Strain identifier

BacDive ID: 14068

Type strain: Yes

Species: Shewanella denitrificans

Strain Designation: OS217

Strain history: CIP <- 2003, I. Brettar, GBF, Braunschweig, Germany: strain OS217

NCBI tax ID(s): 192073 (species)

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

@ref: 5667

BacDive-ID: 14068

DSM-Number: 15013

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, motile

description: Shewanella denitrificans OS217 is an obligate aerobe, motile bacterium that was isolated from water sample, 130 m depth.

NCBI tax id

  • NCBI tax id: 192073
  • Matching level: species

strain history

@refhistory
5667<- I. Brettar and M. G. Höfle, GBF; OS217
399512003, I. Brettar, GBF, Braunschweig, Germany: strain OS217
118906CIP <- 2003, I. Brettar, GBF, Braunschweig, Germany: strain OS217

doi: 10.13145/bacdive14068.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Alteromonadales
  • family: Shewanellaceae
  • genus: Shewanella
  • species: Shewanella denitrificans
  • full scientific name: Shewanella denitrificans Brettar et al. 2002

@ref: 5667

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Shewanellaceae

genus: Shewanella

species: Shewanella denitrificans

full scientific name: Shewanella denitrificans Brettar et al. 2002

strain designation: OS217

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes95.98
6948099.994negative
118906yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5667HALF STRENGTH BACTO MARINE BROTH (DSMZ Medium 514a)yeshttps://mediadive.dsmz.de/medium/514aName: HALF STRENGTH BACTO MARINE BROTH (DSMZ Medium 514a) Composition: Agar 15.0 g/l NaCl 9.725 g/l MgCl2 2.95 g/l Bacto peptone 2.5 g/l Na2SO4 1.62 g/l CaCl2 0.9 g/l Yeast extract 0.5 g/l KCl 0.275 g/l NaHCO3 0.08 g/l Fe(III) citrate 0.05 g/l KBr 0.04 g/l SrCl2 0.017 g/l H3BO3 0.011 g/l Na2HPO4 0.004 g/l Na-silicate 0.002 g/l NaF 0.0012 g/l (NH4)NO3 0.0008 g/l Distilled water
39951Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
118906CIP Medium 186yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=186
118906CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
5667positivegrowth20-25
39951positivegrowth25mesophilic
118906positivegrowth5-30
118906nogrowth37mesophilic
118906nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118906
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.974

halophily

@refsaltgrowthtested relationconcentration
118906NaClpositivegrowth2-4 %
118906NaClnogrowth0 %
118906NaClnogrowth6 %
118906NaClnogrowth8 %
118906NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11890616947citrate-carbon source
1189064853esculin+hydrolysis
11890617632nitrate+reduction
11890616301nitrite+reduction
118906132112sodium thiosulfate-builds gas from

metabolite production

  • @ref: 118906
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
118906oxidase+
118906beta-galactosidase-3.2.1.23
118906alcohol dehydrogenase-1.1.1.1
118906gelatinase+
118906amylase+
118906caseinase+3.4.21.50
118906catalase+1.11.1.6
118906tween esterase+
118906lecithinase+
118906lipase+
118906lysine decarboxylase-4.1.1.18
118906ornithine decarboxylase-4.1.1.17
118906protease+
118906tryptophan deaminase-
118906urease-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
118906-+++-+----++---+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118906++-------++-------+----------------------------------------+---------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryisolation date
5667water sample, 130 m depthBaltic Sea
118906Environment, Water samplesGotland Deep, a basin with anoxic deep water in the central balticBaltic Sea1986

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
56671Risk group (German classification)
1189061Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5667
  • description: Shewanella denitrificans partial 16S rRNA gene, strain OS-217
  • accession: AJ311964
  • length: 1500
  • database: ena
  • NCBI tax ID: 318161

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Shewanella denitrificans OS217GCA_000013765completencbi318161
66792Shewanella denitrificans OS217318161.16completepatric318161
66792Shewanella denitrificans OS2172524023135completeimg318161

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes91.316no
flagellatedyes85.524no
gram-positiveno98.788no
anaerobicno99.039no
halophileno53.064no
spore-formingno94.629no
thermophileno99.46yes
glucose-utilyes91.852no
aerobicyes63.199no
glucose-fermentno72.256no

