Sphingobium aquiterrae (DSM 106441, NCAIM B. 02634, SKLS-A10)

Name: Sphingobium aquiterrae (DSM 106441, NCAIM B. 02634, SKLS-A10)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 159646

Type strain

Strain Designation SKLS-A10

Culture col. no. DSM 106441 NCAIM B. 02634 SKLS-A10

NCBI tax ID(s) 2038656

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Sphingobium aquiterrae SKLS-A10 is an aerobe, Gram-negative, motile prokaryote that forms circular colonies and was isolated from BTEX contaminated groundwater.

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

Name and taxonomic classification

SI-ID 398935

NCAIM B. 02634,DSM 106441

@ref 20215

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

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingobium

Species Sphingobium aquiterrae

Full scientific name Sphingobium aquiterrae Révész et al. 2018

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Flagellum arrangement
66634	negative	rod-shaped		monotrichous, polar

Colony morphology

@ref	Colony color	Colony shape	Incubation period	Medium used
66634	pale yellow	circular	3-4 days	R2A medium

Multimedia

@ref:	66496
multimedia content:	DSM_106441.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_106441.jpg
caption:	DSM 106441 on medium 830 at 28 °C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
66634	Reasoner's 2A agar (R2A)
66496	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
66496	positive	growth	28	mesophilic
66634	positive	growth	4-40

Culture pH

@ref	Ability	Type	PH	PH range
66634	positive	growth	5-11	alkaliphile

Physiology and metabolism

Oxygen tolerance

66634

Oxygen toleranceaerobe

Halophily

@ref	Salt	Growth	Tested relation	Concentration
66634	NaCl	positive	growth	0 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
66634	17128 ChEBI	adipate	-	assimilation
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
66634	27613 ChEBI	amygdalin	+	builds acid from
66634	18305 ChEBI	arbutin	-	builds acid from
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
66634	16716 ChEBI	benzene	-	degradation
66634	17057 ChEBI	cellobiose	-	builds acid from
66634	17108 ChEBI	D-arabinose	-	builds acid from
66634	18333 ChEBI	D-arabitol	-	builds acid from
66634	15824 ChEBI	D-fructose	-	builds acid from
66634	28847 ChEBI	D-fucose	-	builds acid from
66634	12936 ChEBI	D-galactose	-	builds acid from
66634	17634 ChEBI	D-glucose	+	assimilation
66634	17634 ChEBI	D-glucose	+	builds acid from
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
66634	62318 ChEBI	D-lyxose	+	builds acid from
66634	16899 ChEBI	D-mannitol	-	assimilation
66634	16899 ChEBI	D-mannitol	-	builds acid from
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
66634	16024 ChEBI	D-mannose	-	assimilation
66634	16024 ChEBI	D-mannose	-	builds acid from
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
66634	16988 ChEBI	D-ribose	-	builds acid from
66634	17924 ChEBI	D-sorbitol	-	builds acid from
66634	16443 ChEBI	D-tagatose	-	builds acid from
66634	65327 ChEBI	D-xylose	+	builds acid from
66634	27689 ChEBI	decanoate	-	assimilation
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
66634	17113 ChEBI	erythritol	-	builds acid from
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
66634		esculin ferric citrate	+	builds acid from
66634	16101 ChEBI	ethylbenzene	-	degradation
66634	16813 ChEBI	galactitol	-	builds acid from
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
66634	28066 ChEBI	gentiobiose	+	builds acid from
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
66634	17754 ChEBI	glycerol	-	builds acid from
66634	28087 ChEBI	glycogen	-	builds acid from
66634	15443 ChEBI	inulin	-	builds acid from
66634	30849 ChEBI	L-arabinose	-	assimilation
66634	30849 ChEBI	L-arabinose	+	builds acid from
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
66634	18403 ChEBI	L-arabitol	-	builds acid from
66634	18287 ChEBI	L-fucose	-	builds acid from
66634	62345 ChEBI	L-rhamnose	+	builds acid from
66634	17266 ChEBI	L-sorbose	-	builds acid from
66634	65328 ChEBI	L-xylose	-	builds acid from
66634	17716 ChEBI	lactose	-	builds acid from
66634	28488 ChEBI	m-xylene	+	degradation
66634	25115 ChEBI	malate	-	assimilation
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
66634	17306 ChEBI	maltose	-	assimilation
66634	17306 ChEBI	maltose	-	builds acid from
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
66634	6731 ChEBI	melezitose	-	builds acid from
66634	28053 ChEBI	melibiose	-	builds acid from
66634	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from
66634	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from
66634	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from
66634	17268 ChEBI	myo-inositol	-	builds acid from
66634	59640 ChEBI	N-acetylglucosamine	-	assimilation
66634	59640 ChEBI	N-acetylglucosamine	-	builds acid from
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
66634	27417 ChEBI	p-xylene	+	degradation
66634	18401 ChEBI	phenylacetate	-	assimilation
66634		potassium 2-dehydro-D-gluconate	-	builds acid from
66634		potassium 5-dehydro-D-gluconate	-	builds acid from
66634	32032 ChEBI	potassium gluconate	-	assimilation
66634	32032 ChEBI	potassium gluconate	-	builds acid from
66634	16634 ChEBI	raffinose	-	builds acid from
66634	15963 ChEBI	ribitol	-	builds acid from
66634	17814 ChEBI	salicin	-	builds acid from
66634	53258 ChEBI	sodium citrate	-	assimilation
66634	28017 ChEBI	starch	-	builds acid from
66634	17992 ChEBI	sucrose	-	builds acid from
66634	17578 ChEBI	toluene	+	degradation
66634	27082 ChEBI	trehalose	-	builds acid from
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
66634	32528 ChEBI	turanose	-	builds acid from
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE
66634	17151 ChEBI	xylitol	-	builds acid from

