Name: Novosphingobium capsulatum 28
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 14144

Type strain:

Species: Novosphingobium capsulatum

Strain Designation: 28

Culture col. no.: DSM 30196, ATCC 14666, GIFU 11526, IAM 14271, IFO 12533, JCM 7508, NBRC 12533, NCIB 9890, JCM 7452, BCRC 10676, CCM 2832, CCUG 17697, CCUG 31202, CECT 4388, CIP 82.103, LMG 2830, NCIMB 9890, VKM B-1564, VTT E-91059

Strain history: H. Oyaizu KS 0413 <-- IFO 12533 <-- AJ 2514 <-- ATCC 14666 <-- E. Leifson 28.

NCBI tax ID(s): 1219042 (strain), 13688 (species)

Section

Novosphingobium capsulatum 28 is a mesophilic bacterium that was isolated from distilled water.

mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	07-12-2022 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Sphingomonadales*
	Family	*Erythrobacteraceae*
	Genus	*Novosphingobium*
	Species	**Novosphingobium capsulatum**
	Full Scientific Name (PNU)	Novosphingobium capsulatum (Leifson 1962) Takeuchi et al. 2001

	Synonym	Flavobacterium capsulatum
	Synonym	Sphingomonas capsulata

Information on morphological and physiological properties Morphology

Multimedia content

[Ref.: #9195]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #9195]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #9195]

Culture medium growth

[Ref.: #9195]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #9195]

Culture medium composition

expand / minimize

[Ref.: #38753]

Culture medium

MEDIUM 3 - Columbia agar

[Ref.: #38753]

Culture medium growth

[Ref.: #38753]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #9195]	growth	26 °C
[Ref.: #38753]	growth	30 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #9195]	Temperature range	mesophilic
[Ref.: #38753]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67770]

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
[Ref.: #68369]		indole ChEBI	* 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.: #9195]	20806	+	-	-	-	-	+	-	+	+	+	+	-	+	+	+	-	-	+	-	-	+

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

[Ref.: #9195]	Sample type/isolated from	distilled water

[Ref.: #67770]	Sample type/isolated from	Distilled water
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	-
#Engineered	#Industrial	#Engineered product
#Engineered	#Treatment	#Sterilized (Desinfected)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence D16147 (>99% sequence identity) for Novosphingobium capsulatum from Microbeatlas

Aquatic Samples	532
Soil Samples	144
Animal Samples	416
Plant Samples	71
Total Samples	1163

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

[Ref.: #9195]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #20218]	Novosphingobium capsulatum gene for 16S rRNA, partial sequence	D16147	1443	ENA	13688 tax ID	*
[Ref.: #20218]	Sphingomonas capsulata 16S ribosomal RNA, partial sequence	D38431	156	ENA	13688 tax ID	*
[Ref.: #20218]	Novosphingobium capsulatum gene for 16S ribosomal RNA	D84532	1387	ENA	13688 tax ID	*
[Ref.: #20218]	16S rRNA [Sphingomonas capsulata, LMG 2830T, Genomic, 268 nt]	S56775	268	ENA	13688 tax ID	*
[Ref.: #20218]	Novosphingobium capsulatum gene for 16S rRNA, partial sequence, strain: NBRC 12533	AB680290	1410	ENA	13688 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Novosphingobium capsulatum NBRC 12533	1219042.3	wgs	PATRIC	1219042 tax ID	*
[Ref.: #66792]	Novosphingobium capsulatum NBRC 12533	2681812976	draft	JGI IMG/M	1219042 tax ID	*
[Ref.: #67770]	Novosphingobium capsulatum NBRC 12533 NBRC 12533	GCA_001598375	contig	GenBank	1219042 tax ID
[Ref.: #66792]	uncultured Pelagibacteraceae bacterium AG-325-G04	GCA_902515725	contig	PATRIC	1667051 tax ID	*

[Ref.: #9195]	GC-content	64.3 mol%
[Ref.: #67770]	GC-content	64.3 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #67770]	GC-content	63.1 mol%	high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #9195]

Culture collection no.

DSM 30196, ATCC 14666, GIFU 11526, IAM 14271, IFO 12533, JCM 7508, NBRC 12533, NCIB 9890, JCM 7452, BCRC 10676, CCM 2832, CCUG 17697, CCUG 31202, CECT 4388, CIP 82.103, LMG 2830, NCIMB 9890, VKM B-1564, VTT E-91059

[Ref.: #20218]

Associated Passport(s) in StrainInfo

21674, 21668, 21676, 164411, 21677, 21679, 335325, 97746

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Aromatic-degrading Sphingomonas isolates from the deep subsurface.	Fredrickson JK, Balkwill DL, Drake GR, Romine MF, Ringelberg DB, White DC	Appl Environ Microbiol	10.1128/aem.61.5.1917-1922.1995	1995	*
Enzymology	Prolyl endopeptidase from Sphingomonas capsulata: isolation and characterization of the enzyme and nucleotide sequence of the gene.	Kabashima T, Fujii M, Meng Y, Ito K, Yoshimoto T	Arch Biochem Biophys	10.1006/abbi.1998.0836	1998	*
Metabolism	Production and rheological characterization of biopolymer of Sphingomonas capsulata ATCC 14666 using conventional and industrial media.	Berwanger AL, Domingues NM, Vanzo LT, Di Luccio M, Treichel H, Padilha FF, Scamparini AR	Appl Biochem Biotechnol		2006	*
Phylogeny	Proposal of Novosphingobium rhizosphaerae sp. nov., isolated from the rhizosphere.	Kampfer P, Martin K, McInroy JA, Glaeser SP	Int J Syst Evol Microbiol	10.1099/ijs.0.070375-0	2014	*
Phylogeny	Novosphingobium marinum sp. nov., isolated from seawater.	Huo YY, You H, Li ZY, Wang CS, Xu XW	Int J Syst Evol Microbiol	10.1099/ijs.0.070433-0	2014	*
Phylogeny	Description of Novosphingobiumflavum sp. nov., isolated from soil.	Nguyen TM, Myung SW, Jang H, Kim J	Int J Syst Evol Microbiol	10.1099/ijsem.0.001242	2016	*
Phylogeny	Novosphingobium pokkalii sp nov, a novel rhizosphere-associated bacterium with plant beneficial properties isolated from saline-tolerant pokkali rice.	Krishnan R, Menon RR, Likhitha, Busse HJ, Tanaka N, Krishnamurthi S, Rameshkumar N	Res Microbiol	10.1016/j.resmic.2016.09.001	2016	*

References

#9195

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 30196

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#38753 ; 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) .

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

#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) .

* 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 Novosphingobium capsulatum in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF