Name: Pectobacterium polare NIBIO1006
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158290

Type strain:

Species: Pectobacterium polare

Strain Designation: NIBIO1006

Culture col. no.: DSM 105255, NCPPB 4611

Strain history: <- M. W. Dees, NIBIO - Norwegian Inst. of Bioeconomy Res., Aas, Norway; NIBIO1006 <- J. Perminow

NCBI tax ID(s): 2042057 (species)

Section

Pectobacterium polare NIBIO1006 is a mesophilic, Gram-negative, motile plant pathogen that was isolated from potato tuber of cv. Polaris with severe symptoms of soft rot.

Gram-negative
motile
mesophilic
plant pathogen
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	*Pectobacterium*
	Species	**Pectobacterium polare**
	Full Scientific Name (LPSN)	Pectobacterium polare corrig. Dees et al. 2017

Synonym

Pectobacterium polaris

Information on morphological and physiological properties Morphology

[Ref.: #65229]	Gram stain	negative

[Ref.: #65229]	Motility	yes

Multimedia content

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Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

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Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

lysogeny broth agar

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Culture medium growth

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Culture medium composition

expand / minimize

		Temperature
[Ref.: #64950]	growth	28 °C
[Ref.: #65229]	growth	37 °C
[Ref.: #65229]	growth	39 °C

[Ref.: #64950]	Temperature range	mesophilic
[Ref.: #65229]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #65229]

Observation

causes soft rot on potato tubers.

