Name: Sphingobium naphthae K-3-6
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140984

Type strain:

Species: Sphingobium naphthae

Strain Designation: K-3-6

Culture col. no.: KEMB 9005-449, KACC 19001, JCM 31713

Strain history: J. Kim; Kyonggi Univ., South Korea; K-3-6.

NCBI tax ID(s): 1886786 (species)

Section

Sphingobium naphthae K-3-6 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from oil-contaminatet soil sample of Biratnagar, Morang, Nepal.

colony-forming
Gram-negative
rod-shaped
aerobe
16S sequence
Bacteria

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	*Sphingobium*
	Species	**Sphingobium naphthae**
	Full Scientific Name (LPSN)	Sphingobium naphthae Chaudhary et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #43872]	Gram stain	negative

[Ref.: #43872]	Cell length	1.0-1.2 µm

[Ref.: #43872]	Cell width	0.6-0.8 µm

[Ref.: #43872]	Cell shape	rod-shaped

[Ref.: #43872]	Motility	no

[Ref.: #43872]	Colony color	light yellow
[Ref.: #43872]	Colony shape	circular
[Ref.: #43872]	Cultivation medium used	R2A agar

Information on culture and growth conditions Culture and growth conditions

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Culture medium

Brain-Heart infusion agar

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Culture medium growth

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Culture medium

LB (Luria-Bertani) MEDIUM

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Culture medium growth

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Culture medium

Marine agar (MA)

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Culture medium growth

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Culture medium

Nutrient agar (NA)

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Culture medium growth

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Culture medium

Reasoner's 2A agar (R2A)

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Culture medium growth

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Culture medium

Tryptic soy agar

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Culture medium growth

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Culture medium

Veal infusion agar

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Culture medium growth

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Culture medium

MacConkey agar

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Culture medium growth

		Temperature
[Ref.: #43872]	growth	15-45 °C
[Ref.: #43872]	optimum	20-40 °C
[Ref.: #67770]	growth	30 °C

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Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #43872]			optimum	6.5-7.5
[Ref.: #43872]			growth	5.0-9.5

Information on physiology and metabolism Physiology and metabolism

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Oxygen tolerance

aerobe

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Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43872]		NaCl		optimum	0	%(w/v)
[Ref.: #43872]		NaCl		growth	0-6	%(w/v)