Metabolite production

@ref	Chebi-ID	Metabolite	Production
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
66634	acid phosphatase	+	3.1.3.2
66634	alkaline phosphatase	+	3.1.3.1
66634	alpha-chymotrypsin	+	3.4.21.1
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
66634	beta-glucosidase	+	3.2.1.21
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
66634	cystine arylamidase	+	3.4.11.3
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
66634	esterase (C 4)	+
66634	esterase Lipase (C 8)	+
68369	gelatinase	-		from API 20NE
66634	leucine arylamidase	+	3.4.11.1
66634	naphthol-AS-BI-phosphohydrolase	+
68369	urease	-	3.5.1.5	from API 20NE
66634	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

66634

Fatty acid	Percentage
C18:1 w7c	55.7
C14:0 2OH	12.8
C16:1 w7c/iso C15:0 2OH	9
C17:1 w6c	6.6
C16:0	6.3
C18:1 w7c 11-methyl	1.9
C15:0 2OH	1.5
C16:1 w5c	1.5
C18:1 w5c	0.8

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
66496	-	-	-	-	-	+	-	-	+	-	-	-	-	-	+	-	-	-	-	-	+
66496	-	-	-	-	-	+	-	-	+	-	-	-	-	-	+	-	-	-	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Groundwater
#Engineered	#Contamination	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture	Enrichment culture duration	Enrichment culture temperature	Isolation procedure
66496	BTEX contaminated groundwater	Siklós (45° 51' 25.8'' N, 18° 17' 32.3'' E)	Hungary	HUN	Europe
66634	groundwater sample (ca. 3m depth)	Siklós BTEX contaminated site	Hungary	HUN	Europe	45.8571	18.2923 45.8571/18.2923	R2A	5 days	15	a groundwater sample was serially diluted with 0.9 % (w/v) saline solution, spread onReasoner's 2A agar and incubated at 15°C for 5 days for isolation of bacterial strains

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID	Score
124043	ASM3715413v1 assembly for Sphingobium aquiterrae DSM 106441	scaffold	GCA_037154135	2038656.4	2038656	59.87

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
66634	Sphingobium aquiterrae strain SKLS-A10 16S ribosomal RNA gene, partial sequence	MF980915	1409		2038656

GC content

@ref	GC-content (mol%)	Method
66634	65.9	high performance liquid chromatography (HPLC)

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingobium aquiterrae sp. nov., a toluene, meta- and para-xylene-degrading bacterium isolated from petroleum hydrocarbon-contaminated groundwater.	Revesz F, Toth EM, Kriszt B, Boka K, Benedek T, Sarkany O, Nagy Z, Tancsics A	Int J Syst Evol Microbiol	10.1099/ijsem.0.002898	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 )
#66496	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 106441
#66634	Fruzsina Revesz, Erika M. Toth, Balazs Kriszt, Karoly Boka, Tibor Benedek, Orsolya Sarkany, Zsuzsa Nagy, Andras Tancsics: Sphingobium aquiterrae sp. nov., a toluene, meta- and para-xylene-degrading bacterium isolated from petroleum hydrocarbon-contaminated groundwater. IJSEM 68: 2807 - 2812 2018 ( DOI 10.1099/ijsem.0.002898 , PubMed 29975186 )
#68369	Automatically annotated from API 20NE .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Sphingobium aquiterrae (DSM 106441, NCAIM B. 02634, SKLS-A10)

Name and taxonomic classification