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65229]	3-[(4-nitrophenyl)carbamoylamino]propanoic acid	-	builds acid from
[Ref.: #65229]	4-nitrophenyl alpha-D-galactoside ChEBI	+	builds acid from
[Ref.: #65229]	4-nitrophenyl alpha-D-glucopyranoside ChEBI	-	builds acid from
[Ref.: #65229]	4-nitrophenyl beta-D-galactopyranoside ChEBI	+	builds acid from
[Ref.: #65229]	4-nitrophenyl beta-D-glucopyranoside ChEBI	+	builds acid from
[Ref.: #65229]	4-nitrophenyl beta-D-glucuronide ChEBI	-	builds acid from
[Ref.: #65229]	4-nitrophenyl-alpha-D-maltopyranoside	-	builds acid from
[Ref.: #65229]	5-bromo-3-indolyl nonanoate	-	builds acid from
[Ref.: #65229]	amygdalin ChEBI	+	builds acid from
[Ref.: #68368]	amygdalin ChEBI	+	fermentation	* from API 20E
[Ref.: #65229]	arbutin ChEBI	+	builds acid from
[Ref.: #68368]	arginine ChEBI	-	hydrolysis	* from API 20E
[Ref.: #65229]	cellobiose ChEBI	+	builds acid from
[Ref.: #68368]	citrate ChEBI	+	assimilation	* from API 20E
[Ref.: #65229]	D-arabinose ChEBI	-	builds acid from
[Ref.: #65229]	D-arabitol ChEBI	-	builds acid from
[Ref.: #65229]	D-fructose ChEBI	+	builds acid from
[Ref.: #65229]	D-fucose ChEBI	-	builds acid from
[Ref.: #65229]	D-galactose ChEBI	+	builds acid from
[Ref.: #65229]	D-galacturonic acid ChEBI	-	builds acid from
[Ref.: #65229]	D-glucose ChEBI	+	builds acid from
[Ref.: #68368]	D-glucose ChEBI	+	fermentation	* from API 20E
[Ref.: #65229]	D-mannitol ChEBI	+	builds acid from
[Ref.: #68368]	D-mannitol ChEBI	+	fermentation	* from API 20E
[Ref.: #65229]	D-mannose ChEBI	+	builds acid from
[Ref.: #65229]	D-ribose ChEBI	+	builds acid from
[Ref.: #65229]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #65229]	D-tagatose ChEBI	-	builds acid from
[Ref.: #65229]	D-xylose ChEBI	-	builds acid from
[Ref.: #65229]	D-xylose ChEBI	+	builds acid from
[Ref.: #65229]	erythritol ChEBI	-	builds acid from
[Ref.: #65229]	esculin ferric citrate	+	builds acid from
[Ref.: #65229]	galactitol ChEBI	-	builds acid from
[Ref.: #68368]	gelatin ChEBI	+	hydrolysis	* from API 20E
[Ref.: #65229]	gentiobiose ChEBI	+	builds acid from
[Ref.: #65229]	glycerol ChEBI	+	builds acid from
[Ref.: #65229]	glycogen ChEBI	-	builds acid from
[Ref.: #65229]	inulin ChEBI	-	builds acid from
[Ref.: #65229]	L-arabinose ChEBI	+	builds acid from
[Ref.: #68368]	L-arabinose ChEBI	+	fermentation	* from API 20E
[Ref.: #65229]	L-arabitol ChEBI	-	builds acid from
[Ref.: #65229]	L-arginine ChEBI	-	builds acid from
[Ref.: #65229]	L-fucose ChEBI	-	builds acid from
[Ref.: #65229]	L-lysine ChEBI	-	builds acid from
[Ref.: #65229]	L-ornithine ChEBI	-	builds acid from
[Ref.: #65229]	L-rhamnose ChEBI	+	builds acid from
[Ref.: #68368]	L-rhamnose ChEBI	+	fermentation	* from API 20E
[Ref.: #65229]	L-sorbose ChEBI	-	builds acid from
[Ref.: #65229]	L-xylose ChEBI	-	builds acid from
[Ref.: #65229]	lactose ChEBI	+	builds acid from
[Ref.: #68368]	lysine ChEBI	-	degradation	* from API 20E
[Ref.: #65229]	maltose ChEBI	-	builds acid from
[Ref.: #65229]	melezitose ChEBI	-	builds acid from
[Ref.: #65229]	melibiose ChEBI	+	builds acid from
[Ref.: #68368]	melibiose ChEBI	+	fermentation	* from API 20E
[Ref.: #65229]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from
[Ref.: #65229]	methyl alpha-D-mannoside ChEBI	-	builds acid from
[Ref.: #65229]	methyl alpha-D-xylopyranoside	-	builds acid from
[Ref.: #65229]	myo-inositol ChEBI	+	builds acid from
[Ref.: #68368]	myo-inositol ChEBI	+	fermentation	* from API 20E
[Ref.: #65229]	N-acetylglucosamine ChEBI	+	builds acid from
[Ref.: #68368]	nitrate ChEBI	-	reduction	* from API 20E
[Ref.: #68368]	ornithine ChEBI	-	degradation	* from API 20E
[Ref.: #65229]	palatinose ChEBI	-	builds acid from
[Ref.: #65229]	potassium 2-dehydro-D-gluconate	-	builds acid from
[Ref.: #65229]	potassium 5-dehydro-D-gluconate	-	builds acid from
[Ref.: #65229]	potassium gluconate ChEBI	-	builds acid from
[Ref.: #65229]	raffinose ChEBI	+	builds acid from
[Ref.: #65229]	ribitol ChEBI	-	builds acid from
[Ref.: #65229]	salicin ChEBI	+	builds acid from
[Ref.: #65229]	sodium malonate ChEBI	-	builds acid from
[Ref.: #65229]	sodium pyruvate ChEBI	-	builds acid from
[Ref.: #68368]	sorbitol ChEBI	-	fermentation	* from API 20E
[Ref.: #65229]	starch ChEBI	-	builds acid from
[Ref.: #65229]	sucrose ChEBI	+	builds acid from
[Ref.: #68368]	sucrose ChEBI	+	fermentation	* from API 20E
[Ref.: #65229]	trehalose ChEBI	+	builds acid from
[Ref.: #68368]	tryptophan ChEBI	-	energy source	* from API 20E
[Ref.: #65229]	turanose ChEBI	-	builds acid from
[Ref.: #65229]	urea ChEBI	-	builds acid from
[Ref.: #68368]	urea ChEBI	-	hydrolysis	* from API 20E
[Ref.: #65229]	xylitol ChEBI	-	builds acid from
	Only first 10 entries are displayed. Click here to see all.

