Strain identifier

BacDive ID: 22978

Type strain: Yes

Species: Variovorax defluvii

Strain Designation: 2C1-b

Strain history: <- ST Lee, KAIST

NCBI tax ID(s): 913761 (species)

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General

@ref: 19162

BacDive-ID: 22978

DSM-Number: 27259

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

description: Variovorax defluvii 2C1-b is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sewage.

NCBI tax id

  • NCBI tax id: 913761
  • Matching level: species

strain history

@refhistory
19162<- KCTC <- H.-M. Oh and C.-Y. Ahn, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
67770L. Jin 2C1-b.
67771<- ST Lee, KAIST

doi: 10.13145/bacdive22978.20230509.8.1

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 defluvii
  • full scientific name: Variovorax defluvii Jin et al. 2012

@ref: 19162

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Variovorax

species: Variovorax defluvii

full scientific name: Variovorax defluvii Jin et al. 2012

strain designation: 2C1-b

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
30407negative1.4 µm0.45 µmovoid-shapedyes
67771negative

pigmentation

  • @ref: 30407
  • production: yes

multimedia

  • @ref: 19162
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_27259.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

  • @ref: 19162
  • name: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830c
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
19162positivegrowth28mesophilic
30407positivegrowth08-37
30407positiveoptimum30mesophilic
67770positivegrowth30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
30407positivegrowth06-09alkaliphile
30407positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

spore formation

  • @ref: 30407
  • spore formation: no

halophily

  • @ref: 30407
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 1-2 %

observation

  • @ref: 67770
  • observation: quinones: Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
30407168082-dehydro-D-gluconate+carbon source
30407161933-hydroxybenzoate+carbon source
30407370543-hydroxybutyrate+carbon source
30407178794-hydroxybenzoate+carbon source
3040730089acetate+carbon source
3040717128adipate+carbon source
3040716449alanine+carbon source
3040722599arabinose+carbon source
3040724265gluconate+carbon source
3040727570histidine+carbon source
3040717240itaconate+carbon source
3040724996lactate+carbon source
3040725115malate+carbon source
3040715792malonate+carbon source
3040717272propionate+carbon source
304079300suberic acid+carbon source
3040731011valerate+carbon source
304074853esculin+hydrolysis
3040717632nitrate+reduction

enzymes

@refvalueactivityec
30407catalase+1.11.1.6
30407cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
19162sewageRiver GeumhoRepublic of KoreaKORAsia
67770Sewage flowing into River GeumhoRepublic of KoreaKORAsia
67771From sewage flowing into River GeumhoRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Wastewater

Safety information

risk assessment

  • @ref: 19162
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 19162
  • description: Variovorax defluvii strain 2C1-b 16S ribosomal RNA gene, partial sequence
  • accession: HQ385753
  • length: 1498
  • database: ena
  • NCBI tax ID: 913761

GC content

@refGC-contentmethod
1916265.5
6777065.5high performance liquid chromatography (HPLC)

External links

@ref: 19162

culture collection no.: DSM 27259, JCM 17804, KCTC 12768

straininfo link

  • @ref: 87225
  • straininfo: 399132

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
19162Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27259)https://www.dsmz.de/collection/catalogue/details/culture/DSM-27259
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
30407Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2674428776041
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
87225Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID399132.1StrainInfo: A central database for resolving microbial strain identifiers