Strain identifier

BacDive ID: 3782

Type strain: Yes

Species: Dyadobacter psychrophilus

Strain Designation: BZ26

Strain history: CIP <- 2010, R. Margesin, Innsbruck Univ., Innsbruck Austria: strain BZ26

NCBI tax ID(s): 651661 (species)

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General

@ref: 16246

BacDive-ID: 3782

DSM-Number: 22270

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

description: Dyadobacter psychrophilus BZ26 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from hydrocarbon-contaminated soil.

NCBI tax id

  • NCBI tax id: 651661
  • Matching level: species

strain history

@refhistory
379202010, R. Margesin, Innsbruck Univ., Innsbruck Austria: strain BZ26
16246<- R. Margesin, Inst. Microbiology, Univ. Innsbruck, Austria; BZ26
67771<- DSM <- R. Margesin, Inst. Microbiology, Univ. Innsbruck, Austria, BZ26
122029CIP <- 2010, R. Margesin, Innsbruck Univ., Innsbruck Austria: strain BZ26

doi: 10.13145/bacdive3782.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Spirosomataceae
  • genus: Dyadobacter
  • species: Dyadobacter psychrophilus
  • full scientific name: Dyadobacter psychrophilus Zhang et al. 2010

@ref: 16246

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Spirosomaceae

genus: Dyadobacter

species: Dyadobacter psychrophilus

full scientific name: Dyadobacter psychrophilus Zhang et al. 2010

strain designation: BZ26

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29626negative1.5-3 µm0.9-1.2 µmovoid-shapedno
67771negative
69480negative99.99
69480no91.687
122029negativerod-shapedno

pigmentation

  • @ref: 29626
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16246NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
37920MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
122029CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
16246positivegrowth28mesophilic
29626positivegrowth01-30
29626positiveoptimum10-15psychrophilic
37920positivegrowth20psychrophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepH
29626positivegrowth06-08
29626positiveoptimum06-08

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29626aerobe
67771aerobe
122029obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.977

halophily

@refsaltgrowthtested relationconcentration
29626NaClpositivegrowth0-1 %
29626NaClpositiveoptimum0-1 %

observation

  • @ref: 29626
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2962617234glucose+carbon source
2962617992sucrose+carbon source
296264853esculin+hydrolysis
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine+hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
12202917632nitrate-reduction
12202916301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12202935581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
29626acid phosphatase+3.1.3.2
29626alkaline phosphatase+3.1.3.1
29626catalase+1.11.1.6
29626cytochrome oxidase+1.9.3.1
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
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase+3.5.3.6
122029oxidase+
122029catalase+1.11.1.6
122029urease-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
122029-+---++++-+++++++++-

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
16246---+-+-++-+-++------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
16246hydrocarbon-contaminated soilSouth Tyrol, BozenItalyITAEurope
67771From hydrocarbon-contaminated soilSouth Tyrol, BozenItalyITAEurope
122029Environment, SoilTyrolItalyITAEurope2008

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Environmental#Terrestrial#Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
162461Risk group (German classification)
1220291Risk group (French classification)

Sequence information

16S sequences

  • @ref: 16246
  • description: Dyadobacter psychrophilus strain BZ26 16S ribosomal RNA gene, partial sequence
  • accession: GQ131577
  • length: 1501
  • database: ena
  • NCBI tax ID: 651661

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dyadobacter psychrophilus DSM 22270GCA_900167945scaffoldncbi651661
66792Dyadobacter psychrophilus strain DSM 22270651661.3wgspatric651661
66792Dyadobacter psychrophilus DSM 222702595698219draftimg651661

GC content

@refGC-contentmethod
1624648.9thermal denaturation, midpoint method (Tm)
2962648.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.212no
flagellatedno97.359yes
gram-positiveno97.646yes
anaerobicno99.415yes
aerobicyes90.367yes
halophileno95.085no
spore-formingno94.4no
thermophileno99.41yes
glucose-utilyes88.465yes
glucose-fermentno89.469yes

External links

@ref: 16246

culture collection no.: DSM 22270, CGMCC 1.8951, KCTC 23640, CIP 110129

straininfo link

  • @ref: 73294
  • straininfo: 370174

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19717578Dyadobacter psychrophilus sp. nov., a psychrophilic bacterium isolated from soil.Zhang DC, Liu HC, Xin YH, Zhou YG, Schinner F, Margesin RInt J Syst Evol Microbiol10.1099/ijs.0.017236-02009Base Composition, Base Sequence, Fatty Acids/analysis, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Sphingobacterium/*classification/genetics/isolation & purification/physiologyGenetics
Phylogeny31595323Dyadobacter luteus sp. nov., isolated from rose rhizosphere soil.Chen L, Gao X, Ma Q, Liu H, Wang X, Xu Y, Liu YArch Microbiol10.1007/s00203-019-01738-52019Bacterial Typing Techniques, Base Composition, Cytophagaceae/chemistry/*classification/genetics, DNA, Bacterial/genetics, Fatty Acids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Rosa/microbiology, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Vitamin K 2/analysisTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16246Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22270)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22270
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
29626Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2601628776041
37920Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7953
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68369Automatically annotated from API 20NE
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
73294Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID370174.1StrainInfo: A central database for resolving microbial strain identifiers
122029Curators of the CIPCollection of Institut Pasteur (CIP 110129)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110129