Strain identifier

BacDive ID: 8179

Type strain: Yes

Species: Psychrobacter glacincola

Strain history: CIP <- 1997, ACAM <- D. Nichols, Tasmania Univ., Australia

NCBI tax ID(s): 56810 (species)

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

@ref: 4640

BacDive-ID: 8179

DSM-Number: 12194

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

description: Psychrobacter glacincola CCUG 34874 is an aerobe, psychrophilic bacterium that was isolated from ice core .

NCBI tax id

  • NCBI tax id: 56810
  • Matching level: species

strain history

@refhistory
4640<- ACAM <- D. Nichols and J. P. Bowman
119634CIP <- 1997, ACAM <- D. Nichols, Tasmania Univ., Australia

doi: 10.13145/bacdive8179.20230509.8.1

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 glacincola
  • full scientific name: Psychrobacter glacincola Bowman et al. 1997

@ref: 4640

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Moraxellaceae

genus: Psychrobacter

species: Psychrobacter glacincola

full scientific name: Psychrobacter glacincola Bowman et al. 1997

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no92.446
6948099.999negative
119634nonegativecoccus-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4640BACTO 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
32939Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
119634CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
4640positivegrowth15psychrophilic
32939positivegrowth15psychrophilic
52376positivegrowth10-15psychrophilic
52376positivegrowth20-22psychrophilic
119634positivegrowth5-22psychrophilic
119634nogrowth30mesophilic
119634nogrowth37mesophilic
119634nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
52376aerobe
119634obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.992

halophily

@refsaltgrowthtested relationconcentration
119634NaClpositivegrowth0-8 %
119634NaClnogrowth10 %

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
68371maltose-builds acid from17306
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
119634esculin-hydrolysis4853
119634glucose-fermentation17234
119634lactose-fermentation17716
119634nitrate+reduction17632
119634nitrite-reduction16301
119634sodium thiosulfate-builds gas from132112
119634glucose-degradation17234

antibiotic resistance

  • @ref: 119634
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 119634
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11963415688acetoin-
11963417234glucose+

enzymes

@refvalueactivityec
119634oxidase+
119634beta-galactosidase-3.2.1.23
119634alcohol dehydrogenase-1.1.1.1
119634gelatinase-
119634amylase-
119634DNase-
119634caseinase-3.4.21.50
119634catalase+1.11.1.6
119634tween esterase-
119634gamma-glutamyltransferase+2.3.2.2
119634lecithinase-
119634lipase-
119634lysine decarboxylase-4.1.1.18
119634ornithine decarboxylase-4.1.1.17
119634tryptophan deaminase-
119634urease+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

fatty acid profile

  • @reffatty acidpercentageECL
    52376C10:05.810
    52376C16:01.216
    52376C18:00.818
    52376C11:0 iso0.410.605
    52376C12:0 2OH0.213.178
    52376C12:0 3OH6.513.455
    52376C14:0 3OH/C16:1 ISO I0.215.485
    52376C14:1 ω5c0.313.899
    52376C16:1 ω7c3715.819
    52376C16:1 ω9c1.115.774
    52376C17:0 iso1.416.629
    52376C17:1 ω8c2.516.792
    52376C18:1 ω9c39.817.769
    52376C18:2 ω6,9c/C18:0 ANTE1.517.724
    52376TBSA 10Me18:00.218.392
    52376Unidentified0.811.96
    52376unknown 12.4860.512.486
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG
  • @reffatty acidpercentageECL
    52376C10:09.210
    52376C16:00.816
    52376C18:00.518
    52376C11:0 iso110.605
    52376C12:0 3OH8.513.455
    52376C15:0 ISO 3OH3.516.135
    52376C16:1 ω11c1.115.757
    52376C16:1 ω7c29.615.819
    52376C17:0 iso1.516.629
    52376C17:1 ω9c1.716.773
    52376C18:1 ω9c29.917.769
    52376C18:2 ω6,9c/C18:0 ANTE2.817.724
    52376Unidentified0.49.24
    52376Unidentified310.246
    52376Unidentified111.943
    52376Unidentified2.512.674
    52376Unidentified2.118.091
    52376unknown 12.486112.486
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG
  • @reffatty acidpercentageECL
    52376C10:010.310
    52376C16:00.916
    52376C11:0 iso1.210.605
    52376C12:0 3OH9.713.455
    52376C16:1 ω7c32.315.819
    52376C16:1 ω9c1.215.774
    52376C17:0 iso216.629
    52376C17:1 ω8c1.816.792
    52376C18:1 ω9c33.217.769
    52376C18:2 ω6,9c/C18:0 ANTE3.217.724
    52376Unidentified3.410.259
    52376unknown 12.4860.912.486
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119634-+++++-----+--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119634-------------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119634---------------------------------------------------------------------------+-----+------+-+---+-+++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcontinentlatitudelongitudecountryorigin.countryisolation date
4640ice core (-350m)Amery Ice Shelf, S69°29', E71°38'Australia and Oceania-69.483371.6333
52376Sea iceAnery Ice shelfAustralia and OceaniaAntarcticaATA
119634Environment, Shelf sea iceAntarcticaAntarcticaATA1993

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Ice
#Environmental#Terrestrial#Core sample

taxonmaps

  • @ref: 69479
  • File name: preview.99_279.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_80;96_193;97_209;98_234;99_279&stattab=map
  • Last taxonomy: Psychrobacter
  • 16S sequence: AJ312213
  • Sequence Identity:
  • Total samples: 7634
  • soil counts: 925
  • aquatic counts: 3187
  • animal counts: 3350
  • plant counts: 172

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
46401Risk group (German classification)
1196341Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Psychrobacter glacincola ACAM 483T 16S ribosomal RNA geneU461451467ena56810
20218Psychrobacter glacincola 16S rRNA gene, strain DSM 12194TAJ3122131515ena56810

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Psychrobacter glacincola Psychrobacter glacincola ACAM483GCA_904846215contigncbi56810
66792Psychrobacter glacincola strain Psychrobacter glacincola ACAM48356810.15wgspatric56810

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.229no
anaerobicno98.964no
halophileyes69.822no
spore-formingno96.74no
glucose-utilno63.571no
thermophileno99.414yes
flagellatedno93.117no
motileno89.829no
aerobicyes86.366no
glucose-fermentno94.434no

External links

@ref: 4640

culture collection no.: CCUG 34874, DSM 12194, ACAM 483, CIP 105313

straininfo link

  • @ref: 77582
  • straininfo: 44118

literature

  • topic: Phylogeny
  • Pubmed-ID: 14657134
  • title: Psychrobacter okhotskensis sp. nov., a lipase-producing facultative psychrophile isolated from the coast of the Okhotsk Sea.
  • authors: Yumoto I, Hirota K, Sogabe Y, Nodasaka Y, Yokota Y, Hoshino T
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02686-0
  • year: 2003
  • mesh: Base Composition, Base Sequence, DNA, Bacterial/chemistry, Japan, Molecular Sequence Data, Moraxellaceae/*classification/enzymology/genetics/isolation & purification, *Phylogeny, Seawater/microbiology, Temperature
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4640Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12194)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12194
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
32939Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17319
52376Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 34874)https://www.ccug.se/strain?id=34874
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
77582Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44118.1StrainInfo: A central database for resolving microbial strain identifiers
119634Curators of the CIPCollection of Institut Pasteur (CIP 105313)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105313