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

	Physiological tests	Metabolite	Voges-Proskauer-test	Indole test
[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.: #64950]	18066	+	-	-	-	+	-	-	-	-	+	+	+	+	+	-	+	+	+	+	+	-	-	+	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.
[Ref.: #64950]	17735	+	-	-	-	+	-	-	-	-	+	+	+	+	+	-	+	+	+	+	+	-	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.: #64950]	Sample type/isolated from	potato tuber of cv. Polaris with severe symptoms of soft rot
[Ref.: #64950]	Geographic location (country and/or sea, region)	Minne Gård, Minnesund
[Ref.: #64950]	Country	Norway
[Ref.: #64950]	Country ISO 3 Code	NOR
[Ref.: #64950]	Continent	Europe

[Ref.: #65229]	Sample type/isolated from	potato (Solanum tuberosum) tubers showing severe symptoms of soft rot
[Ref.: #65229]	Sampling date	2010
[Ref.: #65229]	Country	Norway
[Ref.: #65229]	Country ISO 3 Code	NOR
[Ref.: #65229]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root (Rhizome)
#Infection	#Plant infections	#Rot (Root,Stem)

What are isolation sources categories?

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

[Ref.: #64950]	Pathogenicity (plant)	yes
[Ref.: #64950]	Biosafety level	1	Risk group (German classification) According to TRBA 466

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

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pectobacterium polaris NIBIO1006	GCA_002307355	complete	GenBank	2042057 tax ID	*
[Ref.: #66792]	Pectobacterium polaris NIBIO1006	2843152325	complete	JGI IMG/M	2042057 tax ID	*

[Ref.: #64950]	GC-content	52 mol%	sequence analysis
[Ref.: #65229]	GC-content	52 mol%	genome sequence analysis

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pectobacterium polaris NIBIO1006 NCBI: GCA_002307355.1
[Ref.: #69480]	flagellated	yes	56.05	no
[Ref.: #69480]	gram-positive	no	98.002	yes
[Ref.: #69480]	anaerobic	no	97.324	no
[Ref.: #69480]	aerobic	yes	58.276	no
[Ref.: #69480]	halophile	no	84.987	no
[Ref.: #69480]	spore-forming	no	93.621	no
[Ref.: #69480]	glucose-util	yes	93.204	no
[Ref.: #69480]	thermophile	no	99.139	yes
[Ref.: #69480]	motile	yes	91.53	yes
[Ref.: #69480]	glucose-ferment	yes	92.076	yes

Availability in culture collections External links

[Ref.: #64950]

Culture collection no.

DSM 105255, NCPPB 4611

Literature:

	Title	Authors	Journal	DOI	Year
Phylogeny	Pectobacterium polaris sp. nov., isolated from potato (Solanum tuberosum).	Dees MW, Lysoe E, Rossmann S, Perminow J, Brurberg MB	Int J Syst Evol Microbiol	10.1099/ijsem.0.002448	2017	*
Phylogeny	Occurrence, Characteristics, and PCR-Based Detection of Pectobacterium polaris Causing Soft Rot of Chinese Cabbage in China.	Chen C, Li X, Bo Z, Du W, Fu L, Tian Y, Cui S, Shi Y, Xie H	Plant Dis	10.1094/PDIS-12-20-2752-RE	2021	*
	First Report of Pectobacterium polaris Causing Soft Rot and Black Leg of Potato in Russia.	Voronina MV, Lukianova AA, Shneider MM, Korzhenkov AA, Toschakov SV, Miroshnikov KA, Vasiliev DM, Ignatov A	Plant Dis	10.1094/PDIS-09-20-1864-PDN	2021	*
	First Report of Pectobacterium polaris Causing Aerial Stem Rot of Potato in China.	Wang J, Han W, Li Z, Cheng J, Pan Y, Zhao D, Zhang D, Li Q, Yang Z, Zhu J	Plant Dis	10.1094/PDIS-06-21-1269-PDN	2021	*

References

#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 )

#64950

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 105255

#65229

Merete Wiken Dees, Erik Lysøe, Simeon Rossmann, Juliana Perminow, May Bente Brurberg: Pectobacterium polaris sp. nov., isolated from potato (Solanum tuberosum). IJSEM 67: 5222 - 5229 2017 ( DOI 10.1099/ijsem.0.002448 , PubMed 29068285 )

#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) .

* These data were automatically processed and therefore are not curated

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Pectobacterium polaris NIBIO1006

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