Name: Novosphingobium pentaromativorans US6-1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 14152

Type strain:

Species: Novosphingobium pentaromativorans

Strain Designation: US6-1

Culture col. no.: CCUG 56449, CIP 108548, DSM 17173, JCM 12182, KCTC 10454, NCIMB 14244

Strain history: K. K. Kwon US6-1.

NCBI tax ID(s): 205844 (species)

Section

Novosphingobium pentaromativorans US6-1 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from muddy sediment.

Gram-negative
rod-shaped
facultative anaerobe
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 pentaromativorans**
	Full Scientific Name (PNU)	Novosphingobium pentaromativorans Sohn et al. 2004

Information on morphological and physiological properties Morphology

[Ref.: #30105]	Gram stain	negative
[Ref.: #30105]	Cell length	0.97-1.95 µm
[Ref.: #30105]	Cell width	0.36-0.45 µm
[Ref.: #30105]	Cell shape	rod-shaped
[Ref.: #30105]	Motility	no

[Ref.: #60963]

Incubation period

2 days

[Ref.: #30105]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6807]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #6807]

Culture medium growth

[Ref.: #6807]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #6807]

Culture medium composition

expand / minimize

[Ref.: #6807]

Culture medium

MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457)

[Ref.: #6807]

Culture medium growth

[Ref.: #6807]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #6807]

Culture medium composition

expand / minimize

[Ref.: #38179]

Culture medium

Marine agar (MA)

[Ref.: #38179]

Culture medium growth

[Ref.: #38179]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #6807]	growth	30 °C
[Ref.: #30105]	optimum	30 °C
[Ref.: #38179]	growth	30 °C
[Ref.: #60963]	growth	30 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #6807]	Temperature range	mesophilic
[Ref.: #30105]	Temperature range	mesophilic
[Ref.: #38179]	Temperature range	mesophilic
[Ref.: #60963]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH	pH range
[Ref.: #30105]			optimum	6.5
[Ref.: #30105]			growth	06-09	alkaliphile

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30105]	Oxygen tolerance	facultative anaerobe
[Ref.: #60963]	Oxygen tolerance	aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30105]		NaCl		growth	01-06	%
[Ref.: #30105]		NaCl		optimum	2.5	%

	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.: #30105]	esculin ChEBI	+	hydrolysis
[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.: #30105]	glucose ChEBI	+	carbon source
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	-	assimilation	* from API 20NE
[Ref.: #30105]	maltose ChEBI	+	carbon source
[Ref.: #68369]	maltose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #30105]	nitrate ChEBI	+	reduction
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #30105]	phenylacetate ChEBI	+	carbon source
[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.: #30105]	catalase	+	1.11.1.6
[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.: #6807]	20617	-	-	-	-	-	+	-	-	+	-	-	-	-	+	-	-	-	-	-	+	+

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

[Ref.: #6807]	Sample type/isolated from	muddy sediment
[Ref.: #6807]	Geographic location (country and/or sea, region)	Ulsan Bay
[Ref.: #6807]	Country	Republic of Korea
[Ref.: #6807]	Country ISO 3 Code	KOR
[Ref.: #6807]	Continent	Asia

[Ref.: #60963]	Sample type/isolated from	Muddy sediment
[Ref.: #60963]	Geographic location (country and/or sea, region)	Ulsan Bay
[Ref.: #60963]	Country	Republic of Korea
[Ref.: #60963]	Country ISO 3 Code	KOR
[Ref.: #60963]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Muddy sediment of Ulsan Bay
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Mud (Sludge)
#Environmental	#Terrestrial	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence LC507451 (>99% sequence identity) for Novosphingobium from Microbeatlas

Aquatic Samples	31
Soil Samples	66
Animal Samples	32
Plant Samples	4
Total Samples	133

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

[Ref.: #6807]

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.: #30105]	Novosphingobium pentaromativorans strain US6-1 16S ribosomal RNA gene, partial sequence	AF502400	1481	GenBank	1088721 tax ID
[Ref.: #67770]	Novosphingobium pentaromativorans JCM 12182 gene for 16S ribosomal RNA, partial sequence	LC507451	1411	ENA	205844 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Novosphingobium pentaromativorans US6-1 US6-1	GCA_000767465	complete	GenBank	1088721 tax ID	*
[Ref.: #66792]	Novosphingobium pentaromativorans US6-1	1088721.7	complete	PATRIC	1088721 tax ID	*
[Ref.: #66792]	Novosphingobium pentaromativorans US6-1	1088721.11	plasmid	PATRIC	1088721 tax ID	*
[Ref.: #66792]	Novosphingobium pentaromativorans US6-1	1088721.3	wgs	PATRIC	1088721 tax ID	*
[Ref.: #66792]	Novosphingobium pentaromativorans US6-1	1088721.13	plasmid	PATRIC	1088721 tax ID	*
[Ref.: #66792]	Novosphingobium pentaromativorans US6-1	1088721.15	plasmid	PATRIC	1088721 tax ID	*

[Ref.: #30105]	GC-content	61.1 mol%
[Ref.: #67770]	GC-content	61.1 mol%	high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #6807]

Culture collection no.

