Name: Agrobacterium skierniewicense Ch11
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13647

Type strain:

Species: Agrobacterium skierniewicense

Strain Designation: Ch11

Culture col. no.: DSM 26438, CFBP 7420, HAMBI 3460, LMG 26191

Strain history: <- LMG <- J. Pulawska; Ch11

NCBI tax ID(s): 984260 (species)

SI-ID 376037

LMG 26191, CFBP 7420

Section

Agrobacterium skierniewicense Ch11 is an aerobe, mesophilic, Gram-negative plant pathogen that was isolated from gall on chrysanthemum.

Gram-negative
rod-shaped
aerobe
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	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Rhizobiaceae*
	Genus	*Agrobacterium*
	Species	**Agrobacterium skierniewicense**
	Full Scientific Name (LPSN)	Agrobacterium skierniewicense (Pu?awska et al. 2012) Mousavi et al. 2016

Synonym

Rhizobium skierniewicense

Information on morphological and physiological properties Morphology

[Ref.: #30286]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.983

[Ref.: #30286]	Cell length	2.5-3.0 µm

[Ref.: #30286]	Cell width	0.5 µm

[Ref.: #30286]	Cell shape	rod-shaped

[Ref.: #18222]

Incubation period

3-7 days

[Ref.: #30286]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #18222]

Culture medium

RHIZOBIUM MEDIUM (DSMZ Medium 98)

[Ref.: #18222]

Culture medium growth

[Ref.: #18222]

Culture medium link

Medium recipe at MediaDive

[Ref.: #18222]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #18222]			growth	30 °C
[Ref.: #30286]			growth	26 °C

[Ref.: #18222]	Temperature range	mesophilic
[Ref.: #30286]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30286]

Oxygen tolerance

aerobe

[Ref.: #30286]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.998

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30286]		NaCl		growth	2	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30286]	3-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #30286]	acetate ChEBI	+	carbon source
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #30286]	arabinose ChEBI	+	carbon source
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #30286]	asparagine ChEBI	+	carbon source
[Ref.: #68369]	D-glucose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #30286]	fructose ChEBI	+	carbon source
[Ref.: #30286]	fucose ChEBI	+	carbon source
[Ref.: #30286]	galactonate ChEBI	+	carbon source
[Ref.: #30286]	galactose ChEBI	+	carbon source
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #30286]	gluconate ChEBI	+	carbon source
[Ref.: #68369]	gluconate ChEBI	+	assimilation	* from API 20NE
[Ref.: #30286]	glucose ChEBI	+	carbon source
[Ref.: #30286]	glutamate ChEBI	+	carbon source
[Ref.: #30286]	glycerol ChEBI	+	carbon source
[Ref.: #30286]	inosine ChEBI	+	carbon source
[Ref.: #68369]	L-arabinose ChEBI	+	assimilation	* from API 20NE
[Ref.: #30286]	L-arabitol ChEBI	+	carbon source
[Ref.: #30286]	lactose ChEBI	+	carbon source
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #30286]	malonate ChEBI	+	carbon source
[Ref.: #68369]	maltose ChEBI	+	assimilation	* from API 20NE
[Ref.: #30286]	mannitol ChEBI	+	carbon source
[Ref.: #30286]	mannose ChEBI	+	carbon source
[Ref.: #30286]	melibiose ChEBI	+	carbon source
[Ref.: #30286]	methyl D-glucoside ChEBI	+	carbon source
[Ref.: #30286]	myo-inositol ChEBI	+	carbon source
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #30286]	ornithine ChEBI	+	carbon source
[Ref.: #30286]	proline ChEBI	+	carbon source
[Ref.: #30286]	quinate ChEBI	+	carbon source
[Ref.: #30286]	rhamnose ChEBI	+	carbon source
[Ref.: #30286]	ribitol ChEBI	+	carbon source
[Ref.: #30286]	succinate ChEBI	+	carbon source
[Ref.: #30286]	sucrose ChEBI	+	carbon source
[Ref.: #30286]	trehalose ChEBI	+	carbon source
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #30286]	uridine ChEBI	+	carbon source
[Ref.: #30286]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #30286]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE
[Ref.: #18222]	catalase	-	1.11.1.6
[Ref.: #30286]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #18222]	cytochrome-c oxidase	+	1.9.3.1
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #68369]	urease	+	3.5.1.5	* from API 20NE

