Name: Sphingomonas naphthae DKC-5-1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133230

Type strain:

Species: Sphingomonas naphthae

Strain Designation: DKC-5-1

Culture col. no.: KEMB 9005-380, KACC 18716, JCM 31294

Strain history: J. Kim; Kyonggi Univ., South Korea; DKC-5-1.

NCBI tax ID(s): 1813468 (species)

Section

Sphingomonas naphthae DKC-5-1 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from oil-contaminated soil.

colony-forming
Gram-negative
motile
rod-shaped
aerobe
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	*Sphingomonas*
	Species	**Sphingomonas naphthae**
	Full Scientific Name (LPSN)	Sphingomonas naphthae Chaudhary and Kim 2016

Information on morphological and physiological properties Morphology

[Ref.: #25006]	Gram stain	negative

[Ref.: #25006]	Cell length	1.26-1.80 µm

[Ref.: #25006]	Cell width	0.31-0.51 µm

[Ref.: #25006]	Cell shape	rod-shaped

[Ref.: #25006]	Motility	yes

[Ref.: #25006]	Flagellum arrangement	polar

[Ref.: #25006]	Colony size	0.5-1.0 mm
[Ref.: #25006]	Colony color	yellow
[Ref.: #25006]	Colony shape	circular
[Ref.: #25006]	Incubation period	5 days
[Ref.: #25006]	Cultivation medium used	R2A agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #25006]

Culture medium

Reasoner's 2A agar (R2A)

[Ref.: #25006]

Culture medium growth

		Temperature
[Ref.: #25006]	growth	4-33 °C
[Ref.: #25006]	optimum	25-28 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #25006]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #25006]			optimum	6.5-8.0
[Ref.: #25006]			growth	6.0-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #25006]

Oxygen tolerance

aerobe

[Ref.: #25006]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #25006]		NaCl		optimum	0	%
[Ref.: #25006]		NaCl		maximum	1.5	%(w/v)

[Ref.: #67770]