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Observation

quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43872]	2-dehydro-D-gluconate ChEBI	-	carbon source
[Ref.: #43872]	3-hydroxybenzoate ChEBI	-	carbon source
[Ref.: #43872]	3-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #43872]	4-hydroxybenzoate ChEBI	+	carbon source
[Ref.: #43872]	4-nitrophenyl beta-D-galactopyranoside ChEBI	+	builds acid from
[Ref.: #43872]	5-dehydro-D-gluconate ChEBI	-	carbon source
[Ref.: #43872]	adipate ChEBI	-	assimilation
[Ref.: #43872]	carboxymethylcellulose ChEBI	-	hydrolysis
[Ref.: #43872]	casein	+	hydrolysis
[Ref.: #43872]	crab shell chitin	-	hydrolysis
[Ref.: #43872]	D-glucose ChEBI	+	assimilation
[Ref.: #43872]	D-glucose ChEBI	+	carbon source
[Ref.: #43872]	D-mannitol ChEBI	-	assimilation
[Ref.: #43872]	D-mannitol ChEBI	-	carbon source
[Ref.: #43872]	D-mannose ChEBI	+	assimilation
[Ref.: #43872]	D-ribose ChEBI	-	carbon source
[Ref.: #43872]	D-sorbitol ChEBI	-	carbon source
[Ref.: #43872]	decanoate ChEBI	-	assimilation
[Ref.: #43872]	decanoate ChEBI	-	carbon source
[Ref.: #43872]	dna ChEBI	+	hydrolysis
[Ref.: #43872]	esculin ChEBI	+	hydrolysis
[Ref.: #43872]	esculin ferric citrate	+	builds acid from
[Ref.: #43872]	gelatin ChEBI	+	builds acid from
[Ref.: #43872]	gelatin ChEBI	+	hydrolysis
[Ref.: #43872]	glucose ChEBI	-	fermentation
[Ref.: #43872]	glycogen ChEBI	-	carbon source
[Ref.: #43872]	itaconate ChEBI	-	carbon source
[Ref.: #43872]	L-alanine 4-nitroanilide	+	carbon source
[Ref.: #43872]	L-arabinose ChEBI	+	assimilation
[Ref.: #43872]	L-arabinose ChEBI	+	carbon source
[Ref.: #43872]	L-arginine ChEBI	-	fermentation
[Ref.: #43872]	L-fucose ChEBI	-	carbon source
[Ref.: #43872]	L-histidine ChEBI	+	carbon source
[Ref.: #43872]	L-proline ChEBI	+/-	carbon source
[Ref.: #43872]	L-rhamnose ChEBI	+	carbon source
[Ref.: #43872]	L-serine ChEBI	+/-	carbon source
[Ref.: #43872]	L-tryptophan ChEBI	-	fermentation
[Ref.: #43872]	lactate ChEBI	+/-	carbon source
[Ref.: #43872]	malate ChEBI	+	assimilation
[Ref.: #43872]	maltose ChEBI	+	assimilation
[Ref.: #43872]	maltose ChEBI	+	carbon source
[Ref.: #43872]	melibiose ChEBI	-	carbon source
[Ref.: #43872]	myo-inositol ChEBI	-	carbon source
[Ref.: #43872]	N-acetylglucosamine ChEBI	-	carbon source
[Ref.: #43872]	N-acetylglucosamine ChEBI	+	assimilation
[Ref.: #43872]	nitrate ChEBI	+	reduction
[Ref.: #43872]	phenylacetate ChEBI	-	assimilation
[Ref.: #43872]	potassium gluconate ChEBI	+	assimilation
[Ref.: #43872]	propionate ChEBI	-	carbon source
[Ref.: #43872]	salicin ChEBI	-	carbon source
[Ref.: #43872]	sodium acetate ChEBI	+	carbon source
[Ref.: #43872]	sodium citrate ChEBI	-	assimilation
[Ref.: #43872]	sodium citrate ChEBI	-	carbon source
[Ref.: #43872]	sodium malonate ChEBI	-	carbon source
[Ref.: #43872]	starch ChEBI	-	hydrolysis
[Ref.: #43872]	suberic acid ChEBI	-	carbon source
[Ref.: #43872]	sucrose ChEBI	+	carbon source
[Ref.: #43872]	tween 40 ChEBI	+	hydrolysis
[Ref.: #43872]	tween 80 ChEBI	+	hydrolysis
[Ref.: #43872]	tyrosine ChEBI	-	hydrolysis
[Ref.: #43872]	urea ChEBI	-	fermentation
[Ref.: #43872]	valerate ChEBI	-	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #43872]	acetoin ChEBI	no
[Ref.: #43872]	hydrogen sulfide ChEBI	no
[Ref.: #43872]	indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #43872]		acetoin ChEBI	-
[Ref.: #43872]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #43872]	acid phosphatase	+	3.1.3.2
[Ref.: #43872]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43872]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #43872]	alpha-fucosidase	-	3.2.1.51
[Ref.: #43872]	alpha-galactosidase	+/-	3.2.1.22
[Ref.: #43872]	alpha-glucosidase	+	3.2.1.20
[Ref.: #43872]	alpha-mannosidase	-	3.2.1.24
[Ref.: #43872]	beta-galactosidase	+	3.2.1.23
[Ref.: #43872]	beta-glucosidase	+	3.2.1.21
[Ref.: #43872]	beta-glucuronidase	+/-	3.2.1.31
[Ref.: #43872]	catalase	-	1.11.1.6
[Ref.: #43872]	cystine arylamidase	+	3.4.11.3
[Ref.: #43872]	cytochrome oxidase	+	1.9.3.1
[Ref.: #43872]	esterase (C 4)	+
[Ref.: #43872]	esterase Lipase (C 8)	-
[Ref.: #43872]	leucine arylamidase	+	3.4.11.1
[Ref.: #43872]	lipase (C 14)	-
[Ref.: #43872]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #43872]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #43872]	trypsin	+	3.4.21.4
[Ref.: #43872]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #43872]

Fatty acid	Percentage
C18:1ω7c / C18:1ω6c	52.5
C16:1ω7c / C16:1ω6c	11.1
C14:0	8.8
C16:0	7
C14:0 2OH	6.2
C17:1ω6c	1.4
C18:1ω5c	1.2
C18:0	1
C16:1ω5c	0.9
C16:0 2OH	0.3
C18:1 2OH	0.3

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

[Ref.: #43872]	Sample type/isolated from	oil-contaminatet soil sample of Biratnagar, Morang, Nepal
[Ref.: #43872]	Geographic location (country and/or sea, region)	Biratnagar, Morang
[Ref.: #43872]	Country	Nepal
[Ref.: #43872]	Country ISO 3 Code	NPL
[Ref.: #43872]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Oil-contaminated soil of Biratnagar
[Ref.: #67770]	Geographic location (country and/or sea, region)	Morang
[Ref.: #67770]	Country	Nepal
[Ref.: #67770]	Country ISO 3 Code	NPL
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Contamination	#Oil (Fuel)
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

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Global distribution of 16S sequence KX672813 (>99% sequence identity) for Sphingomonadaceae from Microbeatlas

Aquatic Samples	602
Soil Samples	140
Animal Samples	333
Plant Samples	88
Total Samples	1163

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.: #43872]	16S rRNA gene sequence	KX672813		GenBank

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GC-content

65.6 mol%

high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #43872]

Culture collection no.

KEMB 9005-449, KACC 19001, JCM 31713

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingobium naphthae sp. nov., with the ability to degrade aliphatic hydrocarbons, isolated from oil-contaminated soil.	Chaudhary DK, Jeong SW, Kim J	Int J Syst Evol Microbiol	10.1099/ijsem.0.002064	2017	*

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 )

#43872

Dhiraj Kumar Chaudhary, Seung-Woo Jeong, Jaisoo Kim: Sphingobium naphthae sp. nov., with the ability to degrade aliphatic hydrocarbons, isolated from oil-contaminated soil. IJSEM 67: 2986 - 2993 2017 ( DOI 10.1099/ijsem.0.002064 , PubMed 28820116 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 .

* These data were automatically processed and therefore are not curated

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