Name: Sphingomonas turrisvirgatae MCT13
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 157911

Type strain:

Species: Sphingomonas turrisvirgatae

Strain Designation: MCT13

Culture col. no.: DSM 105457, BAC RE RSCIC 7

Strain history: <- M. C. Thaller, Univ. of Rome Tor Vergata; MCT13 <- M.M. D'Andrea, Department of Medical Biotechnologies, University of Siena, Italy

NCBI tax ID(s): 1888892 (species)

SI-ID 399274

DSM 105457

Section

Sphingomonas turrisvirgatae MCT13 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from water from a drainage ditch within a disused system of constructed wetlands.

colony-forming
Gram-negative
motile
rod-shaped
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 turrisvirgatae**
	Full Scientific Name (LPSN)	Sphingomonas turrisvirgatae Thaller et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #66632]	Gram stain	negative

[Ref.: #66632]	Cell length	1.08-1.34 µm

[Ref.: #66632]	Cell width	0.29-0.44 µm

[Ref.: #66632]	Cell shape	rod-shaped

[Ref.: #66632]	Motility	yes

[Ref.: #66632]	Colony size	1-2 mm
[Ref.: #66632]	Colony color	yellow
[Ref.: #66632]	Colony shape	circular
[Ref.: #66632]	Incubation period	2 days

Multimedia content

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Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

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Culture medium

R2A MEDIUM (DSMZ Medium 830)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

Brunner mineral medium

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Culture medium growth

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Culture medium

home-made ZoBell w/o NaCl

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Culture medium growth

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Culture medium

LB (Luria-Bertani) agar

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Culture medium growth

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Culture medium

Mueller-Hinton agar

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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

tryptic soy agar (TSA)

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Culture medium growth

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Culture medium

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Culture medium growth

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Culture medium

MacConkey agar

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Culture medium growth

	Temperatures	Kind of temperature		Temperature
[Ref.: #64484]			growth	28 °C
[Ref.: #66632]			growth	20-35 °C

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Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #66632]			growth	6.5-9

Information on physiology and metabolism Physiology and metabolism

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Oxygen tolerance

aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #66632]		NaCl		growth	0-1.5	%

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Observation

Agarase activity can be observed on LBA after 48-72 h of incubation, and is more apparent on ZoBell or agarized Brunner medium.

