Name: Sphingopyxis fribergensis Kp5.2
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 131425

Type strain:

Species: Sphingopyxis fribergensis

Strain Designation: Kp5.2

Culture col. no.: DSM 28731, LMG 28478

Strain history: <- M. Oelschlaegel, TU Freiberg, Inst. of Bioscience, Germany; Kp5.2

NCBI tax ID(s): 1515612 (species)

SI-ID 396395

LMG 28478, DSM 28731

Section

Sphingopyxis fribergensis Kp5.2 is a mesophilic, Gram-negative bacterium that was isolated from soil of meadow within the city.

Gram-negative
mesophilic
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	*Sphingomonadales*
	Family	*Sphingomonadaceae*
	Genus	*Sphingopyxis*
	Species	**Sphingopyxis fribergensis**
	Full Scientific Name (LPSN)	Sphingopyxis fribergensis Oelschlägel et al. 2015

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.868

Information on culture and growth conditions Culture and growth conditions

[Ref.: #22652]

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

[Ref.: #22652]

Culture medium composition

expand / minimize

[Ref.: #22652]

Culture medium

MINERAL MEDIUM WITH VITAMINS (DSMZ Medium 462)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

[Ref.: #22652]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #22652]			growth	28 °C

[Ref.: #22652]

Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.947

[Ref.: #22652]

Name of produced compound

styrene oxide isomerase

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[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.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	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.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE
[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.: #22652]	24481	-	-	-	-	-	+	-	+	+	-	+	-	-	+	-	-	-	+	-	+	+
[Ref.: #22652]	23287	-	-	-	-	-	+	-	-	+	-	+	-	-	+	-	-	-	+	-	+	-

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

[Ref.: #22652]	Sample type/isolated from	soil of meadow within the city
[Ref.: #22652]	Geographic location (country and/or sea, region)	Saxony, Freiberg
[Ref.: #22652]	Country	Germany
[Ref.: #22652]	Country ISO 3 Code	DEU
[Ref.: #22652]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered	#Agriculture	#Meadow
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KF540261 (>99% sequence identity) for Sphingopyxis from Microbeatlas

Aquatic Samples	132
Soil Samples	153
Animal Samples	47
Plant Samples	218
Total Samples	550

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

[Ref.: #22652]

Biosafety level

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.: #22652]	Sphingopyxis fribergensis strain Kp5.2 16S ribosomal RNA gene, partial sequence	KF540261	1374	ENA	1515612 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sphingopyxis fribergensis Kp5.2	GCA_000803645	complete	GenBank	1515612 tax ID	*
[Ref.: #66792]	Sphingopyxis fribergensis strain Kp5.2	1515612.6	plasmid	PATRIC	1515612 tax ID	*
[Ref.: #66792]	Sphingopyxis fribergensis Kp5.2	2636415409	complete	JGI IMG/M	1515612 tax ID	*

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GC-content

63.7 mol%

sequence analysis

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: Sphingopyxis fribergensis Kp5.2 NCBI: GCA_000803645.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sphingopyxis fribergensis Kp5.2 NCBI: GCA_000803645.1
[Ref.: #69480]	motile	yes	70.209	no
[Ref.: #69480]	flagellated	no	84.933	no
[Ref.: #69480]	gram-positive	no	96.431	no
[Ref.: #69480]	anaerobic	no	99.501	no
[Ref.: #69480]	aerobic	yes	94.397	no
[Ref.: #69480]	halophile	no	94.348	no
[Ref.: #69480]	spore-forming	no	93.442	no
[Ref.: #69480]	glucose-util	yes	89.537	yes
[Ref.: #69480]	thermophile	no	98.15	yes
[Ref.: #69480]	glucose-ferment	no	93.031	no

Availability in culture collections External links

[Ref.: #22652]

Culture collection no.

DSM 28731, LMG 28478

[Ref.: #89853]

SI-ID 396395

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingopyxis solisilvae sp. nov., isolated from forest soil.	Chaudhary DK, Dahal RH, Kim J	Int J Syst Evol Microbiol	10.1099/ijsem.0.001869	2017	*
Metabolism	Heterologous production of different styrene oxide isomerases for the highly efficient synthesis of phenylacetaldehyde.	Oelschlagel M, Richter L, Stuhr A, Hofmann S, Schlomann M	J Biotechnol	10.1016/j.jbiotec.2017.04.038	2017	*
Phylogeny	Sphingopyxis fribergensis sp. nov., a soil bacterium with the ability to degrade styrene and phenylacetic acid.	Oelschlagel M, Ruckert C, Kalinowski J, Schmidt G, Schlomann M, Tischler D	Int J Syst Evol Microbiol	10.1099/ijs.0.000371	2015	*
Enzymology	Biochemical Characterization of Phenylacetaldehyde Dehydrogenases from Styrene-degrading Soil Bacteria.	Zimmerling J, Oelschlagel M, Grossmann C, Voitel M, Schlomann M, Tischler D	Appl Biochem Biotechnol	10.1007/s12010-020-03421-8	2020	*

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 )

#22652

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28731

#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 )

#89853

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-ID396395.1 )

* These data were automatically processed and therefore are not curated

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