Strain identifier

BacDive ID: 6169

Type strain: Yes

Species: Devosia geojensis

Strain Designation: BD-c194

Strain history: <- CO Jeon, Gyungsang Univ.

NCBI tax ID(s): 443610 (species)

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General

@ref: 8094

BacDive-ID: 6169

DSM-Number: 19414

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

description: Devosia geojensis BD-c194 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from diesel-contaminated soil.

NCBI tax id

  • NCBI tax id: 443610
  • Matching level: species

strain history

@refhistory
8094<- C. O. Jeon, Gyeongsang Natl. Univ. (GSNU), Jinju, Korea; BD-c194
67771<- CO Jeon, Gyungsang Univ.

doi: 10.13145/bacdive6169.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Devosiaceae
  • genus: Devosia
  • species: Devosia geojensis
  • full scientific name: Devosia geojensis Ryu et al. 2008

@ref: 8094

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Devosiaceae

genus: Devosia

species: Devosia geojensis

full scientific name: Devosia geojensis Ryu et al. 2008

strain designation: BD-c194

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32428negative1.5 µm0.65 µmrod-shapedyes
67771negative
69480negative99.967

Culture and growth conditions

culture medium

  • @ref: 8094
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: 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 water

culture temp

@refgrowthtypetemperaturerange
8094positivegrowth30mesophilic
32428positivegrowth30-35mesophilic
32428positiveoptimum32.5mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
32428positivegrowth7.5-9alkaliphile
32428positiveoptimum8.25

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32428aerobe
67771aerobe

spore formation

@refspore formationconfidence
32428no
69481no95
69480no99.983

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3242817234glucose+carbon source
3242817306maltose+carbon source
3242829864mannitol+carbon source
3242837684mannose+carbon source
32428506227N-acetylglucosamine+carbon source
324284853esculin+hydrolysis

enzymes

@refvalueactivityec
32428acid phosphatase+3.1.3.2
32428alkaline phosphatase+3.1.3.1
32428catalase+1.11.1.6
32428cytochrome oxidase+1.9.3.1
32428urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8094diesel-contaminated soilGeojeRepublic of KoreaKORAsia
67771From contaminated soil(Diesel)Republic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_4211.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_2129;97_2564;98_3176;99_4211&stattab=map
  • Last taxonomy: Devosia geojensis
  • 16S sequence: EF575560
  • Sequence Identity:
  • Total samples: 1918
  • soil counts: 791
  • aquatic counts: 771
  • animal counts: 256
  • plant counts: 100

Safety information

risk assessment

  • @ref: 8094
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8094
  • description: Devosia geojensis strain BD-c194 16S ribosomal RNA gene, partial sequence
  • accession: EF575560
  • length: 1449
  • database: ena
  • NCBI tax ID: 443610

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Devosia geojensis BD-c194GCA_000969415contigncbi443610
66792Devosia geojensis strain BD-c194443610.3wgspatric443610
66792Devosia geojensis BD-c1942636415796draftimg443610

GC content

@refGC-contentmethod
809460.8high performance liquid chromatography (HPLC)
3242860.8
6777160.83

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno95no
gram-positiveno97.34no
anaerobicno98.857yes
halophileno91.115no
spore-formingno96.521no
glucose-utilyes88.863yes
aerobicyes93.329no
flagellatedno74.125no
motileyes86.528yes
thermophileno97.921yes
glucose-fermentno87.471no

External links

@ref: 8094

culture collection no.: DSM 19414, KCTC 22082

straininfo link

  • @ref: 75653
  • straininfo: 405479

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18319469Devosia geojensis sp. nov., isolated from diesel-contaminated soil in Korea.Ryu SH, Chung BS, Le NT, Jang HH, Yun PY, Park W, Jeon COInt J Syst Evol Microbiol10.1099/ijs.0.65481-02008Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, *Gasoline, Genes, rRNA, Genotype, Hyphomicrobiaceae/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Soil Pollutants, Species SpecificityGenetics
Phylogeny19329609Devosia albogilva sp. nov. and Devosia crocina sp. nov., isolated from a hexachlorocyclohexane dump site.Verma M, Kumar M, Dadhwal M, Kaur J, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.005447-02009Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, *Environmental Microbiology, Fatty Acids/analysis, *Hexachlorocyclohexane, Hyphomicrobiaceae/*classification/*isolation & purification, India, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic AcidGenetics
Phylogeny24827705Devosia pacifica sp. nov., isolated from deep-sea sediment.Jia YY, Sun C, Pan J, Zhang WY, Zhang XQ, Huo YY, Zhu XF, Wu MInt J Syst Evol Microbiol10.1099/ijs.0.059626-02014Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Hyphomicrobiaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryGenetics
Phylogeny26391996Devosia honganensis sp. nov., isolated from the soil of a chemical factory.Zhang L, Song M, Chen XL, Xu RJ, Chen K, Li SP, Xia ZY, Jiang JDAntonie Van Leeuwenhoek10.1007/s10482-015-0582-42015Aerobiosis, Base Composition, China, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Glycolipids/analysis, Hydrogen-Ion Concentration, Hyphomicrobiaceae/*classification/genetics/*isolation & purification/physiology, Industrial Waste, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Pigments, Biological/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, TemperatureGenetics
Phylogeny28647822Devosia nitraria sp. nov., a novel species isolated from the roots of Nitraria sibirica in China.Xu L, Zhang Y, Read N, Liu S, Friman VPAntonie Van Leeuwenhoek10.1007/s10482-017-0901-z2017Bacterial Proton-Translocating ATPases/genetics, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Glutamate-Ammonia Ligase/genetics, Glycolipids/analysis, Hyphomicrobiaceae/chemistry/*classification/genetics, Phospholipids/analysis, *Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Soil Microbiology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
8094Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19414)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19414
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
32428Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2865128776041
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
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
75653Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID405479.1StrainInfo: A central database for resolving microbial strain identifiers