Strain identifier

BacDive ID: 2957

Type strain: Yes

Species: Diaphorobacter oryzae

Strain Designation: RF3

Strain history: <- SK Rhee, Chungbuk Natl. Univ.

NCBI tax ID(s): 1121478 (strain), 491745 (species)

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General

@ref: 16513

BacDive-ID: 2957

DSM-Number: 22780

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

description: Diaphorobacter oryzae RF3 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from thiosulfate-oxidizing enrichment culture from paddy soils.

NCBI tax id

NCBI tax idMatching level
1121478strain
491745species

strain history

@refhistory
16513<- KCTC <- S.-K. Rhee, Chungbuk Natl. Univ., Korea
67771<- SK Rhee, Chungbuk Natl. Univ.

doi: 10.13145/bacdive2957.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Diaphorobacter
  • species: Diaphorobacter oryzae
  • full scientific name: Diaphorobacter oryzae Pham et al. 2009

@ref: 16513

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Diaphorobacter

species: Diaphorobacter oryzae

full scientific name: Diaphorobacter oryzae Pham et al. 2009

strain designation: RF3

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
28923negative1.55 µm0.65 µmrod-shapedyes
67771negative

Culture and growth conditions

culture medium

  • @ref: 16513
  • name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/535
  • composition: Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16513positivegrowth28mesophilic
28923positivegrowth07-35
28923positiveoptimum30mesophilic
67771positivegrowth25mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
28923aerobe
67771aerobe

observation

  • @ref: 28923
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
28923168082-dehydro-D-gluconate+carbon source
28923370543-hydroxybutyrate+carbon source
28923178794-hydroxybenzoate+carbon source
2892330089acetate+carbon source
2892316449alanine+carbon source
2892327689decanoate+carbon source
2892324265gluconate+carbon source
2892317234glucose+carbon source
2892327570histidine+carbon source
2892324996lactate+carbon source
2892325115malate+carbon source
2892326271proline+carbon source
2892317272propionate+carbon source
2892317822serine+carbon source
2892331011valerate+carbon source
2892317632nitrate+reduction

enzymes

@refvalueactivityec
28923catalase+1.11.1.6
28923cytochrome oxidase+1.9.3.1
28923urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16513thiosulfate-oxidizing enrichment culture from paddy soilsCheongjuRepublic of KoreaKORAsia
67771From a thiosulfate-oxidizing enrichment cultureRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Engineered#Laboratory#Lab enrichment
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_110402.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_491;97_892;98_1045;99_110402&stattab=map
  • Last taxonomy: Diaphorobacter oryzae
  • 16S sequence: EU342381
  • Sequence Identity:
  • Total samples: 223
  • soil counts: 16
  • aquatic counts: 183
  • animal counts: 13
  • plant counts: 11

Safety information

risk assessment

  • @ref: 16513
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16513
  • description: Diaphorobacter oryzae strain RF3 16S ribosomal RNA gene, partial sequence
  • accession: EU342381
  • length: 1401
  • database: ena
  • NCBI tax ID: 491745

Genome sequences

  • @ref: 66792
  • description: Diaphorobacter oryzae DSM 22780
  • accession: 2574179700
  • assembly level: draft
  • database: img
  • NCBI tax ID: 1121478

GC content

@refGC-contentmethod
1651362.9high performance liquid chromatography (HPLC)
2892362.9

External links

@ref: 16513

culture collection no.: DSM 22780, KCTC 22225, LMG 24467

straininfo link

  • @ref: 72479
  • straininfo: 323909

literature

  • topic: Phylogeny
  • Pubmed-ID: 19196757
  • title: Diaphorobacter oryzae sp. nov., isolated from a thiosulfate-oxidizing enrichment culture.
  • authors: Pham VH, Park SJ, Roh Y, Roh DH, Rhee SK
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.001669-0
  • year: 2009
  • mesh: Bacteriological Techniques, Comamonadaceae/chemistry/*classification/genetics/metabolism, Culture Media, Fatty Acids, Molecular Sequence Data, Oxidation-Reduction, Phenotype, RNA, Ribosomal, 16S/genetics, Species Specificity, Thiosulfates/*metabolism
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16513Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22780)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22780
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
28923Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2536228776041
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
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
72479Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID323909.1StrainInfo: A central database for resolving microbial strain identifiers