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)

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	07-12-2022 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Enterobacterales*
	Family	*Pectobacteriaceae*
	Genus	*Dickeya*
	Species	**Dickeya dianthicola**
	Full Scientific Name (PNU)	Dickeya dianthicola Samson et al. 2005

Information on morphological and physiological properties Morphology

[Ref.: #29987]	Gram stain	negative
[Ref.: #29987]	Cell length	2 µm
[Ref.: #29987]	Cell width	0.75 µm
[Ref.: #29987]	Cell shape	rod-shaped
[Ref.: #29987]	Motility	yes

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 provided by DSMZ

[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.: #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
[Ref.: #68368]	acetoin ChEBI	* from API 20E
[Ref.: #68368]	hydrogen sulfide ChEBI	* from API 20E
[Ref.: #29987]	indole ChEBI
[Ref.: #68368]	indole ChEBI	* from API 20E

	Metabolite	Voges-Proskauer-test	Indole test
[Ref.: #68368]	acetoin ChEBI	+		* from API 20E
[Ref.: #29987]	indole ChEBI		+
[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]	15078	+	+	-	-	+	-	-	-	+	+	-	+	+	-	-	+	+	+	+	+	-	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.: #20218]	Dickeya dianthicola strain NCPPB 453 16S-23S ribosomal RNA intergenic spacer, partial sequence	KC844729	339	ENA	204039 tax ID	*
[Ref.: #7273]	Dickeya dianthicola strain CFBP 1200 16S ribosomal RNA gene, partial sequence	AF520708	1427	ENA	204039 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Dickeya dianthicola NCPPB 453 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.: #66792]	Methanobacterium sp. Rep1_Bin027	GCA_016839005	contig	PATRIC	2164 tax ID	*

[Ref.: #29987]

GC-content

59.5 mol%

Availability in culture collections External links

[Ref.: #7273]

Culture collection no.

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

[Ref.: #20218]

Associated Passport(s) in StrainInfo

691251, 278264, 42892, 42894, 42895

Literature:

Topic	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	*
	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	*
	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	*

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) .

#26354

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

* These data were automatically processed and therefore are not curated

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