Strain identifier

BacDive ID: 4352

Type strain: Yes

Species: Dickeya zeae

Strain Designation: Sr58

Strain history: <- CFBP <- A. Kelman; Sr58

NCBI tax ID(s): 1223573 (strain), 204042 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 7361

BacDive-ID: 4352

DSM-Number: 18068

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

description: Dickeya zeae Sr58 is a facultative anaerobe, mesophilic, Gram-negative plant pathogen that was isolated from Zea mays.

NCBI tax id

NCBI tax idMatching level
204042species
1223573strain

strain history

  • @ref: 7361
  • history: <- CFBP <- A. Kelman; Sr58

doi: 10.13145/bacdive4352.20230509.8.1

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 zeae
  • full scientific name: Dickeya zeae Samson et al. 2005

@ref: 7361

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Pectobacteriaceae

genus: Dickeya

species: Dickeya zeae

full scientific name: Dickeya zeae Samson et al. 2005

strain designation: Sr58

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29987negative2 µm0.75 µmrod-shapedyes
69480yes97.057
69480negative99.978

Culture and growth conditions

culture medium

  • @ref: 7361
  • name: REACTIVATION WITH LIQUID MEDIUM (DSMZ Medium 535b)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/535b
  • composition: Name: REACTIVATION WITH LIQUID MEDIUM (DSMZ Medium 535b) Composition: Trypticase soy broth 30.0 g/l Casein peptone 17.0 g/l Agar 15.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l K2HPO4 2.5 g/l D(+)-Glucose 2.5 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
7361positivegrowth30mesophilic
29987positivegrowth36-39mesophilic
29987positiveoptimum37.5mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 29987
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.831

observation

  • @ref: 29987
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2998716449alanine+carbon source
2998722599arabinose+carbon source
2998717057cellobiose+carbon source
2998717234glucose+carbon source
2998717716lactose+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
7361+---+---++++++-+++++-

Isolation, sampling and environmental information

isolation

  • @ref: 7361
  • sample type: Zea mays
  • host species: Zea mays
  • country: USA
  • origin.country: USA
  • continent: North America

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_7526.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_451;97_1020;98_1203;99_7526&stattab=map
  • Last taxonomy: Dickeya
  • 16S sequence: AF520711
  • Sequence Identity:
  • Total samples: 44
  • soil counts: 2
  • aquatic counts: 1
  • animal counts: 29
  • plant counts: 12

Safety information

risk assessment

  • @ref: 7361
  • pathogenicity plant: yes
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Dickeya zeae strain NCPPB 2538 16S-23S ribosomal RNA intergenic spacer, partial sequenceKC844739317ena204042
7361Dickeya zeae strain CFBP 2052 16S ribosomal RNA gene, partial sequenceAF5207111422ena204042

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dickeya zeae NCPPB 2538GCA_000406165chromosomencbi1223573
66792Dickeya zeae NCPPB 25381223573.12wgspatric1223573
66792Dickeya zeae NCPPB 25382558860215draftimg1223573

GC content

  • @ref: 29987
  • GC-content: 56.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileyes90.933no
flagellatedyes59.781no
gram-positiveno98.686yes
anaerobicno95.565yes
aerobicno69.328yes
halophileno93.98no
spore-formingno92.832no
thermophileno99.185yes
glucose-utilyes94.262yes
glucose-fermentyes89.152yes

External links

@ref: 7361

culture collection no.: DSM 18068, CFBP 2052, ICMP 5704, NCPPB 2538

straininfo link

  • @ref: 73843
  • straininfo: 2606

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
30699660First Report of Bacterial Stalk Rot of Maize Caused by Dickeya zeae in Mexico.Martinez-Cisneros BA, Juarez-Lopez G, Valencia-Torres N, Duran-Peralta E, Mezzalama MPlant Dis10.1094/PDIS-02-14-0198-PDN2014
Phylogeny32552985Dickeya oryzae sp. nov., isolated from the roots of rice.Wang X, He SW, Guo HB, Han JG, Thin KK, Gao JS, Wang Y, Zhang XXInt J Syst Evol Microbiol10.1099/ijsem.0.0042652020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Enterobacteriaceae/*classification/isolation & purification, Fatty Acids/chemistry, Genes, Bacterial, Nucleic Acid Hybridization, Oryza/*microbiology, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome
Phylogeny34726587Diversity within the Dickeya zeae complex, identification of Dickeya zeae and Dickeya oryzae members, proposal of the novel species Dickeya parazeae sp. nov.Hugouvieux-Cotte-Pattat N, Van Gijsegem FInt J Syst Evol Microbiol10.1099/ijsem.0.0050592021Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Dickeya/classification/isolation & purification, France, Nucleic Acid Hybridization, *Phylogeny, Plant Diseases/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
7361Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18068)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18068
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
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
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
73843Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID2606.1StrainInfo: A central database for resolving microbial strain identifiers