Observation

quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25006]	2-dehydro-D-gluconate ChEBI	-	carbon source
[Ref.: #25006]	3-hydroxybenzoate ChEBI	-	carbon source
[Ref.: #25006]	3-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #25006]	4-hydroxybenzoate ChEBI	+	carbon source
[Ref.: #25006]	4-nitrophenyl beta-D-galactopyranoside ChEBI	-	fermentation
[Ref.: #25006]	5-dehydro-D-gluconate ChEBI	-	carbon source
[Ref.: #25006]	adipate ChEBI	-	assimilation
[Ref.: #25006]	carboxymethylcellulose ChEBI	-	hydrolysis
[Ref.: #25006]	casein	-	hydrolysis
[Ref.: #25006]	chitin ChEBI	-	hydrolysis
[Ref.: #25006]	D-glucose ChEBI	+	assimilation
[Ref.: #25006]	D-glucose ChEBI	+	carbon source
[Ref.: #25006]	D-mannitol ChEBI	-	assimilation
[Ref.: #25006]	D-mannitol ChEBI	-	carbon source
[Ref.: #25006]	D-mannose ChEBI	-	assimilation
[Ref.: #25006]	D-ribose ChEBI	-	carbon source
[Ref.: #25006]	D-sorbitol ChEBI	-	carbon source
[Ref.: #25006]	decanoate ChEBI	-	assimilation
[Ref.: #25006]	decanoate ChEBI	-	carbon source
[Ref.: #25006]	esculin ferric citrate	+	hydrolysis
[Ref.: #25006]	gelatin ChEBI	-	hydrolysis
[Ref.: #25006]	gelatin ChEBI	-	fermentation
[Ref.: #25006]	glucose ChEBI	-	fermentation
[Ref.: #25006]	glycogen ChEBI	-	carbon source
[Ref.: #25006]	hypoxanthine ChEBI	-	hydrolysis
[Ref.: #25006]	itaconate ChEBI	-	carbon source
[Ref.: #25006]	L-alanine ChEBI	-	carbon source
[Ref.: #25006]	L-arabinose ChEBI	+	assimilation
[Ref.: #25006]	L-arabinose ChEBI	+	carbon source
[Ref.: #25006]	L-arginine ChEBI	-	fermentation
[Ref.: #25006]	L-fucose ChEBI	-	carbon source
[Ref.: #25006]	L-histidine ChEBI	-	carbon source
[Ref.: #25006]	L-proline ChEBI	-	carbon source
[Ref.: #25006]	L-rhamnose ChEBI	-	carbon source
[Ref.: #25006]	L-serine ChEBI	-	carbon source
[Ref.: #25006]	L-tryptophan ChEBI	-	fermentation
[Ref.: #25006]	lactate ChEBI	-	carbon source
[Ref.: #25006]	malate ChEBI	-	assimilation
[Ref.: #25006]	maltose ChEBI	+	assimilation
[Ref.: #25006]	maltose ChEBI	+	carbon source
[Ref.: #25006]	melibiose ChEBI	-	carbon source
[Ref.: #25006]	myo-inositol ChEBI	-	carbon source
[Ref.: #25006]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #25006]	N-acetylglucosamine ChEBI	-	carbon source
[Ref.: #25006]	nitrate ChEBI	-	reduction
[Ref.: #25006]	phenylacetate ChEBI	-	assimilation
[Ref.: #25006]	potassium gluconate ChEBI	-	assimilation
[Ref.: #25006]	propionate ChEBI	-	carbon source
[Ref.: #25006]	salicin ChEBI	-	carbon source
[Ref.: #25006]	sodium acetate ChEBI	-	carbon source
[Ref.: #25006]	sodium citrate ChEBI	+	assimilation
[Ref.: #25006]	sodium citrate ChEBI	+	carbon source
[Ref.: #25006]	sodium malonate ChEBI	-	carbon source
[Ref.: #25006]	starch ChEBI	-	hydrolysis
[Ref.: #25006]	suberic acid ChEBI	-	carbon source
[Ref.: #25006]	sucrose ChEBI	-	carbon source
[Ref.: #25006]	tryptophan ChEBI	-	energy source
[Ref.: #25006]	tween 80 ChEBI	-	hydrolysis
[Ref.: #25006]	urea ChEBI	-	fermentation
[Ref.: #25006]	valerate ChEBI	-	carbon source
[Ref.: #25006]	xanthine ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #25006]	ampicillin ChEBI				yes	30	µg (disc)
[Ref.: #25006]	chloramphenicol ChEBI				yes	100	µg (disc)
[Ref.: #25006]	cycloheximide ChEBI				yes	30	µg (disc)
[Ref.: #25006]	gentamicin ChEBI	yes	10	µg (disc)
[Ref.: #25006]	kanamycin ChEBI				yes	30	µg (disc)
[Ref.: #25006]	nalidixic acid ChEBI	yes	30	µg (disc)
[Ref.: #25006]	neomycin ChEBI	yes	30	µg (disc)
[Ref.: #25006]	novobiocin ChEBI	yes	30	µg (disc)
[Ref.: #25006]	penicillin ChEBI				yes	10	µg (disc)
[Ref.: #25006]	rifampicin ChEBI	yes	10	µg (disc)
[Ref.: #25006]	streptomycin ChEBI	yes	10	µg (disc)
[Ref.: #25006]	sulfamethoxazole ChEBI				yes	30	µg (disc)
[Ref.: #25006]	tetracycline ChEBI	yes	30	µg (disc)
[Ref.: #25006]	trimethoprim ChEBI				yes	30	µg (disc)
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #25006]		acetoin ChEBI	no
[Ref.: #25006]		indole ChEBI	no

	Metabolite	Voges-Proskauer-test	Methylred-test	Indole test
[Ref.: #25006]	acetoin ChEBI	-
[Ref.: #25006]	glucose ChEBI		-
[Ref.: #25006]	indole ChEBI			-