CCUG 56449, CIP 108548, DSM 17173, JCM 12182, KCTC 10454, NCIMB 14244

[Ref.: #20218]

Associated Passport(s) in StrainInfo

556099, 381482, 381483

Literature:

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

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Novosphingobium pentaromativorans sp. nov., a high-molecular-mass polycyclic aromatic hydrocarbon-degrading bacterium isolated from estuarine sediment.	Sohn JH, Kwon KK, Kang JH, Jung HB, Kim SJ	Int J Syst Evol Microbiol	10.1099/ijs.0.02945-0	2004	*
Phylogeny	[Predominant strains of polycyclic aromatic hydrocarbon-degrading consortia from deep sea of the Middle Atlantic Ridge].	Cui Z, Shao Z	Wei Sheng Wu Xue Bao		2009	*
Genetics	Genome sequence of benzo(a)pyrene-degrading bacterium Novosphingobium pentaromativorans US6-1.	Luo YR, Kang SG, Kim SJ, Kim MR, Li N, Lee JH, Kwon KK	J Bacteriol	10.1128/JB.06476-11	2012	*
Metabolism	Proteomic characterization of plasmid pLA1 for biodegradation of polycyclic aromatic hydrocarbons in the marine bacterium, Novosphingobium pentaromativorans US6-1.	Yun SH, Choi CW, Lee SY, Lee YG, Kwon J, Leem SH, Chung YH, Kahng HY, Kim SJ, Kwon KK, Kim SI	PLoS One	10.1371/journal.pone.0090812	2014	*
Enzymology	Experimental results and integrated modeling of bacterial growth on an insoluble hydrophobic substrate (phenanthrene).	Adam IK, Rein A, Miltner A, Fulgencio AC, Trapp S, Kastner M	Environ Sci Technol	10.1021/es500004z	2014	*
Metabolism	Biodegradation of polycyclic aromatic hydrocarbons by Novosphingobium pentaromativorans US6-1.	Lyu Y, Zheng W, Zheng T, Tian Y	PLoS One	10.1371/journal.pone.0101438	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	Novosphingobium endophyticum sp. nov. isolated from roots of Glycyrrhiza uralensis.	Li YQ, Li L, Chen W, Duan YQ, Nimaichand S, Guo JW, Gao R, Li WJ	Arch Microbiol	10.1007/s00203-015-1124-1	2015	*
Genetics	Complete genome sequence of Novosphingobium pentaromativorans US6-1(T).	Choi DH, Kwon YM, Kwon KK, Kim SJ	Stand Genomic Sci	10.1186/s40793-015-0102-1	2015	*
Phylogeny	Novosphingobium profundi sp. nov. isolated from a deep-sea seamount.	Zhang DC, Liu YX, Huang HJ	Antonie Van Leeuwenhoek	10.1007/s10482-016-0769-3	2016	*
Metabolism	Proteomic characterization of the outer membrane vesicle of the halophilic marine bacterium Novosphingobium pentaromativorans US6-1.	Yun SH, Lee SY, Choi CW, Lee H, Ro HJ, Jun S, Kwon YM, Kwon KK, Kim SJ, Kim GH, Kim SI	J Microbiol	10.1007/s12275-017-6581-6	2016	*
Transcriptome	Transcriptome Analysis of Novosphingobium pentaromativorans US6-1 Reveals the Rsh Regulon and Potential Molecular Mechanisms of N-acyl-l-homoserine Lactone Accumulation.	Lu H, Huang Y	Int J Mol Sci	10.3390/ijms19092631	2018	*
Phylogeny	Novosphingobium aquimarinum sp. nov., isolated from seawater.	Le VV, Ko SR, Lee SA, Jin L, Ahn CY, Oh HM	Int J Syst Evol Microbiol	10.1099/ijsem.0.004493	2020	*
Phylogeny	Novosphingobium aureum sp. nov., a marine bacterium isolated from salt flat sediment.	Yoo Y, Kim D, Lee H, Khim JS, Kim B, Yang D, Pathiraja D, Choi IG, Kim JJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.004930	2021	*
	Benzo[a]pyrene might be transported by a TonB-dependent transporter in Novosphingobium pentaromativorans US6-1.	Liang J, Xu J, Zhao W, Wang J, Chen K, Li Y, Tian Y	J Hazard Mater	10.1016/j.jhazmat.2020.124037	2020	*
	Oxygen availability affects the synthesis of quorum sensing signal in the facultative anaerobe Novosphingobium pentaromativorans US6-1.	Huang Y, Lu Z, Jiang T, Zeng Y, Zeng Y, Chen B	Appl Microbiol Biotechnol	10.1007/s00253-021-11089-1	2021	*
	Finding novel chemoreceptors that specifically sense and trigger chemotaxis toward polycyclic aromatic hydrocarbons in Novosphingobium pentaromativorans US6-1.	Li Y, Liang J, Yang S, Yao J, Chen K, Yang L, Zheng W, Tian Y	J Hazard Mater	10.1016/j.jhazmat.2021.126246	2021	*

References

#6807

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17173

#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 )

#30105

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26461 (see below)

#38179 ; Curators of the CIP;
#60963 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 56449

#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) .

#26461

IJSEM 1483 2004 ( DOI 10.1099/ijs.0.02945-0 , PubMed 15388699 )

* These data were automatically processed and therefore are not curated

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