Strain identifier

BacDive ID: 14081

Type strain: Yes

Species: Shewanella atlantica

Strain Designation: HAW-EB5

Strain history: <- J.-S. Zhao, Biotechnol. Res. Inst., Natl. Res. Council of Canada, Montreal; HAW-EB5

NCBI tax ID(s): 271099 (species)

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General

@ref: 7527

BacDive-ID: 14081

DSM-Number: 18400

keywords: genome sequence, 16S sequence, Bacteria, aerobe, psychrophilic, Gram-negative, motile, rod-shaped

description: Shewanella atlantica HAW-EB5 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from marine sediment.

NCBI tax id

  • NCBI tax id: 271099
  • Matching level: species

strain history

  • @ref: 7527
  • history: <- J.-S. Zhao, Biotechnol. Res. Inst., Natl. Res. Council of Canada, Montreal; HAW-EB5

doi: 10.13145/bacdive14081.20230509.8.1

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 atlantica
  • full scientific name: Shewanella atlantica Zhao et al. 2007

@ref: 7527

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Shewanellaceae

genus: Shewanella

species: Shewanella atlantica

full scientific name: Shewanella atlantica Zhao et al. 2007

strain designation: HAW-EB5

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31886negative3.5 µm0.55 µmrod-shapedyes
69480yes98.687
69480negative99.996

colony morphology

  • @ref: 60228
  • incubation period: 2-3 days

pigmentation

  • @ref: 31886
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7527MODIFIED MEDIUM 514 (DSMZ Medium 1173)yeshttps://mediadive.dsmz.de/medium/1173Name: MODIFIED MEDIUM 514 (DSMZ Medium 1173) Composition: NaCl 39.45 g/l Bacto peptone 10.0 g/l MgCl2 5.9 g/l Yeast extract 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 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
7527BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium514.pdf

culture temp

@refgrowthtypetemperaturerange
7527positivegrowth10psychrophilic
31886positivegrowth04-25
31886positiveoptimum10psychrophilic
60228positivegrowth22psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 60228
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
31886no
69481no100
69480no99.995

halophily

@refsaltgrowthtested relationconcentration
31886NaClpositivegrowth01-04 %
31886NaClpositiveoptimum2.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3188630089acetate+carbon source
3188616449alanine+carbon source
3188635391aspartate+carbon source
3188628757fructose+carbon source
3188617596inosine+carbon source
3188624996lactate+carbon source
3188625017leucine+carbon source
3188625115malate+carbon source
3188651850methyl pyruvate+carbon source
31886506227N-acetylglucosamine+carbon source
3188626271proline+carbon source
3188617822serine+carbon source
3188630031succinate+carbon source
3188617992sucrose+carbon source
3188626986threonine+carbon source
3188617748thymidine+carbon source
3188653423tween 40+carbon source
3188653426tween 80+carbon source
3188616704uridine+carbon source
3188631011valerate+carbon source
3188617632nitrate+reduction

metabolite production

  • @ref: 31886
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

enzymes

@refvalueactivityec
31886alkaline phosphatase+3.1.3.1
31886catalase+1.11.1.6
31886cytochrome oxidase+1.9.3.1
31886urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
7527marine sedimentAtlantic Ocean, near Halifax harbour, Emerald BasinCanadaCANNorth America
60228Marine sedimentnear Halifax,Atlantic OceanCanadaCANNorth America2003-06-01

isolation source categories

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

Safety information

risk assessment

  • @ref: 7527
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7527
  • description: Shewanella atlantica strain HAW-EB5 16S ribosomal RNA gene, partial sequence
  • accession: AY579752
  • length: 1295
  • database: ena
  • NCBI tax ID: 271099

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Shewanella atlantica HAW-EB5GCA_003966265scaffoldncbi271099
66792Shewanella atlantica HAW-EB52900429846draftimg271099

GC content

  • @ref: 31886
  • GC-content: 46.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes92.621yes
flagellatedyes91.505no
gram-positiveno98.949yes
anaerobicno95.469yes
aerobicno73.89no
halophileyes59.127no
spore-formingno94.556yes
glucose-utilyes90.655no
thermophileno99.548yes
glucose-fermentno58.292no

External links

@ref: 7527

culture collection no.: CIP 109519, DSM 18400, CCUG 54554, NCIMB 14239

straininfo link

  • @ref: 83250
  • straininfo: 407346

literature

  • topic: Phylogeny
  • Pubmed-ID: 17766891
  • title: Shewanella canadensis sp. nov. and Shewanella atlantica sp. nov., manganese dioxide- and hexahydro-1,3,5-trinitro-1,3,5-triazine-reducing, psychrophilic marine bacteria.
  • authors: Zhao JS, Manno D, Thiboutot S, Ampleman G, Hawari J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64596-0
  • year: 2007
  • mesh: Atlantic Ocean, Bacterial Typing Techniques, Canada, Carbohydrate Metabolism, Carbon/metabolism, Carboxylic Acids/metabolism, Cell Membrane/chemistry, DNA Gyrase/genetics, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Geologic Sediments/microbiology, Manganese Compounds/*metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidation-Reduction, Oxides/*metabolism, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Shewanella/chemistry/*classification/isolation & purification/*metabolism, Triazines/*metabolism, beta-Galactosidase/biosynthesis
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7527Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18400)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18400
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
31886Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2814628776041
60228Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 54554)https://www.ccug.se/strain?id=54554
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)
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
83250Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID407346.1StrainInfo: A central database for resolving microbial strain identifiers