Strain identifier

BacDive ID: 391

Type strain: Yes

Species: Alcanivorax borkumensis

Strain Designation: SK2

Strain history: CIP <- 1998, P.N. Golyshin, GBF Nat. Res. Center Biotechnol., Braunschweig, Germany: strain SK2 <- S. Lang, TU Braunschweig, Germany: strain SK2

NCBI tax ID(s): 59754 (species)

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General

@ref: 4326

BacDive-ID: 391

DSM-Number: 11573

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, rod-shaped

description: Alcanivorax borkumensis SK2 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from seawater sediment sample.

NCBI tax id

  • NCBI tax id: 59754
  • Matching level: species

strain history

@refhistory
4326<- M. Yakimov, GBF Braunschweig <- S. Lang, TU Braunschweig, SK2
116897CIP <- 1998, P.N. Golyshin, GBF Nat. Res. Center Biotechnol., Braunschweig, Germany: strain SK2 <- S. Lang, TU Braunschweig, Germany: strain SK2

doi: 10.13145/bacdive391.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Oceanospirillales
  • family: Alcanivoracaceae
  • genus: Alcanivorax
  • species: Alcanivorax borkumensis
  • full scientific name: Alcanivorax borkumensis Yakimov et al. 1998

@ref: 4326

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Alcanivoracaceae

genus: Alcanivorax

species: Alcanivorax borkumensis

full scientific name: Alcanivorax borkumensis Yakimov et al. 1998

strain designation: SK2

type strain: yes

Morphology

cell morphology

  • @ref: 116897
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4326ALCANIVORAX BORKUMENSIS MEDIUM (DSMZ Medium 809)yeshttps://mediadive.dsmz.de/medium/809Name: ALCANIVORAX BORKUMENSIS MEDIUM (DSMZ Medium 809) Composition: NaCl 23.0 g/l Sodium pyruvate 10.0 g/l MgCl2 x 2 H2O 6.16 g/l MgSO4 x 7 H2O 5.8 g/l NaNO3 5.0 g/l CaCl2 x 2 H2O 1.47 g/l Na2HPO4 x 7 H2O 0.89 g/l FeSO4 x 7 H2O 0.03 g/l Distilled water
4326BACTO 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
4326ONR7a MEDIUM (DSMZ Medium 950)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium950.pdf
37215MEDIUM 325 - for AlcanivoraxyesDistilled water make up to (1000.000 ml);Sodium chloride (2.300 g);Sodium nitrate (5.000 g);Magnesium chloride hexahydrate (6.160 g);Magnesium sulphate heptahydrate(5.800 g);Calcium chloride dihydrate (1.470 g);Agar (15.000 g);Pyruvic acid (10.000 g)
116897CIP Medium 325yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=325

culture temp

@refgrowthtypetemperaturerange
4326positivegrowth28mesophilic
37215positivegrowth30mesophilic
116897positivegrowth15-41
116897nogrowth5psychrophilic

Physiology and metabolism

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
116897esculin-hydrolysis4853
116897nitrate+reduction17632
116897nitrite-reduction16301

metabolite production

  • @ref: 116897
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase+3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)-
68382alkaline phosphatase-3.1.3.1
116897oxidase+
116897beta-galactosidase-3.2.1.23
116897alcohol dehydrogenase-1.1.1.1
116897gelatinase-
116897amylase-
116897caseinase-3.4.21.50
116897catalase+1.11.1.6
116897tween esterase+
116897gamma-glutamyltransferase+2.3.2.2
116897lecithinase-
116897lipase-
116897lysine decarboxylase-4.1.1.18
116897ornithine decarboxylase-4.1.1.17
116897phenylalanine ammonia-lyase-4.3.1.24
116897protease-
116897tryptophan deaminase-
116897urease+3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116897---+-+-+--++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116897-------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
4326seawater sediment sampleNorth Sea, BorkumGermanyDEUEurope
116897Environment, Seawater sedimentsBorkum IslandGermanyDEUEurope

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_3218.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15837;96_250;97_273;98_2466;99_3218&stattab=map
  • Last taxonomy: Alcanivorax sp.
  • 16S sequence: Y12579
  • Sequence Identity:
  • Total samples: 2592
  • soil counts: 26
  • aquatic counts: 2464
  • animal counts: 100
  • plant counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
43261Risk group (German classification)
1168971Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Alcanivorax borkumensis strain SK2 16S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, complete sequence; tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF197571584ena393595
20218Alcanivorax borkumensis strain SK2 16S ribosomal RNA gene, partial sequence; tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF1979011142ena393595
20218Alcanivorax borkumensis strain SK2 16S ribosomal RNA and 23S ribosomal RNA genes, partial sequenceAF197903949ena393595
20218Alcanivorax borkumensis 16S rRNA geneY125791503ena393595

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Alcanivorax borkumensis SK2GCA_000009365completencbi393595
66792Alcanivorax borkumensis SK2393595.15completepatric393595
66792Alcanivorax borkumensis SK2637000004completeimg393595

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno77.882no
flagellatedno74.361no
gram-positiveno99.032no
anaerobicno99.327no
halophileyes90.877no
spore-formingno97.438no
thermophileno99.635no
glucose-utilno73.982no
aerobicyes95.797no
glucose-fermentno90.591no

External links

@ref: 4326

culture collection no.: DSM 11573, ATCC 700651, CIP 105606

straininfo link

  • @ref: 70071
  • straininfo: 45443

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4326Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11573)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11573
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
37215Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17643
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
70071Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID45443.1StrainInfo: A central database for resolving microbial strain identifiers
116897Curators of the CIPCollection of Institut Pasteur (CIP 105606)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105606