	Enzyme	Enzyme activity	EC number
[Ref.: #25006]	acid phosphatase	+	3.1.3.2
[Ref.: #25006]	alkaline phosphatase	+	3.1.3.1
[Ref.: #25006]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #25006]	alpha-fucosidase	+	3.2.1.51
[Ref.: #25006]	alpha-glucosidase	+	3.2.1.20
[Ref.: #25006]	alpha-mannosidase	+	3.2.1.24
[Ref.: #25006]	beta-galactosidase	+	3.2.1.23
[Ref.: #25006]	beta-glucosidase	+	3.2.1.21
[Ref.: #25006]	beta-glucuronidase	+	3.2.1.31
[Ref.: #25006]	catalase	-	1.11.1.6
[Ref.: #25006]	cystine arylamidase	+	3.4.11.3
[Ref.: #25006]	cytochrome oxidase	+	1.9.3.1
[Ref.: #25006]	esterase (C 4)	+
[Ref.: #25006]	esterase lipase (C 8)	+
[Ref.: #25006]	leucine arylamidase	+	3.4.11.1
[Ref.: #25006]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #25006]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #25006]	trypsin	+	3.4.21.4
[Ref.: #25006]	tryptophan deaminase	-	4.1.99.1
[Ref.: #25006]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #25006]	Sample type/isolated from	oil-contaminated soil
[Ref.: #25006]	Geographic location (country and/or sea, region)	Gunsan, North Jeolla Province
[Ref.: #25006]	Country	Republic of Korea
[Ref.: #25006]	Country ISO 3 Code	KOR
[Ref.: #25006]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Oil-contaminated soil of Gunsan
[Ref.: #67770]	Geographic location (country and/or sea, region)	North Jeolla Province
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

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.: #25006]	Sphingomonas naphthae strain DKC-5-1 16S ribosomal RNA gene, partial sequence	KU312690	1432	GenBank	1813468 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sphingomonas naphthae KACC 18716	GCA_028607085	complete	GenBank	1813468 tax ID	*

[Ref.: #25006]

GC-content

65.9 mol%

high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sphingomonas naphthae KACC 18716 NCBI: GCA_028607085.1
[Ref.: #69480]	flagellated	no	88.488	no
[Ref.: #69480]	gram-positive	no	97.03	yes
[Ref.: #69480]	anaerobic	no	98.702	no
[Ref.: #69480]	aerobic	yes	95.867	yes
[Ref.: #69480]	halophile	no	93.996	yes
[Ref.: #69480]	spore-forming	no	94.748	yes
[Ref.: #69480]	glucose-ferment	no	92.172	yes
[Ref.: #69480]	thermophile	no	97.057	yes
[Ref.: #69480]	glucose-util	yes	89.718	yes
[Ref.: #69480]	motile	yes	72.312	yes

Availability in culture collections External links

[Ref.: #25006]

Culture collection no.

KEMB 9005-380, KACC 18716, JCM 31294

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingomonas naphthae sp. nov., isolated from oil-contaminated soil.	Chaudhary DK, Kim J	Int J Syst Evol Microbiol	10.1099/ijsem.0.001400	2016	*
Phylogeny	Sphingomonas crocodyli sp. nov., isolated from a crocodile pond.	Sheu SY, Xie YR, Kwon SW, Sheu C, Chen WM	Int J Syst Evol Microbiol	10.1099/ijsem.0.003455	2019	*

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 )

#25006

D. K. K. Chaudhary, J.: Sphingomonas naphthae sp. nov., isolated from oil-contaminated soil. IJSEM 66: 4621 - 4627 2016 ( DOI 10.1099/ijsem.0.001400 , PubMed 27506439 )

#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) .

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

#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) .

* These data were automatically processed and therefore are not curated

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Sphingomonas naphthae KACC 18716

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