Name: Dickeya zeae Sr58
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 4352

Type strain:

Species: Dickeya zeae

Strain Designation: Sr58

Culture col. no.: DSM 18068, CFBP 2052, ICMP 5704, NCPPB 2538

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

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

SI-ID 2606

LMG 2505, ICMP 5704, NCPPB 2538, PDDCC 5704, CFBP 2052, BCRC 13205, CCRC 13205, DSM 18068, CFBP 1452, CIP 109102

Special Collections

Section

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

Gram-negative
motile
rod-shaped
facultative anaerobe
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 zeae**
	Full Scientific Name (LPSN)	Dickeya zeae Samson et al. 2005

Information on morphological and physiological properties Morphology

[Ref.: #29987]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %100

[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.: #7361]

Culture medium

REACTIVATION WITH LIQUID MEDIUM (DSMZ Medium 535b)

[Ref.: #7361]

Culture medium growth

[Ref.: #7361]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7361]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7361]	growth	30 °C
[Ref.: #29987]	growth	36-39 °C
[Ref.: #29987]	optimum	37.5 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29987]

Oxygen tolerance

facultative anaerobe

[Ref.: #69481]

Ability of spore formation

no Confidence in %99

[Ref.: #29987]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29987]	alanine ChEBI	+	carbon source
[Ref.: #68368]	amygdalin ChEBI	+	fermentation	* from API 20E
[Ref.: #29987]	arabinose ChEBI	+	carbon source
[Ref.: #68368]	arginine ChEBI	-	hydrolysis	* from API 20E
[Ref.: #29987]	cellobiose ChEBI	+	carbon source
[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.: #29987]	lactose ChEBI	+	carbon source
[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.: #7361]	17666	+	-	-	-	+	-	-	-	+	+	+	+	+	+	-	+	+	+	+	+	-	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.: #7361]	Sample type/isolated from	Zea mays
[Ref.: #7361]	Host species	Zea mays
[Ref.: #7361]	Country	USA
[Ref.: #7361]	Country ISO 3 Code	USA
[Ref.: #7361]	Continent	North America
* marker position based on {}

Isolation sources categories

#Host

#Plants

#Herbaceous plants (Grass,Crops)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AF520711 (>99% sequence identity) for Dickeya from Microbeatlas

Aquatic Samples	1
Soil Samples	2
Animal Samples	29
Plant Samples	12
Total Samples	44

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

[Ref.: #7361]	Pathogenicity (plant)	yes
[Ref.: #7361]	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.: #7361]	Dickeya zeae strain CFBP 2052 16S ribosomal RNA gene, partial sequence	AF520711	1422	GenBank ENA	204042 tax ID
[Ref.: #20218]	Dickeya zeae strain NCPPB 2538 16S-23S ribosomal RNA intergenic spacer, partial sequence	KC844739	317	GenBank ENA	204042 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Dickeya zeae NCPPB 2538	GCA_000406165	chromosome	GenBank ENA	1223573 tax ID	*
[Ref.: #66792]	Dickeya zeae NCPPB 2538	1223573.12	wgs	PATRIC	1223573 tax ID	*
[Ref.: #66792]	Dickeya zeae NCPPB 2538	2558860215	draft	JGI IMG/M	1223573 tax ID	*

[Ref.: #29987]

GC-content

56.4 mol%

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Dickeya zeae NCPPB 2538 NCPPB 2538 NCBI: GCA_000406165.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	99	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Dickeya zeae NCPPB 2538 NCPPB 2538 NCBI: GCA_000406165.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	100	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	96.994	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	71.748	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	88.04	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	99	no
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	79.14	no

Availability in culture collections External links

[Ref.: #7361]

Culture collection no.

DSM 18068, CFBP 2052, ICMP 5704, NCPPB 2538

[Ref.: #73843]

SI-ID 2606

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Diversity 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 F	Int J Syst Evol Microbiol	10.1099/ijsem.0.005059	2021	*
Phylogeny	Dickeya oryzae sp. nov., isolated from the roots of rice.	Wang X, He SW, Guo HB, Han JG, Thin KK, Gao JS, Wang Y, Zhang XX	Int J Syst Evol Microbiol	10.1099/ijsem.0.004265	2020	*
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 Bacterial Stalk Rot of Maize Caused by Dickeya zeae in Mexico.	Martinez-Cisneros BA, Juarez-Lopez G, Valencia-Torres N, Duran-Peralta E, Mezzalama M	Plant Dis	10.1094/PDIS-02-14-0198-PDN	2014	*

References

#7361

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18068

#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 .

#69479

João 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 beta .

#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 )

#73843

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-ID2606.1 )

#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 zeae in external resources:
SILVA
BRENDA
PANGAEA
GBIF

Dickeya zeae NCPPB 2538 NCPPB 2538

Dickeya zeae NCPPB 2538 NCPPB 2538

Change proposal

Change proposal