External links

@ref: 5667

culture collection no.: DSM 15013, LMG 21692, CIP 107825

straininfo link

  • @ref: 83237
  • straininfo: 89621

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12508890Shewanella denitrificans sp. nov., a vigorously denitrifying bacterium isolated from the oxic-anoxic interface of the Gotland Deep in the central Baltic Sea.Brettar I, Christen R, Hofle MGInt J Syst Evol Microbiol10.1099/00207713-52-6-22112002Baltic States, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Microscopy, Electron, Molecular Sequence Data, Nitrogen/metabolism, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Shewanella/*classification/genetics/isolation & purification/metabolism, Species Specificity, Terminology as TopicGenetics
Metabolism19717628Biogenic formation of As-S nanotubes by diverse Shewanella strains.Jiang S, Lee JH, Kim MG, Myung NV, Fredrickson JK, Sadowsky MJ, Hur HGAppl Environ Microbiol10.1128/AEM.00450-092009Arsenicals/*metabolism, Microscopy, Electron, Nanotubes/*chemistry/*ultrastructure, Shewanella/*metabolism, Spectrometry, X-Ray Emission, Sulfides/*metabolism, X-Ray Absorption Spectroscopy
Enzymology19959582The periplasmic nitrate reductase in Shewanella: the resolution, distribution and functional implications of two NAP isoforms, NapEDABC and NapDAGHB.Simpson PJL, Richardson DJ, Codd RMicrobiology (Reading)10.1099/mic.0.034421-02009Amino Acid Sequence, Gene Expression Regulation, Bacterial, Genome, Bacterial, Isoenzymes/genetics/*metabolism, Molecular Sequence Data, Nitrate Reductase/genetics/*metabolism, Nitrates/metabolism, Operon, Periplasm/enzymology, Protein Subunits/genetics/metabolism, Quinones/metabolism, Shewanella/*enzymology/genetics, Transcriptional ActivationMetabolism
Metabolism23396327Shewanella spp. Use acetate as an electron donor for denitrification but not ferric iron or fumarate reduction.Yoon S, Sanford RA, Loffler FEAppl Environ Microbiol10.1128/AEM.03872-122013Acetates/*metabolism, *Denitrification, Electron Transport, Electrons, Energy Metabolism, Ferric Compounds/metabolism, Fumarates/metabolism, Iron/metabolism, Oxidation-Reduction, Reducing Agents/*metabolism, Shewanella/*metabolism
Phylogeny23950150Shewanella aestuarii sp. nov., a marine bacterium isolated from a tidal flat.Park HY, Jeon COInt J Syst Evol Microbiol10.1099/ijs.0.055178-02013Bacterial Typing Techniques, Base Composition, DNA Gyrase/genetics, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Quinones/chemistry, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Shewanella/*classification/genetics/isolation & purificationGenetics
Metabolism24621294Comparisons of Shewanella strains based on genome annotations, modeling, and experiments.Ong WK, Vu TT, Lovendahl KN, Llull JM, Serres MH, Romine MF, Reed JLBMC Syst Biol10.1186/1752-0509-8-312014Carbon/metabolism, Cluster Analysis, Electron Transport, Genes, Bacterial/genetics, *Models, Biological, *Molecular Sequence Annotation, Mutation, Phenotype, Shewanella/*genetics/*metabolism, Species SpecificityPhenotype
Enzymology25224746Spectroscopic characterization and mechanistic investigation of P-methyl transfer by a radical SAM enzyme from the marine bacterium Shewanella denitrificans OS217.Allen KD, Wang SCBiochim Biophys Acta10.1016/j.bbapap.2014.09.0092014
29422884Redox Sensing within the Genus Shewanella.Harris HW, Sanchez-Andrea I, McLean JS, Salas EC, Tran W, El-Naggar MY, Nealson KHFront Microbiol10.3389/fmicb.2017.025682018

Reference

@idauthorscataloguedoi/urltitle
5667Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15013)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15013
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
39951Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5379
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
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
83237Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID89621.1StrainInfo: A central database for resolving microbial strain identifiers
118906Curators of the CIPCollection of Institut Pasteur (CIP 107825)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107825