API® 20NE:

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

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #18222]	24944	-	-	-	-	+	+	-	+	+	+	+	+	+	+	+	-	-	+	-	-	+
[Ref.: #18222]	23942	-	-	-	-	+	+	-	+	+	+	+	+	+/-	+	+	-	-	+	-	-	not determinedn.d.

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

[Ref.: #18222]	Sample type/isolated from	gall on chrysanthemum
[Ref.: #18222]	Geographic location (country and/or sea, region)	Skierniewice
[Ref.: #18222]	Country	Poland
[Ref.: #18222]	Country ISO 3 Code	POL
[Ref.: #18222]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Infection	#Plant infections	#Gall

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence HQ823551 (>99% sequence identity) for Agrobacterium from Microbeatlas

Aquatic Samples	101
Soil Samples	173
Animal Samples	477
Plant Samples	797
Total Samples	1548

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

[Ref.: #18222]	Pathogenicity (plant)	yes
[Ref.: #18222]	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.: #18222]	Rhizobium skierniewicense strain Ch11 16S ribosomal RNA gene, partial sequence	HQ823551	1400	ENA	1368417 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rhizobium skierniewicense DSM 26438	GCA_014196515	contig	GenBank	984260 tax ID	*
[Ref.: #66792]	Rhizobium skierniewicense strain DSM 26438	984260.5	wgs	PATRIC	984260 tax ID	*
[Ref.: #66792]	Rhizobium skierniewicense DSM 26438	2829908084	draft	JGI IMG/M	984260 tax ID	*
[Ref.: #66792]	Rhizobium skierniewicense DSM 26438	2738541311	draft	JGI IMG/M	984260 tax ID	*

[Ref.: #18222]

GC-content

57.2 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: Rhizobium skierniewicense strain DSM 26438 PATRIC: 984260.4
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhizobium skierniewicense strain DSM 26438 PATRIC: 984260.5
[Ref.: #69480]	motile	yes	77.509	no
[Ref.: #69480]	flagellated	no	85.168	no
[Ref.: #69480]	gram-positive	no	98.106	no
[Ref.: #69480]	anaerobic	no	97.616	yes
[Ref.: #69480]	halophile	no	87.801	no
[Ref.: #69480]	spore-forming	no	96.161	yes
[Ref.: #69480]	thermophile	no	99.136	yes
[Ref.: #69480]	glucose-util	yes	91.337	no
[Ref.: #69480]	aerobic	yes	90.946	yes
[Ref.: #69480]	glucose-ferment	no	88.326	yes

Availability in culture collections External links

[Ref.: #18222]

Culture collection no.

DSM 26438, CFBP 7420, HAMBI 3460, LMG 26191

[Ref.: #82830]

SI-ID 376037

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rhizobium skierniewicense sp. nov., isolated from tumours on chrysanthemum and cherry plum.	Pulawska J, Willems A, Sobiczewski P	Int J Syst Evol Microbiol	10.1099/ijs.0.032532-0	2011	*

References

#18222

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26438

#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 )

#30286

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 #26627 (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) .

#68369

Automatically annotated from API 20NE .

#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 )

#82830

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-ID376037.1 )

#26627

IJSEM 895 2012 ( DOI 10.1099/ijs.0.032532-0 , PubMed 21642489 )

* These data were automatically processed and therefore are not curated

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Rhizobium skierniewicense strain DSM 26438

Rhizobium skierniewicense strain DSM 26438

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