Name: Dickeya dianthicola DSM 18054
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 4351

Type strain:

Species: Dickeya dianthicola

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

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

NCBI tax ID(s): 1223568 (strain), 204039 (species)

SI-ID 10989

LMG 2966, ICMP 6427, LMG 2485, NCPPB 453, PDDCC 6427, CFBP 1200, BCRC 13211, CCRC 13211, DSM 18054

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Enterobacterales*
	Family	*Pectobacteriaceae*
	Genus	*Dickeya*
	Species	**Dickeya dianthicola**
	Full Scientific Name (LPSN)	Dickeya dianthicola Samson et al. 2005

Information on morphological and physiological properties Morphology

[Ref.: #29987]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.985

[Ref.: #29987]	Cell length	2 µm

[Ref.: #29987]	Cell width	0.75 µm

[Ref.: #29987]	Cell shape	rod-shaped

[Ref.: #29987]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %98.423

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7273]

Culture medium

REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)

[Ref.: #7273]

Culture medium growth

[Ref.: #7273]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7273]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #7273]			growth	30 °C
[Ref.: #29987]			optimum	36 °C

[Ref.: #7273]	Temperature range	mesophilic
[Ref.: #29987]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29987]

Oxygen tolerance

facultative anaerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.825

[Ref.: #29987]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68368]	amygdalin ChEBI	+	fermentation	* from API 20E
[Ref.: #29987]	arabinose ChEBI	+	carbon source
[Ref.: #68368]	arginine ChEBI	+	hydrolysis	* from API 20E
[Ref.: #68368]	citrate ChEBI	+	assimilation	* from API 20E
[Ref.: #68368]	D-glucose ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	D-mannitol ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	gelatin ChEBI	-	hydrolysis	* from API 20E
[Ref.: #29987]	glucose ChEBI	+	carbon source
[Ref.: #68368]	L-arabinose ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	L-rhamnose ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	lysine ChEBI	-	degradation	* from API 20E
[Ref.: #29987]	malate ChEBI	+	carbon source
[Ref.: #29987]	malonate ChEBI	+	carbon source
[Ref.: #29987]	mannitol ChEBI	+	carbon source
[Ref.: #29987]	mannose ChEBI	+	carbon source
[Ref.: #29987]	melibiose ChEBI	+	carbon source
[Ref.: #68368]	melibiose ChEBI	+	fermentation	* from API 20E
[Ref.: #29987]	myo-inositol ChEBI	+	carbon source
[Ref.: #68368]	myo-inositol ChEBI	-	fermentation	* from API 20E
[Ref.: #29987]	nitrate ChEBI	+	reduction
[Ref.: #68368]	ornithine ChEBI	-	degradation	* from API 20E
[Ref.: #29987]	raffinose ChEBI	+	carbon source
[Ref.: #68368]	sorbitol ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	sucrose ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	tryptophan ChEBI	+	energy source	* from API 20E
[Ref.: #68368]	urea ChEBI	-	hydrolysis	* from API 20E
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #29987]	indole ChEBI	yes
[Ref.: #68368]	acetoin ChEBI	yes	* from API 20E
[Ref.: #68368]	hydrogen sulfide ChEBI	no	* from API 20E
[Ref.: #68368]	indole ChEBI	yes	* from API 20E

	Metabolite	Voges-Proskauer-test	Indole test
[Ref.: #29987]	indole ChEBI		+
[Ref.: #68368]	acetoin ChEBI	+		* from API 20E
[Ref.: #68368]	indole ChEBI		+	* from API 20E

	Enzyme	Enzyme activity	EC number
[Ref.: #68368]	arginine dihydrolase	+	3.5.3.6	* from API 20E
[Ref.: #68368]	beta-galactosidase	+	3.2.1.23	* from API 20E
[Ref.: #68368]	cytochrome oxidase	-	1.9.3.1	* from API 20E
[Ref.: #68368]	gelatinase	-		* from API 20E
[Ref.: #68368]	lysine decarboxylase	-	4.1.1.18	* from API 20E
[Ref.: #68368]	ornithine decarboxylase	-	4.1.1.17	* from API 20E
[Ref.: #68368]	tryptophan deaminase	-	4.1.99.1	* from API 20E
[Ref.: #68368]	urease	-	3.5.1.5	* from API 20E

