Strain identifier

BacDive ID: 23909

Type strain: Yes

Species: Dickeya solani

Strain history: <- J.M. van der Wolf, Plant Res. International, Wageningen, Netherlands; IPO 2222

NCBI tax ID(s): 1225786 (strain), 1089444 (species)

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General

@ref: 20529

BacDive-ID: 23909

DSM-Number: 28711

keywords: 16S sequence, Bacteria, mesophilic, plant pathogen

description: Dickeya solani DSM 28711 is a mesophilic plant pathogen that was isolated from potato plant showing symptoms of blackleg and slow wilt.

NCBI tax id

NCBI tax idMatching level
1089444species
1225786strain

strain history

  • @ref: 20529
  • history: <- J.M. van der Wolf, Plant Res. International, Wageningen, Netherlands; IPO 2222

doi: 10.13145/bacdive23909.20230509.8.1

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 solani
  • full scientific name: Dickeya solani van der Wolf et al. 2014

@ref: 20529

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Pectobacteriaceae

genus: Dickeya

species: Dickeya solani

full scientific name: Dickeya solani van der Wolf et al. 2014

type strain: yes

Morphology

multimedia

@refmultimedia contentintellectual property rightscaption
20529https://www.dsmz.de/microorganisms/photos/DSM_28711.jpg© Leibniz-Institut DSMZ
20529https://www.dsmz.de/microorganisms/photos/DSM_28711.jpgLeibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbHDSM 28711 on medium 535 at 28 °C

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
20529TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
20529TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)yeshttps://mediadive.dsmz.de/medium/545Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water

culture temp

  • @ref: 20529
  • growth: positive
  • type: growth
  • temperature: 25
  • range: mesophilic

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836817632nitrate-reduction
6836830849L-arabinose+fermentation
6836827613amygdalin+fermentation
6836828053melibiose+fermentation
6836817992sucrose+fermentation
6836862345L-rhamnose+fermentation
6836830911sorbitol-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
6836817997dinitrogenyes
6836816301nitriteno
6836835581indoleyes
6836816136hydrogen sulfideno

metabolite tests

  • @ref: 68368
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
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 TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOXNO2N2
20529+---+---+-+++--+++++--+
20529+---+---++++++-+++++-
20529+---+---++++++-++++++

Isolation, sampling and environmental information

isolation

  • @ref: 20529
  • sample type: potato plant (Melody) showing symptoms of blackleg and slow wilt
  • country: Netherlands
  • origin.country: NLD
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Infection#Disease
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_1714.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_451;97_1020;98_1353;99_1714&stattab=map
  • Last taxonomy: Dickeya solani
  • 16S sequence: KF639914
  • Sequence Identity:
  • Total samples: 113
  • soil counts: 4
  • aquatic counts: 28
  • animal counts: 68
  • plant counts: 13

Safety information

risk assessment

  • @ref: 20529
  • pathogenicity plant: yes
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20529
  • description: Dickeya solani strain NCPPB 4575 16S ribosomal RNA gene, partial sequence
  • accession: KF639914
  • length: 1401
  • database: ena
  • NCBI tax ID: 1089444

