Strain identifier

BacDive ID: 3015

Type strain: Yes

Species: Variovorax dokdonensis

Strain Designation: DS-43

Strain history: CIP <- 2005, J.H. Yoon, KRIBB, Taejon, South Korea: strain DS-43

NCBI tax ID(s): 344883 (species)

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General

@ref: 7496

BacDive-ID: 3015

DSM-Number: 18312

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

description: Variovorax dokdonensis DS-43 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 344883
  • Matching level: species

strain history

@refhistory
7496<- KCTC <- K. Oh, KRIBB, Korea; DS-43
67771<- JH Yoon, KRIBB
118958CIP <- 2005, J.H. Yoon, KRIBB, Taejon, South Korea: strain DS-43

doi: 10.13145/bacdive3015.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Variovorax
  • species: Variovorax dokdonensis
  • full scientific name: Variovorax dokdonensis Yoon et al. 2006

@ref: 7496

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Variovorax

species: Variovorax dokdonensis

full scientific name: Variovorax dokdonensis Yoon et al. 2006

strain designation: DS-43

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31695negative0.7-2.8 µm0.3-0.5 µmrod-shapedyes
67771negative
118958negativerod-shapedyes

colony morphology

  • @ref: 118958

pigmentation

  • @ref: 31695
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7496REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c)yeshttps://mediadive.dsmz.de/medium/830cName: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c) Composition: Agar 15.0 g/l Yeast extract 0.5 g/l Proteose peptone 0.5 g/l Casamino acids 0.5 g/l Glucose 0.5 g/l Starch 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
40251MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
118958CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7496positivegrowth28mesophilic
31695positivegrowth10-40
31695positiveoptimum30mesophilic
40251positivegrowth30mesophilic
63058positivegrowth37mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31695positivegrowth5-9.5alkaliphile
31695positiveoptimum07-08

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31695aerobe
63058aerobe
67771aerobe
118958obligate aerobe

spore formation

  • @ref: 31695
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31695NaClpositivegrowth0-5 %
31695NaClpositiveoptimum0.5 %

observation

  • @ref: 31695
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3169517128adipate+carbon source
11895817632nitrate-reduction
11895816301nitrite-reduction

metabolite production

  • @ref: 118958
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31695alkaline phosphatase+3.1.3.1
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
118958oxidase+
118958alcohol dehydrogenase-1.1.1.1
118958catalase+1.11.1.6
118958lysine decarboxylase-4.1.1.18
118958ornithine decarboxylase-4.1.1.17
118958urease+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
118958-+++-+----+----+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
7496soilDokdoRepublic of KoreaKORAsia
63058SoilDokdo IslandRepublic of KoreaKORAsia2005
67771From soilDokdoRepublic of KoreaKORAsia
118958Environment, SoilDokdo IslandRepublic of KoreaKORAsia2004

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_64525.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_21250;97_35316;98_45615;99_64525&stattab=map
  • Last taxonomy: Variovorax
  • 16S sequence: DQ178978
  • Sequence Identity:
  • Total samples: 22
  • soil counts: 11
  • aquatic counts: 5
  • animal counts: 5
  • plant counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
74961Risk group (German classification)
1189581Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7496
  • description: Variovorax dokdonensis strain DS-43 16S ribosomal RNA gene, partial sequence
  • accession: DQ178978
  • length: 1486
  • database: ena
  • NCBI tax ID: 344883

GC content

  • @ref: 31695
  • GC-content: 66

External links

@ref: 7496

culture collection no.: DSM 18312, CIP 108838, KCTC 12544, CCUG 64011

straininfo link

  • @ref: 72537
  • straininfo: 291006

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16585700Variovorax dokdonensis sp. nov., isolated from soil.Yoon JH, Kang SJ, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.64070-02006Comamonadaceae/*classification/genetics/growth & development/*isolation & purification, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyGenetics
Phylogeny17158995Variovorax soli sp. nov., isolated from greenhouse soil.Kim BY, Weon HY, Yoo SH, Lee SY, Kwon SW, Go SJ, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.64390-02006Bacterial Typing Techniques, Comamonadaceae/chemistry/*classification/genetics/isolation & purification, DNA, Bacterial/analysis, Fatty Acids/analysis, Korea, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyGenetics
Phylogeny18175723Variovorax boronicumulans sp. nov., a boron-accumulating bacterium isolated from soil.Miwa H, Ahmed I, Yoon J, Yokota A, Fujiwara TInt J Syst Evol Microbiol10.1099/ijs.0.65315-02008Bacterial Typing Techniques, Base Composition, Boron/*metabolism, Comamonadaceae/*classification/genetics/*isolation & purification/physiology, DNA, Bacterial/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny21948092Variovorax defluvii sp. nov., isolated from sewage.Jin L, Kim KK, Ahn CY, Oh HMInt J Syst Evol Microbiol10.1099/ijs.0.035295-02011Bacterial Typing Techniques, Base Composition, Comamonadaceae/*classification/genetics/*isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rivers/microbiology, Sequence Analysis, DNA, Sewage/*microbiologyGenetics
Phylogeny25504533Variovorax guangxiensis sp. nov., an aerobic, 1-aminocyclopropane-1-carboxylate deaminase producing bacterium isolated from banana rhizosphere.Gao JL, Yuan M, Wang XM, Qiu TL, Li JW, Liu HC, Li XA, Chen J, Sun JGAntonie Van Leeuwenhoek10.1007/s10482-014-0304-32014Bacterial Typing Techniques, Base Composition, Carbon-Carbon Lyases/*metabolism, China, Cluster Analysis, Comamonadaceae/*classification/enzymology/genetics/*isolation & purification, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Musa, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, *Soil MicrobiologyEnzymology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7496Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18312)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18312
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
31695Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2797228776041
40251Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6512
63058Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 64011)https://www.ccug.se/strain?id=64011
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
72537Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID291006.1StrainInfo: A central database for resolving microbial strain identifiers
118958Curators of the CIPCollection of Institut Pasteur (CIP 108838)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108838