Name: Sphingosinicella soli KSL-125
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 14295

Type strain:

Species: Sphingosinicella soli

Strain Designation: KSL-125

Culture col. no.: DSM 17328, KCTC 12482

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 333708 (species)

SI-ID 401686

DSM 17328

Special Collections

Section

Sphingosinicella soli KSL-125 is an aerobe, Gram-negative, motile bacterium that was isolated from alkaline soil.

Gram-negative
motile
rod-shaped
aerobe
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	*Sphingosinicellaceae*
	Genus	*Sphingosinicella*
	Species	**Sphingosinicella soli**
	Full Scientific Name (LPSN)	Sphingosinicella soli Yoon et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #32275]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %95.233

[Ref.: #32275]	Cell length	2.35 µm

[Ref.: #32275]	Cell width	0.4 µm

[Ref.: #32275]	Cell shape	rod-shaped

[Ref.: #32275]	Motility	yes

[Ref.: #32275]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6896]

Culture medium

TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)

[Ref.: #6896]

Culture medium growth

[Ref.: #6896]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6896]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #6896]	growth	28 °C
[Ref.: #32275]	growth	04-37 °C
[Ref.: #32275]	optimum	30 °C
[Ref.: #67771]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #32275]			optimum	7.75
[Ref.: #32275]			growth	6-9.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32275]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe
[Ref.: #69480]	Oxygen tolerance	aerobe Confidence in %92.43

[Ref.: #32275]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %90.422
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32275]		NaCl		growth	0-2	%
[Ref.: #32275]		NaCl		optimum	0.5	%

[Ref.: #67771]

Observation

quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32275]	2-oxopentanoate ChEBI	+	carbon source
[Ref.: #32275]	methyl pyruvate ChEBI	+	carbon source
[Ref.: #32275]	ornithine ChEBI	+	carbon source

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

[Ref.: #6896]	Sample type/isolated from	alkaline soil
[Ref.: #6896]	Geographic location (country and/or sea, region)	Kwangchun
[Ref.: #6896]	Country	Republic of Korea
[Ref.: #6896]	Country ISO 3 Code	KOR
[Ref.: #6896]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From alkaline soil from Kwangchun
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Soil
#Condition	#Alkaline	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence DQ087403 (>99% sequence identity) for Sphingosinicella from Microbeatlas

Aquatic Samples	7685
Soil Samples	5974
Animal Samples	2606
Plant Samples	1345
Total Samples	17610

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

[Ref.: #6896]

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.: #6896]	Sphingosinicella soli strain KSL-125 16S ribosomal RNA gene, partial sequence	DQ087403	1409	GenBank ENA	333708 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sphingosinicella soli DSM 17328	GCA_014199685	contig	GenBank ENA	333708 tax ID	*
[Ref.: #66792]	Sphingosinicella soli strain DSM 17328	333708.3	wgs	PATRIC	333708 tax ID	*
[Ref.: #66792]	Sphingosinicella soli DSM 17328	2828629153	draft	JGI IMG/M	333708 tax ID	*

[Ref.: #6896]	GC-content	65.1 mol%	high performance liquid chromatography (HPLC)
[Ref.: #32275]	GC-content	65.1 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Sphingosinicella soli strain DSM 17328 PATRIC: 333708.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sphingosinicella soli strain DSM 17328 PATRIC: 333708.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	95.233	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	96.171	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	90.422	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	92.43	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	97.076	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	65.49	no

Availability in culture collections External links

[Ref.: #6896]

Culture collection no.

DSM 17328, KCTC 12482

[Ref.: #83448]

SI-ID 401686

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingosinicella humi sp. nov., isolated from arsenic-contaminated farmland soil and emended description of the genus Sphingosinicella.	Qiao Z, Cao M, Wang D, Liao S, Wang G	Int J Syst Evol Microbiol	10.1099/ijsem.0.003186	2018	*
Phylogeny	Parablastomonas arctica gen. nov., sp. nov., isolated from high Arctic glacial till.	Ren L, Chang X, Jiang F, Kan W, Qu Z, Qiu X, Fang C, Peng F	Int J Syst Evol Microbiol	10.1099/ijs.0.067231-0	2014	*
Phylogeny	Sphingosinicella vermicomposti sp. nov., isolated from vermicompost, and emended description of the genus Sphingosinicella.	Yasir M, Aslam Z, Song GC, Jeon CO, Chung YR	Int J Syst Evol Microbiol	10.1099/ijs.0.010777-0	2009	*
Phylogeny	Sphingosinicella soli sp. nov., isolated from an alkaline soil in Korea.	Yoon JH, Kang SJ, Lee JS, Nam SW, Kim W, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.65242-0	2008	*

References

#6896

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17328

#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 )

#32275

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 #28515 (see below)

#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;

#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 )

#83448

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-ID401686.1 )

#28515

IJSEM 173 2008 ( DOI 10.1099/ijs.0.65242-0 , PubMed 18175705 )

* These data were automatically processed and therefore are not curated

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Sphingosinicella soli strain DSM 17328

Sphingosinicella soli strain DSM 17328

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