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #66632]	3-hydroxybutyrate ChEBI	+	assimilation
[Ref.: #66632]	adipate ChEBI	+	assimilation
[Ref.: #68369]	adipate ChEBI	+	assimilation	* from API 20NE
[Ref.: #66632]	amygdalin ChEBI	-	assimilation
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #66632]	cellobiose ChEBI	-	assimilation
[Ref.: #66632]	citric acid ChEBI	-	assimilation
[Ref.: #66632]	D-arabinose ChEBI	-	assimilation
[Ref.: #66632]	D-galactose ChEBI	+	assimilation
[Ref.: #66632]	D-glucose ChEBI	+	assimilation
[Ref.: #68369]	D-glucose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #66632]	D-lyxose ChEBI	-	assimilation
[Ref.: #66632]	D-mannitol ChEBI	-	assimilation
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #66632]	D-mannose ChEBI	+	assimilation
[Ref.: #68369]	D-mannose ChEBI	-	assimilation	* from API 20NE
[Ref.: #66632]	D-ribose ChEBI	-	assimilation
[Ref.: #66632]	D-sorbitol ChEBI	-	assimilation
[Ref.: #66632]	D-tagatose ChEBI	-	assimilation
[Ref.: #66632]	D-xylose ChEBI	-	assimilation
[Ref.: #66632]	decanoate ChEBI	-	assimilation
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #66632]	erythritol ChEBI	-	assimilation
[Ref.: #66632]	galactitol ChEBI	-	assimilation
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #66632]	gentiobiose ChEBI	-	assimilation
[Ref.: #66632]	gluconate ChEBI	-	assimilation
[Ref.: #66632]	glucose ChEBI	-	builds acid from
[Ref.: #66632]	glycerol ChEBI	-	assimilation
[Ref.: #66632]	glycine ChEBI	-	assimilation
[Ref.: #66632]	glycogen ChEBI	-	assimilation
[Ref.: #66632]	inulin ChEBI	-	assimilation
[Ref.: #66632]	L-alanine ChEBI	-	assimilation
[Ref.: #66632]	L-arabinose ChEBI	-	assimilation
[Ref.: #68369]	L-arabinose ChEBI	+	assimilation	* from API 20NE
[Ref.: #66632]	L-arginine ChEBI	-	assimilation
[Ref.: #66632]	L-asparagine ChEBI	+	assimilation
[Ref.: #66632]	L-aspartate ChEBI	+	assimilation
[Ref.: #66632]	L-cysteine ChEBI	-	assimilation
[Ref.: #66632]	L-fucose ChEBI	-	assimilation
[Ref.: #66632]	L-glutamate ChEBI	+	assimilation
[Ref.: #66632]	L-glutamine ChEBI	+	assimilation
[Ref.: #66632]	L-histidine ChEBI	-	assimilation
[Ref.: #66632]	L-isoleucine ChEBI	-	assimilation
[Ref.: #66632]	L-leucine ChEBI	-	assimilation
[Ref.: #66632]	L-methionine ChEBI	-	assimilation
[Ref.: #66632]	L-ornithine ChEBI	-	assimilation
[Ref.: #66632]	L-proline ChEBI	+	assimilation
[Ref.: #66632]	L-rhamnose ChEBI	-	assimilation
[Ref.: #66632]	L-serine ChEBI	-	assimilation
[Ref.: #66632]	L-sorbose ChEBI	-	assimilation
[Ref.: #66632]	L-threonine ChEBI	-	assimilation
[Ref.: #66632]	L-xylose ChEBI	-	assimilation
[Ref.: #66632]	lactose ChEBI	-	assimilation
[Ref.: #66632]	lysine ChEBI	-	assimilation
[Ref.: #66632]	malate ChEBI	-	assimilation
[Ref.: #66632]	maltose ChEBI	-	assimilation
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #66632]	melezitose ChEBI	-	assimilation
[Ref.: #66632]	melibiose ChEBI	-	assimilation
[Ref.: #66632]	methyl alpha-D-glucopyranoside ChEBI	-	assimilation
[Ref.: #66632]	methyl alpha-D-mannoside ChEBI	-	assimilation
[Ref.: #66632]	methyl beta-D-xylopyranoside ChEBI	-	assimilation
[Ref.: #66632]	myo-inositol ChEBI	-	assimilation
[Ref.: #66632]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #66632]	nitrate ChEBI	-	reduction
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #66632]	phenylacetate ChEBI	-	assimilation
[Ref.: #66632]	phenylalanine ChEBI	-	assimilation
[Ref.: #66632]	potassium 2-dehydro-D-gluconate	-	assimilation
[Ref.: #66632]	potassium 5-dehydro-D-gluconate	-	assimilation
[Ref.: #66632]	raffinose ChEBI	-	assimilation
[Ref.: #66632]	ribitol ChEBI	-	assimilation
[Ref.: #66632]	salicin ChEBI	-	assimilation
[Ref.: #66632]	starch ChEBI	-	assimilation
[Ref.: #66632]	sucrose ChEBI	-	assimilation
[Ref.: #66632]	trehalose ChEBI	-	assimilation
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #66632]	turanose ChEBI	-	assimilation
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #66632]	xylitol ChEBI	-	assimilation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #66632]	ampicillin ChEBI	yes	10	µg (disc)
[Ref.: #66632]	chloramphenicol ChEBI	yes	30	µg (disc)
[Ref.: #66632]	ciprofloxacin ChEBI	yes	5	µg (disc)
[Ref.: #66632]	kanamycin ChEBI	yes	30	µg (disc)
[Ref.: #66632]	streptomycin ChEBI				yes	50	µg (disc)
[Ref.: #66632]	tetracycline ChEBI	yes	30	µg (disc)