External links

@ref: 20529

culture collection no.: DSM 28711, LMG 25993, NCPPB 4479, IPO 2222

straininfo link

  • @ref: 87919
  • straininfo: 370474

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny24225027Dickeya solani sp. nov., a pectinolytic plant-pathogenic bacterium isolated from potato (Solanum tuberosum).van der Wolf JM, Nijhuis EH, Kowalewska MJ, Saddler GS, Parkinson N, Elphinstone JG, Pritchard L, Toth IK, Lojkowska E, Potrykus M, Waleron M, de Vos P, Cleenwerck I, Pirhonen M, Garlant L, Helias V, Pothier JF, Pfluger V, Duffy B, Tsror L, Manulis SInt J Syst Evol Microbiol10.1099/ijs.0.052944-02013Bacterial Typing Techniques, DNA, Bacterial/genetics, Enterobacteriaceae/*classification/genetics/isolation & purification, Europe, Fatty Acids/chemistry, Genes, Bacterial, Indoles/metabolism, Israel, Molecular Sequence Data, Multilocus Sequence Typing, Nucleic Acid Hybridization, Pectins/*metabolism, *Phylogeny, Plant Diseases/microbiology, RNA, Ribosomal, 16S/genetics, Solanum tuberosum/*microbiology, Spectrometry, Mass, Matrix-Assisted Laser Desorption-IonizationMetabolism
Genetics26467299Population genomics reveals additive and replacing horizontal gene transfers in the emerging pathogen Dickeya solani.Khayi S, Blin P, Pedron J, Chong TM, Chan KG, Moumni M, Helias V, Van Gijsegem F, Faure DBMC Genomics10.1186/s12864-015-1997-z2015Base Sequence, Chromosome Mapping, Enterobacteriaceae/*genetics/pathogenicity, Gene Transfer, Horizontal/*genetics, *Genetics, Population, Genome, Bacterial, *Metagenomics, Phylogeny, Plant Diseases/genetics/microbiology, Polymorphism, Single Nucleotide, Solanum tuberosum/microbiologyPhylogeny
27942352Complete genome anatomy of the emerging potato pathogen Dickeya solani type strain IPO 2222(T).Khayi S, Blin P, Chong TM, Chan KG, Faure DStand Genomic Sci10.1186/s40793-016-0208-02016
Phylogeny28395253The uniform structure of O-polysaccharides isolated from Dickeya solani strains of different origin.Ossowska K, Czerwicka M, Sledz W, Zoledowska S, Motyka A, Golanowska M, Condemine G, Lojkowska E, Kaczynski ZCarbohydr Res10.1016/j.carres.2017.04.0012017Enterobacteriaceae/*chemistry, O Antigens/*chemistry, Species Specificity
29619040Oxygen Availability Influences Expression of Dickeya solani Genes Associated With Virulence in Potato (Solanum tuberosum L.) and Chicory (Cichorium intybus L.).Lisicka W, Fikowicz-Krosko J, Jafra S, Narajczyk M, Czaplewska P, Czajkowski RFront Plant Sci10.3389/fpls.2018.003742018
30673477Systemic Colonization and Expression of Disease Symptoms on Bittersweet Nightshade (Solanum dulcamara) Infected with a GFP-Tagged Dickeya solani IPO2222 (IPO2254).Fikowicz-Krosko J, Czajkowski RPlant Dis10.1094/PDIS-08-17-1147-RE2018Enterobacteriaceae/growth & development/*physiology, Green Fluorescent Proteins, Plant Diseases/*microbiology, Plant Leaves/microbiology, Plant Roots/microbiology, Solanum/*microbiology, Xylem/microbiology
Pathogenicity32983224Genome-Wide Identification of Dickeya solani Transcriptional Units Up-Regulated in Response to Plant Tissues From a Crop-Host Solanum tuberosum and a Weed-Host Solanum dulcamara.Czajkowski R, Fikowicz-Krosko J, Maciag T, Rabalski L, Czaplewska P, Jafra S, Richert M, Krychowiak-Masnicka M, Hugouvieux-Cotte-Pattat NFront Plant Sci10.3389/fpls.2020.5803302020
35750797Resistance of Dickeya solani strain IPO 2222 to lytic bacteriophage PhiD5 results in fitness tradeoffs for the bacterium during infection.Bartnik P, Lewtak K, Fiolka M, Czaplewska P, Narajczyk M, Czajkowski RSci Rep10.1038/s41598-022-14956-72022*Bacteriophages/genetics, Dickeya, Enterobacteriaceae/genetics, Plant Diseases/microbiology, *Solanum tuberosum/microbiology
Phylogeny35812926Peribacillus castrilensis sp. nov.: A Plant-Growth-Promoting and Biocontrol Species Isolated From a River Otter in Castril, Granada, Southern Spain.Rodriguez M, Reina JC, Sampedro I, Llamas I, Martinez-Checa FFront Plant Sci10.3389/fpls.2022.8967282022

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
20529Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28711Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28711)
68368Automatically annotated from API 20E
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
87919Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID370474.1