API® 20E:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	beta-GalactosidaseONPG	Arginine dihydrolaseADH (Arg)	Lysine decarboxylaseLDC (Lys)	Ornithine decarboxylaseODC	Citrate utilizationCIT	H2S productionH2S	Urease/urea hydrolysisURE	Tryptophan deaminaseTDA (Trp)	Indole productionIND	Acetoin production (Voges Proskauer test)VP	Gelatinase/gelatin hydrolysisGEL	Fermentation/oxidation of D-glucoseGLU	Fermentation/oxidation of D-mannitolMAN	Fermentation/oxidation of inositolINO	Fermentation/oxidation of sorbitolSor	Fermentation/oxidation of L-rhamnoseRHA	Fermentation/oxidation of sucroseSAC	Fermentation/oxidation of melibioseMEL	Fermentation/oxidation of amygdalinAMY	Fermentation/oxidation of L-arabinoseARA	Cytochrome oxidaseOX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	Oxidative catabolisation of D-glucoseOF-O	Fermentation of D-glucoseOF-F
[Ref.: #7273]	17672	+	+	-	-	+	-	-	-	+	+	-	+	+	-	-	+	+	+	+	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #7273]	Sample type/isolated from	Dianthus caryophyllus
[Ref.: #7273]	Host species	Dianthus caryophyllus
[Ref.: #7273]	Country	United Kingdom
[Ref.: #7273]	Country ISO 3 Code	GBR
[Ref.: #7273]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Host

#Plants

#Herbaceous plants (Grass,Crops)

What are isolation sources categories?

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #7273]	Pathogenicity (plant)	yes
[Ref.: #7273]	Biosafety level	1	Risk group (German classification) According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #7273]	Dickeya dianthicola strain CFBP 1200 16S ribosomal RNA gene, partial sequence	AF520708	1427	ENA	204039 tax ID
[Ref.: #20218]	Dickeya dianthicola strain NCPPB 453 16S-23S ribosomal RNA intergenic spacer, partial sequence	KC844729	339	ENA	204039 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Dickeya dianthicola NCPPB 453	GCA_000365305	chromosome	GenBank	1223568 tax ID	*
[Ref.: #66792]	Dickeya dianthicola NCPPB 453	1223568.13	wgs	PATRIC	1223568 tax ID	*
[Ref.: #66792]	Dickeya dianthicola NCPPB 453	2551306377	draft	JGI IMG/M	1223568 tax ID	*

[Ref.: #29987]

GC-content

59.5 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Dickeya dianthicola NCPPB 453 NCPPB 453 NCBI: GCA_000365305.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Dickeya dianthicola NCPPB 453 NCPPB 453 NCBI: GCA_000365305.1
[Ref.: #69480]	motile	yes	90.219	yes
[Ref.: #69480]	flagellated	yes	52.52	no
[Ref.: #69480]	gram-positive	no	98.228	no
[Ref.: #69480]	anaerobic	no	97.128	yes
[Ref.: #69480]	aerobic	no	51.759	no
[Ref.: #69480]	halophile	no	94.251	no
[Ref.: #69480]	spore-forming	no	92.279	no
[Ref.: #69480]	glucose-util	yes	92.97	yes
[Ref.: #69480]	thermophile	no	99.358	yes
[Ref.: #69480]	glucose-ferment	yes	89.523	yes

Availability in culture collections External links

[Ref.: #7273]

Culture collection no.

DSM 18054, CFBP 1200, ICMP 6427, LMG 2485, NCPPB 453, CN 26

[Ref.: #73842]

SI-ID 10989

Literature:

	Title	Authors	Journal	DOI	Year
Phylogeny	Transfer 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 L	Int J Syst Evol Microbiol	10.1099/ijs.0.02791-0	2005	*
	First Report of Dickeya dianthicola causing blackleg on New Guinea Impatiens (Impatiens hawkeri) in New York State, USA.	Liu Y, Vasiu S, Daughtrey ML, Filiatrault M	Plant Dis	10.1094/PDIS-09-20-2020-PDN	2020	*
	Bacterial Stem Rot of Oncidium Orchid Caused by a Dickeya sp. (ex Pectobacterium chrysanthemi) in Mainland China.	Li B, Qiu W, Fang Y, Xie GL	Plant Dis	10.1094/PDIS-93-5-0552B	2009	*

References

#7273

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18054

#20215

Parte, 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 DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#29987

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26354 (see below)

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#68368

Automatically annotated from API 20E .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#73842

Reimer, 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 identifiers . ( DOI 10.60712/SI-ID10989.1 )

#26354

IJSEM 1415 2005 ( DOI 10.1099/ijs.0.02791-0 , PubMed 16014461 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Dickeya dianthicola in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Dickeya dianthicola NCPPB 453 NCPPB 453

Dickeya dianthicola NCPPB 453 NCPPB 453

Change proposal

Change proposal