	Metabolite	Production
[Ref.: #66632]	hydrogen sulfide ChEBI	no
[Ref.: #66632]	indole ChEBI	no
[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.: #66632]	arginine dihydrolase	-	3.5.3.6
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #66632]	beta-galactosidase	-	3.2.1.23
[Ref.: #66632]	catalase	+	1.11.1.6
[Ref.: #66632]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #66632]	gelatinase	-
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #66632]	urease	-	3.5.1.5
[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.: #64484]	24969	-	-	-	-	-	+	-	-	+	+	-	-	-	-	+	-	+	+	+	+/-	+
[Ref.: #64484]	24609	-	-	-	-	-	-	-	-	+	+	-	-	-	-	-	-	+	-	-	-	+

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

[Ref.: #64484]	Sample type/isolated from	water from a drainage ditch within a disused system of constructed wetlands
[Ref.: #64484]	Geographic location (country and/or sea, region)	Rome
[Ref.: #64484]	Country	Italy
[Ref.: #64484]	Country ISO 3 Code	ITA
[Ref.: #64484]	Continent	Europe
[Ref.: #64484]	Geographic location	41.8511°/12.6302°

[Ref.: #66632]	Sample type/isolated from	water sample
[Ref.: #66632]	Geographic location (country and/or sea, region)	constructed wetlands in the L-E.S.A. area of the University of Rome Tor Vergata, Rome
[Ref.: #66632]	Country	Italy
[Ref.: #66632]	Country ISO 3 Code	ITA
[Ref.: #66632]	Continent	Europe
[Ref.: #66632]	Geographic location	41.8511°/12.6301°
[Ref.: #66632]	Enrichment culture duration	1 week
[Ref.: #66632]	Enrichment culture temperature	25 ̊C
[Ref.: #66632]	Isolation/enrichment procedure	Water samples were spread on several culture media containing different salt concentrations for 1 week at roomtemperature
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Wetland (Swamp)
#Environmental	#Aquatic	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence MG077083 (>99% sequence identity) for Sphingomonas from Microbeatlas

Aquatic Samples	184
Soil Samples	149
Animal Samples	493
Plant Samples	48
Total Samples	874

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.: #64484]	Sphingomonas turrisvirgatae strain MCT13 16S ribosomal RNA gene, partial sequence	MG077083	1451	ENA	1888892 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sphingomonas turrisvirgatae MCT13	GCA_001721295	contig	GenBank	1888892 tax ID	*
[Ref.: #66792]	Sphingomonas turrisvirgatae MCT13	2751185898	draft	JGI IMG/M	1888892 tax ID	*

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GC-content

65.3 mol%

genome sequence analysis

Availability in culture collections External links

[Ref.: #64484]

Culture collection no.

DSM 105457, BAC RE RSCIC 7

[Ref.: #110764]

SI-ID 399274

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingomonas suaedae sp. nov., a chitin-degrading strain isolated from rhizosphere soil of Suaeda salsa.	Zhang H, Xu L, Zhang JX, Sun JQ	Int J Syst Evol Microbiol	10.1099/ijsem.0.004238	2020	*
Phylogeny	Sphingomonas turrisvirgatae sp. nov., an agar-degrading species isolated from freshwater.	Thaller MC, D'Andrea MM, Marmo P, Civitareale C, Casu F, Migliore L	Int J Syst Evol Microbiol	10.1099/ijsem.0.002896	2018	*
Phylogeny	Characterization of vB_StuS_MMDA13, a Newly Discovered Bacteriophage Infecting the Agar-Degrading Species Sphingomonas turrisvirgatae.	Marmo P, Thaller MC, Di Lallo G, Henrici De Angelis L, Poerio N, De Santis F, Fraziano M, Migliore L, D'Andrea MM	Viruses	10.3390/v12080894	2020	*

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 )

#64484

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 105457

#66632

Maria Cristina Thaller, Marco Maria D'Andrea, Pasquale Marmo, Cinzia Civitareale, Francesca Casu, Luciana Migliore: Sphingomonas turrisvirgatae sp. nov., an agar-degrading species isolated from freshwater. IJSEM 68: 2794 - 2799 2018 ( DOI 10.1099/ijsem.0.002896 , PubMed 30180924 )

#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) .

#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 .

#110764

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-ID399274.1 )

* These data were automatically processed and therefore are not curated

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