, 132°38'W12.6833-132.633
123347Environment, Seawater at a depth of 300mPacific Ocean1985

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_1920.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_80;96_193;97_209;98_1507;99_1920&stattab=map
  • Last taxonomy: Psychrobacter
  • 16S sequence: AJ309940
  • Sequence Identity:
  • Total samples: 1598
  • soil counts: 91
  • aquatic counts: 1139
  • animal counts: 350
  • plant counts: 18

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
52371Risk group (German classification)
1233471Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5237
  • description: Psychrobacter submarinus 16S rRNA gene, strain KMM 225
  • accession: AJ309940
  • length: 1428
  • database: ena
  • NCBI tax ID: 154108

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Psychrobacter submarinus KMM 225GCA_904846685contigncbi154108
66792Psychrobacter submarinus strain Psychrobacter submarinus KMM225154108.8wgspatric154108

GC content

  • @ref: 5237
  • GC-content: 46.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno89.225no
gram-positiveno98.135no
anaerobicno98.476no
aerobicyes86.532no
halophileyes76.476no
spore-formingno96.421no
thermophileno99.255no
glucose-utilno62.162no
flagellatedno91.809no
glucose-fermentno93.896no

External links

@ref: 5237

culture collection no.: DSM 14161, KMM 225, CIP 107641

straininfo link

  • @ref: 77589
  • straininfo: 88148

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12148642Psychrobacter submarinus sp. nov. and Psychrobacter marincola sp. nov., psychrophilic halophiles from marine environments.Romanenko LA, Schumann P, Rohde M, Lysenko AM, Mikhailov VV, Stackebrandt EInt J Syst Evol Microbiol10.1099/00207713-52-4-12912002Animals, Bacterial Typing Techniques, *Cold Temperature, DNA, Ribosomal/analysis, Gammaproteobacteria/chemistry/*classification/genetics/physiology, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/*metabolism, Urochordata/*microbiologyGenetics
Pathogenicity33838818Structure and in vitro antiproliferative activity of the acidic capsular polysaccharide from the deep-sea bacterium Psychrobacter submarinus KMM 225(T).Kokoulin MS, Kuzmich AS, Romanenko LA, Chikalovets IVCarbohydr Polym10.1016/j.carbpol.2021.1179412021Aquatic Organisms/chemistry, Carbohydrate Sequence, Cell Proliferation/*drug effects, Cell Survival/drug effects, Humans, K562 Cells, Magnetic Resonance Spectroscopy/methods, Polysaccharides, Bacterial/*chemistry/isolation & purification/*pharmacology, Psychrobacter/*chemistry, Seawater/microbiologyEnzymology

Reference

@idauthorscataloguedoi/urltitle
5237Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14161)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14161
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
33154Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5099
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)
68371Automatically annotated from API 50CH acid
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
77589Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID88148.1StrainInfo: A central database for resolving microbial strain identifiers
123347Curators of the CIPCollection of Institut Pasteur (CIP 107641)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107641