Name: Sphingomonas desiccabilis CP1D
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 14239

Type strain:

Species: Sphingomonas desiccabilis

Strain Designation: CP1D

Culture col. no.: DSM 16792, ATCC BAA-1041, CIP 110412

Strain history: CIP <- 2012, DSMZ <- F. Garcia-Pichel, Arizona, USA: strain CP1D <- G.S.N. Reddy

NCBI tax ID(s): 429134 (species)

SI-ID 308625

ATCC BAA-1041, DSM 16792, CIP 110412

Section

Sphingomonas desiccabilis CP1D is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from biological soil crusts.

Gram-negative
rod-shaped
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 desiccabilis**
	Full Scientific Name (LPSN)	Sphingomonas desiccabilis Reddy and Garcia-Pichel 2007

Information on morphological and physiological properties Morphology

[Ref.: #31806]	Gram stain	negative
[Ref.: #118917]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.948

[Ref.: #31806]	Cell length	0.5 µm

[Ref.: #31806]	Cell width	0.25 µm

[Ref.: #31806]	Cell shape	rod-shaped
[Ref.: #118917]	Cell shape	rod-shaped

[Ref.: #31806]	Motility	no

[Ref.: #31806]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6605]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #6605]

Culture medium growth

[Ref.: #6605]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6605]

Culture medium composition

expand / minimize

[Ref.: #34729]

Culture medium

MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromati

[Ref.: #34729]

Culture medium growth

[Ref.: #34729]

Culture medium composition

expand / minimize

[Ref.: #118917]

Culture medium

CIP Medium 566

[Ref.: #118917]

Culture medium growth

[Ref.: #118917]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #6605]	growth	30 °C
[Ref.: #31806]	growth	15-37 °C
[Ref.: #31806]	optimum	25 °C
[Ref.: #34729]	growth	30 °C

[Ref.: #6605]	Temperature range	mesophilic
[Ref.: #31806]	Temperature range	mesophilic
[Ref.: #34729]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31806]			optimum	7

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %98
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.994

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31806]		NaCl		growth	0-4	%
[Ref.: #31806]		NaCl		optimum	2	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31806]	acetate ChEBI	+	carbon source
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #31806]	alanine ChEBI	+	carbon source
[Ref.: #31806]	arabinose ChEBI	+	carbon source
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #31806]	cellobiose ChEBI	+	carbon source
[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.: #31806]	fructose ChEBI	+	carbon source
[Ref.: #31806]	galactose ChEBI	+	carbon source
[Ref.: #31806]	gelatin ChEBI	+	carbon source
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	+	assimilation	* from API 20NE
[Ref.: #31806]	glucose ChEBI	+	carbon source
[Ref.: #31806]	glycerol ChEBI	+	carbon source
[Ref.: #68369]	L-arabinose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	-	assimilation	* from API 20NE
[Ref.: #31806]	maltose ChEBI	+	carbon source
[Ref.: #68369]	maltose ChEBI	+	assimilation	* from API 20NE
[Ref.: #31806]	mannose ChEBI	+	carbon source
[Ref.: #31806]	melibiose ChEBI	+	carbon source
[Ref.: #68369]	N-acetylglucosamine ChEBI	+	assimilation	* from API 20NE
[Ref.: #31806]	nitrate ChEBI	+	reduction
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #31806]	proline ChEBI	+	carbon source
[Ref.: #31806]	pyruvate ChEBI	+	carbon source
[Ref.: #31806]	raffinose ChEBI	+	carbon source
[Ref.: #31806]	rhamnose ChEBI	+	carbon source
[Ref.: #31806]	ribose ChEBI	+	carbon source
[Ref.: #31806]	sucrose ChEBI	+	carbon source
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #31806]	xylose ChEBI	+	carbon source
	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.: #31806]	catalase	+	1.11.1.6
[Ref.: #31806]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #31806]	gelatinase	+
[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.: #6605]	25225	-	-	-	-	-	+	-	+	+	+	+	-	+	+	+	-	-	-	-	-	+

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

[Ref.: #6605]	Sample type/isolated from	biological soil crusts
[Ref.: #6605]	Geographic location (country and/or sea, region)	Colorado Plateau
[Ref.: #6605]	Country	USA
[Ref.: #6605]	Country ISO 3 Code	USA
[Ref.: #6605]	Continent	North America

[Ref.: #118917]	Sample type/isolated from	Environment, Biological soil crusts
[Ref.: #118917]	Country	United States of America
[Ref.: #118917]	Country ISO 3 Code	USA
[Ref.: #118917]	Continent	North America
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AJ871435 (>99% sequence identity) for Sphingomonas from Microbeatlas

Aquatic Samples	141
Soil Samples	121
Animal Samples	437
Plant Samples	31
Total Samples	730

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

[Ref.: #6605]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #118917]	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.: #31806]	Sphingomonas desiccabilis partial 16S rRNA gene, type strain CP1DT	AJ871435	1451	GenBank	429134 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sphingomonas desiccabilis CP1D	GCA_004135605	contig	GenBank	429134 tax ID	*
[Ref.: #66792]	Sphingomonas desiccabilis DSM 16792	GCA_014196135	contig	GenBank	429134 tax ID	*
[Ref.: #66792]	Sphingomonas desiccabilis strain DSM 16792	429134.4	wgs	PATRIC	429134 tax ID	*
[Ref.: #66792]	Sphingomonas desiccabilis CP1D	2922465951	draft	JGI IMG/M	429134 tax ID	*
[Ref.: #66792]	Sphingomonas desiccabilis DSM 16792	2829818831	draft	JGI IMG/M	429134 tax ID	*

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 desiccabilis strain DSM 16792 PATRIC: 429134.4
[Ref.: #69481]	spore-forming	no	98	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sphingomonas desiccabilis strain DSM 16792 PATRIC: 429134.4
[Ref.: #69480]	gram-positive	no	97.54	no
[Ref.: #69480]	anaerobic	no	99.075	no
[Ref.: #69480]	halophile	no	94.422	no
[Ref.: #69480]	spore-forming	no	95.564	no
[Ref.: #69480]	glucose-util	yes	91.382	no
[Ref.: #69480]	aerobic	yes	90.254	no
[Ref.: #69480]	flagellated	no	95.452	yes
[Ref.: #69480]	thermophile	no	98.618	no
[Ref.: #69480]	motile	no	87.09	no
[Ref.: #69480]	glucose-ferment	no	88.296	no

Availability in culture collections External links

[Ref.: #6605]

Culture collection no.

DSM 16792, ATCC BAA-1041, CIP 110412

[Ref.: #83398]

SI-ID 308625

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingomonas mucosissima sp. nov. and Sphingomonas desiccabilis sp. nov., from biological soil crusts in the Colorado Plateau, USA.	Reddy GSN, Garcia-Pichel F	Int J Syst Evol Microbiol	10.1099/ijs.0.64331-0	2007	*

References

#6605

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16792

#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 )

#31806

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 #28075 (see below)

#34729 ; 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) .

#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 )

#83398

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-ID308625.1 )

#118917 Collection of Institut Pasteur ; Curators of the CIP; CIP 110412

#28075

IJSEM 1028 2007 ( DOI 10.1099/ijs.0.64331-0 , PubMed 17473253 )

* These data were automatically processed and therefore are not curated

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Sphingomonas desiccabilis strain DSM 16792

Sphingomonas desiccabilis strain DSM 16792

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