Strain identifier

BacDive ID: 4351

Type strain: Yes

Species: Dickeya dianthicola

Strain history: <- CFBP <- R. A. Lelliott; CN 26

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 7273

BacDive-ID: 4351

DSM-Number: 18054

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, motile, rod-shaped, plant pathogen

description: Dickeya dianthicola DSM 18054 is a facultative anaerobe, mesophilic, Gram-negative plant pathogen that was isolated from Dianthus caryophyllus.

NCBI tax id

NCBI tax idMatching level
1223568strain
204039species

strain history

  • @ref: 7273
  • history: <- CFBP <- R. A. Lelliott; CN 26

doi: 10.13145/bacdive4351.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Pectobacteriaceae
  • genus: Dickeya
  • species: Dickeya dianthicola
  • full scientific name: Dickeya dianthicola Samson et al. 2005

@ref: 7273

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Pectobacteriaceae

genus: Dickeya

species: Dickeya dianthicola

full scientific name: Dickeya dianthicola Samson et al. 2005

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29987negative2 µm0.75 µmrod-shapedyes
69480yes98.423
69480negative99.985

Culture and growth conditions

culture medium

  • @ref: 7273
  • name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1a
  • composition: Name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
7273positivegrowth30mesophilic
29987positiveoptimum36mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 29987
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.825

observation

  • @ref: 29987
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2998722599arabinose+carbon source
2998717234glucose+carbon source
2998725115malate+carbon source
2998715792malonate+carbon source
2998729864mannitol+carbon source
2998737684mannose+carbon source
2998728053melibiose+carbon source
2998717268myo-inositol+carbon source
2998716634raffinose+carbon source
2998717632nitrate+reduction
6836830849L-arabinose+fermentation
6836827613amygdalin+fermentation
6836828053melibiose+fermentation
6836817992sucrose+fermentation
6836862345L-rhamnose+fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol+fermentation
6836817634D-glucose+fermentation
683685291gelatin-hydrolysis
6836827897tryptophan+energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
2998735581indoleyes
6836815688acetoinyes
6836835581indoleyes
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-test
2998735581indole+
6836815688acetoin+
6836835581indole+

enzymes

@refvalueactivityec
68368cytochrome oxidase-1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase+3.2.1.23

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
7273++--+---++-++--+++++-

Isolation, sampling and environmental information

isolation

  • @ref: 7273
  • sample type: Dianthus caryophyllus
  • host species: Dianthus caryophyllus
  • country: United Kingdom
  • origin.country: GBR
  • continent: Europe

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Herbaceous plants (Grass,Crops)

Safety information

risk assessment

  • @ref: 7273
  • pathogenicity plant: yes
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Dickeya dianthicola strain NCPPB 453 16S-23S ribosomal RNA intergenic spacer, partial sequenceKC844729339ena204039
7273Dickeya dianthicola strain CFBP 1200 16S ribosomal RNA gene, partial sequenceAF5207081427ena204039

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dickeya dianthicola NCPPB 453GCA_000365305chromosomencbi1223568
66792Dickeya dianthicola NCPPB 4531223568.13wgspatric1223568
66792Dickeya dianthicola NCPPB 4532551306377draftimg1223568

GC content

  • @ref: 29987
  • GC-content: 59.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes90.219yes
flagellatedyes52.52no
gram-positiveno98.228no
anaerobicno97.128yes
aerobicno51.759no
halophileno94.251no
spore-formingno92.279no
glucose-utilyes92.97yes
thermophileno99.358yes
glucose-fermentyes89.523yes

External links

@ref: 7273

culture collection no.: DSM 18054, CFBP 1200, ICMP 6427, LMG 2485, NCPPB 453, CN 26

straininfo link

  • @ref: 73842
  • straininfo: 10989

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16014461Transfer of Pectobacterium chrysanthemi (Burkholder et al. 1953) Brenner et al. 1973 and Brenneria paradisiaca to the genus Dickeya gen. nov. as Dickeya chrysanthemi comb. nov. and Dickeya paradisiaca comb. nov. and delineation of four novel species, Dickeya dadantii sp. nov., Dickeya dianthicola sp. nov., Dickeya dieffenbachiae sp. nov. and Dickeya zeae sp. nov.Samson R, Legendre JB, Christen R, Saux MF, Achouak W, Gardan LInt J Syst Evol Microbiol10.1099/ijs.0.02791-02005Animals, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Dickeya chrysanthemi/*classification/genetics/physiology, Enterobacteriaceae/*classification/genetics/physiology, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Rabbits, SerotypingGenetics
30764150Bacterial Stem Rot of Oncidium Orchid Caused by a Dickeya sp. (ex Pectobacterium chrysanthemi) in Mainland China.Li B, Qiu W, Fang Y, Xie GLPlant Dis10.1094/PDIS-93-5-0552B2009
33200972First Report of Dickeya dianthicola causing blackleg on New Guinea Impatiens (Impatiens hawkeri) in New York State, USA.Liu Y, Vasiu S, Daughtrey ML, Filiatrault MPlant Dis10.1094/PDIS-09-20-2020-PDN2020

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
7273Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18054)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18054
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
29987Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604126354
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)
68368Automatically annotated from API 20E
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
73842Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10989.1StrainInfo: A central database for resolving microbial strain identifiers