Name: Sphingomonas jinjuensis YC6723
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 14267

Type strain:

Species: Sphingomonas jinjuensis

Strain Designation: YC6723

Culture col. no.: DSM 21457, CIP 110411, KCTC 22477

Strain history: CIP <- 2012, DSMZ <- Y.R. Chung, GSNU Gyeongsang Nat. Univ., Jinju, Korea: strain YC6723 <- Z. Aslam

NCBI tax ID(s): 535907 (species)

SI-ID 378358

DSM 21457, KCTC 22477, CIP 110411

Section

Sphingomonas jinjuensis YC6723 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from rhizosphere of a rice field under conventional practice.

Gram-negative
aerobe
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	*Sphingomonas*
	Species	**Sphingomonas jinjuensis**
	Full Scientific Name (LPSN)	Sphingomonas jinjuensis Chung et al. 2011

Information on morphological and physiological properties Morphology

[Ref.: #67771]	Gram stain	negative
[Ref.: #120353]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.951

[Ref.: #120353]	Cell shape	rod-shaped

[Ref.: #120353]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15717]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #15717]

Culture medium growth

[Ref.: #15717]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15717]

Culture medium composition

expand / minimize

[Ref.: #33358]

Culture medium

MEDIUM 328- for nutrient agar

[Ref.: #33358]

Culture medium growth

[Ref.: #33358]

Culture medium composition

expand / minimize

[Ref.: #120353]

Culture medium

CIP Medium 328

[Ref.: #120353]

Culture medium growth

[Ref.: #120353]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #15717]	growth	30 °C
[Ref.: #33358]	growth	30 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #15717]	Temperature range	mesophilic
[Ref.: #33358]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67771]

Oxygen tolerance

aerobe

[Ref.: #69480]

Ability of spore formation

no Confidence in %99.998

[Ref.: #67771]

Observation

quinones: Q-10

	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]	cytochrome oxidase	+	1.9.3.1	* 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.: #15717]	23251	-	-	-	-	-	+	-	+	+	+	-	-	+	+	-	-	-	-	-	-	+

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

[Ref.: #15717]	Sample type/isolated from	rhizosphere of a rice field under conventional practice
[Ref.: #15717]	Geographic location (country and/or sea, region)	Jinju
[Ref.: #15717]	Country	Republic of Korea
[Ref.: #15717]	Country ISO 3 Code	KOR
[Ref.: #15717]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From rice field
[Ref.: #67771]	Geographic location (country and/or sea, region)	Jinju
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia

[Ref.: #120353]	Sample type/isolated from	Environment, Rhizosphere of a rice field under conventional practice
[Ref.: #120353]	Geographic location (country and/or sea, region)	Jinju
[Ref.: #120353]	Country	Republic of Korea
[Ref.: #120353]	Country ISO 3 Code	KOR
[Ref.: #120353]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Agriculture	#Field
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Rhizosphere

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EU707561 (>99% sequence identity) for Sphingomonas jinjuensis subclade from Microbeatlas

Aquatic Samples	7
Soil Samples
Animal Samples	19
Plant Samples	21
Total Samples	47

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

[Ref.: #15717]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #120353]	Biosafety level	1	Risk group (French classification)

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.: #15717]	Sphingomonas jinjuensis strain YC6723 16S ribosomal RNA gene, partial sequence	EU707561	1375	ENA	535907 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sphingomonas jinjuensis YC6723	GCA_014197105	scaffold	GenBank	535907 tax ID	*
[Ref.: #66792]	Sphingomonas jinjuensis DSM 21457	2830075706	draft	JGI IMG/M	535907 tax ID	*

[Ref.: #15717]

GC-content

61.0 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 GenomeNet Sporulation v. 1 based on: Sphingomonas jinjuensis YC6723 NCBI: GCA_014197105.1
[Ref.: #69481]	spore-forming	no	84	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sphingomonas jinjuensis YC6723 NCBI: GCA_014197105.1
[Ref.: #69480]	flagellated	no	90.453	no
[Ref.: #69480]	gram-positive	no	96.687	yes
[Ref.: #69480]	anaerobic	no	99.499	no
[Ref.: #69480]	aerobic	yes	94.157	yes
[Ref.: #69480]	halophile	no	93.06	no
[Ref.: #69480]	spore-forming	no	95.797	no
[Ref.: #69480]	glucose-util	yes	93.006	no
[Ref.: #69480]	thermophile	no	97.26	no
[Ref.: #69480]	motile	yes	70.54	no
[Ref.: #69480]	glucose-ferment	no	90.643	yes

Availability in culture collections External links

[Ref.: #15717]

Culture collection no.

DSM 21457, CIP 110411, KCTC 22477

[Ref.: #83424]

SI-ID 378358

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingomonas oryziterrae sp. nov. and Sphingomonas jinjuensis sp. nov. isolated from rhizosphere soil of rice (Oryza sativa L.).	Chung EJ, Jo EJ, Yoon HS, Song GC, Jeon CO, Chung YR	Int J Syst Evol Microbiol	10.1099/ijs.0.023846-0	2010	*

References

#15717

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21457

#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 )

#33358 ; Curators of the CIP;

#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) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 )

#83424

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-ID378358.1 )

#120353 Collection of Institut Pasteur ; Curators of the CIP; CIP 110411
* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Sphingomonas jinjuensis in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF