Sphingopyxis lindanitolerans (DSM 106274, PCM 2932, WS5A3p)

Name: Sphingopyxis lindanitolerans (DSM 106274, PCM 2932, WS5A3p)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 159655

Type strain

Strain Designation WS5A3p

Culture col. no. DSM 106274 PCM 2932 WS5A3p

NCBI tax ID(s) 2054227

Special Collections DSMZ Literature strains

Links

Sphingopyxis lindanitolerans WS5A3p is an aerobe, mesophilic, Gram-negative prokaryote that forms circular colonies and was isolated from soil from pesticide burial ground , dichlorodiphenyltrichloroethane and methoxychlor).

Gram-negative rod-shaped colony-forming aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 396856

PCM:2932,ATCC TSD-188,DSM 106274

@ref 20215

Last LPSN update 2025-12-16 10:08:18

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingopyxis

Species Sphingopyxis lindanitolerans

Full scientific name Sphingopyxis lindanitolerans Kaminski et al. 2018

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
66789	negative	1.2 µm	0.46 µm	rod-shaped

Colony morphology

@ref	Colony color	Colony shape	Medium used
66789	whitish-brown	circular	LB (Luria-Bertani) MEDIUM

Multimedia

@ref:	66505
multimedia content:	DSM_106274.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_106274.jpg
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
66505	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
66789	LB (Luria-Bertani) MEDIUM
66505	TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)	Medium recipe at MediaDive	Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
66505	positive	growth	25	mesophilic
66789	positive	growth	12-37
66789	positive	optimum	23-30

Culture pH

@ref	Ability	Type	PH	PH range
66789	positive	growth	8-9	alkaliphile

Physiology and metabolism

Oxygen tolerance

66789

Oxygen toleranceaerobe

Halophily

@ref	Salt	Growth	Tested relation	Concentration
66789	NaCl	positive	growth	0-2 %(w/v)
66789	NaCl	positive	optimum	0 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
66789	73918 ChEBI	3-O-methyl-D-glucose	-	carbon source
66789	18101 ChEBI	4-hydroxyphenylacetic acid	-	carbon source
66789	16411 ChEBI	acetic acid	+	carbon source
66789	13705 ChEBI	acetoacetate	+	carbon source
66789	17128 ChEBI	adipate	+	assimilation
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
66789	17925 ChEBI	alpha-D-glucose	+	carbon source
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
66789	73706 ChEBI	bromosuccinate	-	carbon source
66789	17057 ChEBI	cellobiose	+	carbon source
66789	53258 ChEBI	citric acid	+	carbon source
66789	18333 ChEBI	D-arabitol	-	carbon source
66789	29990 ChEBI	D-aspartate	-	carbon source
66789	15824 ChEBI	D-fructose	+	carbon source
66789	78697 ChEBI	D-fructose 6-phosphate	+	carbon source
66789	28847 ChEBI	D-fucose	+	carbon source
66789	15895 ChEBI	D-galactonic acid lactone	-	carbon source
66789	12936 ChEBI	D-galactose	+	carbon source
66789	18024 ChEBI	D-galacturonic acid	-	carbon source
66789	8391 ChEBI	D-gluconate	-	carbon source
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
66789	14314 ChEBI	D-glucose 6-phosphate	+	carbon source
66789	15748 ChEBI	D-glucuronate	+	carbon source
66789	16899 ChEBI	D-mannitol	-	carbon source
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
66789	16024 ChEBI	D-mannose	-	carbon source
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
66789	16523 ChEBI	D-serine	-	carbon source
66789	17924 ChEBI	D-sorbitol	-	carbon source
66789	27689 ChEBI	decanoate	-	assimilation
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
66789	23652 ChEBI	dextrin	+	carbon source
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
66789	15740 ChEBI	formate	-	carbon source
66789	16865 ChEBI	gamma-aminobutyric acid	-	carbon source
66789	5291 ChEBI	gelatin	+	carbon source
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
66789	28066 ChEBI	gentiobiose	+	carbon source
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
66789	17234 ChEBI	glucose	+	assimilation
66789	17234 ChEBI	glucose	-	fermentation
66789	32323 ChEBI	glucuronamide	+	carbon source
66789	17754 ChEBI	glycerol	-	carbon source
66789	70744 ChEBI	glycine-proline	+	carbon source
66789	17596 ChEBI	inosine	-	carbon source
66789	16977 ChEBI	L-alanine	+	carbon source
66789	30849 ChEBI	L-arabinose	-	assimilation
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
66789	16467 ChEBI	L-arginine	-	carbon source
66789	29991 ChEBI	L-aspartate	+	carbon source
66789	18287 ChEBI	L-fucose	+	carbon source
66789	29985 ChEBI	L-glutamate	+	carbon source
66789	15971 ChEBI	L-histidine	+	carbon source
66789	18183 ChEBI	L-pyroglutamic acid	-	carbon source
66789	62345 ChEBI	L-rhamnose	-	carbon source
66789	17115 ChEBI	L-serine	+	carbon source
66789	24996 ChEBI	lactate	+	carbon source
66789	17716 ChEBI	lactose	-	carbon source
66789	25115 ChEBI	malate	+	assimilation
66789	25115 ChEBI	malate	-	carbon source
66789	25115 ChEBI	malate	+	carbon source
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
66789	17306 ChEBI	maltose	-	assimilation
66789	17306 ChEBI	maltose	+	carbon source
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
66789	29864 ChEBI	mannitol	-	assimilation
66789	37684 ChEBI	mannose	-	assimilation
66789	28053 ChEBI	melibiose	+	carbon source
66789	37657 ChEBI	methyl D-glucoside	-	carbon source
66789	51850 ChEBI	methyl pyruvate	-	carbon source
66789	17268 ChEBI	myo-inositol	+	carbon source
66789	63154 ChEBI	N-acetyl-beta-D-mannosamine	-	carbon source
66789	28800 ChEBI	N-acetylgalactosamine	-	carbon source
66789	59640 ChEBI	N-acetylglucosamine	-	assimilation
66789	59640 ChEBI	N-acetylglucosamine	-	carbon source
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
66789	35418 ChEBI	n-acetylneuraminate	-	carbon source
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
66789	17309 ChEBI	pectin	-	carbon source
66789	18401 ChEBI	phenylacetate	-	assimilation
66789	32032 ChEBI	potassium gluconate	-	assimilation
66789	17272 ChEBI	propionate	-	carbon source
66789	26490 ChEBI	quinate	-	carbon source
66789	16634 ChEBI	raffinose	-	carbon source
66789	17814 ChEBI	salicin	+	carbon source
66789	53258 ChEBI	sodium citrate	-	assimilation
66789	17164 ChEBI	stachyose	-	carbon source
66789	17992 ChEBI	sucrose	-	carbon source
66789	27082 ChEBI	trehalose	+	carbon source
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
66789	32528 ChEBI	turanose	-	carbon source
66789	53423 ChEBI	tween 40	+	carbon source
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
66789	35581 ChEBI	indole
68369	35581 ChEBI	indole		from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
66789	arginine dihydrolase	-	3.5.3.6
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
66789	beta-galactosidase	-	3.2.1.23
66789	beta-glucosidase	+	3.2.1.21
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
66789	cytochrome oxidase	+	1.9.3.1
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68369	gelatinase	-		from API 20NE
66789	nitrate reductase	-	1.7.99.4
66789	protease	-
66789	urease	-	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE

