Strain identifier

BacDive ID: 23258

Type strain: Yes

Species: Daejeonella rubra

Strain Designation: W1

Strain history: CIP <- 2013, DSMZ <- 2011, R. Margesin, Innsbruck Univ., Innsbruck, Austria: strain W1 Pedobacter sp.

NCBI tax ID(s): 990371 (species)

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General

@ref: 19205

BacDive-ID: 23258

DSM-Number: 24536

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

description: Daejeonella rubra W1 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from soil from a petroleum hydrocarbon contaminated former military site.

NCBI tax id

  • NCBI tax id: 990371
  • Matching level: species

strain history

@refhistory
19205<- R. Margesin, Inst. Microbiology, Univ. Innsbruck, Austria; W1
122273CIP <- 2013, DSMZ <- 2011, R. Margesin, Innsbruck Univ., Innsbruck, Austria: strain W1 Pedobacter sp.

doi: 10.13145/bacdive23258.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Sphingobacteriia
  • order: Sphingobacteriales
  • family: Sphingobacteriaceae
  • genus: Daejeonella
  • species: Daejeonella rubra
  • full scientific name: Daejeonella rubra (Margesin and Zhang 2013) García-López et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Pedobacter ruber

@ref: 19205

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Daejeonella

species: Daejeonella rubra

full scientific name: Daejeonella rubra (Margesin and Zhang 2013) García-López et al. 2020

strain designation: W1

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
30578negativerod-shapedno
69480negative99.998
122273negativerod-shapedyes

pigmentation

  • @ref: 30578
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
39721MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
19205R2A MEDIUM (DSMZ Medium 830)yesName: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled waterhttps://mediadive.dsmz.de/medium/830
122273CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
19205positivegrowth15psychrophilic
30578positivegrowth22.5psychrophilic
30578positivegrowth01-36
39721positivegrowth25mesophilic

culture pH

  • @ref: 30578
  • ability: positive
  • type: optimum
  • pH: 7

Physiology and metabolism

oxygen tolerance

  • @ref: 30578
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30578no
69481no100
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
30578NaClpositivegrowth0-1 %
30578NaClpositiveoptimum0.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3057817306maltose+carbon source
3057837684mannose+carbon source
30578506227N-acetylglucosamine+carbon source
12227317632nitrate-reduction
12227316301nitrite-reduction

metabolite production

  • @ref: 122273
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
30578acid phosphatase+3.1.3.2
30578alkaline phosphatase+3.1.3.1
30578alpha-galactosidase+3.2.1.22
30578catalase+1.11.1.6
30578gelatinase+
30578cytochrome oxidase+1.9.3.1
30578urease+3.5.1.5
122273oxidase-
122273catalase+1.11.1.6
122273urease-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
122273-+---+----++-----+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeisolation date
19205soil from a petroleum hydrocarbon contaminated former military siteSouth Tyrol, Welsberg (46° 45' 10.57'' N 12° 06' 47.39'' E)ItalyITAEurope46.752912.1132
122273Environment, SoilWelsberg, south TyrolItalyITAEurope2010

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination#Oil (Fuel)
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_46309.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_115;96_1777;97_2127;98_27082;99_46309&stattab=map
  • Last taxonomy: Daejeonella rubra subclade
  • 16S sequence: HQ882803
  • Sequence Identity:
  • Total samples: 381
  • soil counts: 25
  • aquatic counts: 337
  • animal counts: 18
  • plant counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
192051Risk group (German classification)
1222731Risk group (French classification)

Sequence information

16S sequences

  • @ref: 19205
  • description: Pedobacter ruber strain W1 16S ribosomal RNA gene, partial sequence
  • accession: HQ882803
  • length: 1514
  • database: ena
  • NCBI tax ID: 990371

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Daejeonella rubra DSM 24536GCA_900103545contigncbi990371
66792Pedobacter ruber strain DSM 24536990371.3wgspatric990371
66792Pedobacter ruber DSM 245362675903227draftimg990371

GC content

@refGC-contentmethod
1920539.0high performance liquid chromatography (HPLC)
3057839

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno93.632yes
flagellatedno97.667yes
gram-positiveno97.077yes
anaerobicno98.257yes
halophileno95.938yes
spore-formingno93.825yes
thermophileno94.778yes
glucose-utilyes84.462no
aerobicyes83.185no
glucose-fermentno87.13no

External links

@ref: 19205

culture collection no.: DSM 24536, CIP 110258, LMG 26240

straininfo link

  • @ref: 87481
  • straininfo: 375104

literature

  • topic: Phylogeny
  • Pubmed-ID: 22427447
  • title: Pedobacter ruber sp. nov., a psychrophilic bacterium isolated from soil.
  • authors: Margesin R, Zhang DC
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.039107-0
  • year: 2012
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Italy, Molecular Sequence Data, Pedobacter/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysis
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
19205Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24536)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24536
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
30578Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2690928776041
39721Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8097
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
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
87481Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID375104.1StrainInfo: A central database for resolving microbial strain identifiers
122273Curators of the CIPCollection of Institut Pasteur (CIP 110258)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110258