Fatty acid profile

Metadata FA analysis

@ref

66789

Fatty acid	Percentage
C18:1 w7c and/or C18:1 w6c	44.7
C16:1 w7c and/or C16:1 w6c	29.8
C16:0	10.2
C14:0 2OH	4.4
C17:1 w6c	3.3
C16:0 2OH	2.7
C16:1 w5c	1.2

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
66505	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	+	-	-	+
66505	-	-	-	-	-	+	-	-	+/-	-	-	-	-	-	-	-	-	+	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Contamination	#Pesticide
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture	Enrichment culture composition	Enrichment culture duration	Enrichment culture temperature
66505	soil from pesticide burial ground (organochlorine pesticides, including gamma-hexalchlorocyclohexane (lindane), dichlorodiphenyltrichloroethane (DDT) and methoxychlor)	Wislawie, West Pomeranian Voivoideship (53° 51' 0.7'' N, 15° 04' 32.5'' E)	Poland	POL	Europe	53.8519	15.0675 53.8519/15.0675
66789	soil at a pesticide disposal site during the process of its removal	Wislawie village	Poland	POL	Europe	53.8502	15.0757 53.8502/15.0757	minimal salt medium	MSM: NH4NO3 -1.375, MgSO4.7H2O - 0.44, KCl - 1.1, NaCl - 1.1, CaCl2.2H2O - 0.055 g/L) supplemented with 1 ml of trace elements (FeSO4.7H2O - 0.55, ZnSO4.7H2O - 1.65, MnSO4. H2O - 1.65, CoCl2.6H2O - 0.166, CuSO4.5H2O - 0.166 mg/L). g-HCH was added from stock (30mM dissolved in acetone) to a final concentration of 5 mg/L.	2 weeks	23

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM299388v1 assembly for Sphingopyxis lindanitolerans WS5A3p	chromosome	GCA_002993885	2054227.3	2788500577	2054227	83.35

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
66505	Sphingopyxis lindanitolerans strain WS5A3p 16S ribosomal RNA gene, partial sequence	MF927681	1450		2054227

GC content

@ref	GC-content (mol%)	Method
66505	65.1
66789	65.1	genome sequence analysis

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Genomic Analysis of gamma-Hexachlorocyclohexane-Degrading Sphingopyxis lindanitolerans WS5A3p Strain in the Context of the Pangenome of Sphingopyxis.	Kaminski MA, Sobczak A, Dziembowski A, Lipinski L	Genes (Basel)	10.3390/genes10090688	2019
Phylogeny	Sphingopyxis lindanitolerans sp. nov. strain WS5A3p(T) enriched from a pesticide disposal site.	Kaminski MA, Sobczak A, Spolnik G, Danikiewicz W, Dziembowski A, Lipinski L	Int J Syst Evol Microbiol	10.1099/ijsem.0.003094	2018

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 )
#66505	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 106274
#66789	Michal A. Kaminski, Adam Sobczak, Grzegorz Spolnik, Witold Danikiewicz, Andrzej Dziembowski and Leszek Lipinski: Sphingopyxis lindanitolerans sp. nov. strain WS5A3pT enriched from a pesticide disposal site. IJSEM 68: 3935 - 3941 2018 ( DOI 10.1099/ijsem.0.003094 , PubMed 30394866 )
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Sphingopyxis lindanitolerans (DSM 106274, PCM 2932, WS5A3p)

Name and taxonomic classification