Strain identifier

BacDive ID: 14295

Type strain: Yes

Species: Sphingosinicella soli

Strain Designation: KSL-125

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 333708 (species)

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General

@ref: 6896

BacDive-ID: 14295

DSM-Number: 17328

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped

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

NCBI tax id

  • NCBI tax id: 333708
  • Matching level: species

strain history

@refhistory
6896<- J.-H. Yoon, Korea Res. Inst. of Biosci. and Biotechnol. (KRIBB); KSL-125 <- J.-H. Yoon et al.
67771<- JH Yoon, KRIBB

doi: 10.13145/bacdive14295.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingosinicellaceae
  • genus: Sphingosinicella
  • species: Sphingosinicella soli
  • full scientific name: Sphingosinicella soli Yoon et al. 2008

@ref: 6896

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingosinicellaceae

genus: Sphingosinicella

species: Sphingosinicella soli

full scientific name: Sphingosinicella soli Yoon et al. 2008

strain designation: KSL-125

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32275negative2.35 µm0.4 µmrod-shapedyes
67771negative
69480negative99.948

pigmentation

  • @ref: 32275
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 6896
  • name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/545
  • composition: Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
6896positivegrowth28mesophilic
32275positivegrowth04-37
32275positiveoptimum30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
32275positivegrowth6-9.5alkaliphile
32275positiveoptimum7.75

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32275aerobe
67771aerobe

spore formation

@refspore formationconfidence
32275no
69481no100
69480no99.991

halophily

@refsaltgrowthtested relationconcentration
32275NaClpositivegrowth0-2 %
32275NaClpositiveoptimum0.5 %

observation

  • @ref: 67771
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
32275286442-oxopentanoate+carbon source
3227551850methyl pyruvate+carbon source
3227518257ornithine+carbon source

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6896alkaline soilKwangchunRepublic of KoreaKORAsia
67771From alkaline soil from KwangchunRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Condition#Alkaline

taxonmaps

  • @ref: 69479
  • File name: preview.99_29701.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_14601;97_17816;98_22148;99_29701&stattab=map
  • Last taxonomy: Sphingosinicella
  • 16S sequence: DQ087403
  • Sequence Identity:
  • Total samples: 17610
  • soil counts: 5974
  • aquatic counts: 7685
  • animal counts: 2606
  • plant counts: 1345

Safety information

risk assessment

  • @ref: 6896
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6896
  • description: Sphingosinicella soli strain KSL-125 16S ribosomal RNA gene, partial sequence
  • accession: DQ087403
  • length: 1409
  • database: ena
  • NCBI tax ID: 333708

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingosinicella soli DSM 17328GCA_014199685contigncbi333708
66792Sphingosinicella soli strain DSM 17328333708.3wgspatric333708
66792Sphingosinicella soli DSM 173282828629153draftimg333708

GC content

@refGC-contentmethod
689665.1high performance liquid chromatography (HPLC)
3227565.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno96.931yes
anaerobicno98.708yes
halophileno92.687yes
spore-formingno94.312yes
glucose-utilyes71.363no
motileyes80.945no
flagellatedno89.608no
thermophileno97.859yes
aerobicyes93.939yes
glucose-fermentno93.714no

External links

@ref: 6896

culture collection no.: DSM 17328, KCTC 12482

straininfo link

  • @ref: 83448
  • straininfo: 401686

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18175705Sphingosinicella soli sp. nov., isolated from an alkaline soil in Korea.Yoon JH, Kang SJ, Lee JS, Nam SW, Kim W, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.65242-02008Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, Genes, rRNA, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil/analysis, *Soil Microbiology, Species Specificity, Sphingomonadaceae/*classification/genetics/*isolation & purificationGenetics
Phylogeny19654337Sphingosinicella vermicomposti sp. nov., isolated from vermicompost, and emended description of the genus Sphingosinicella.Yasir M, Aslam Z, Song GC, Jeon CO, Chung YRInt J Syst Evol Microbiol10.1099/ijs.0.010777-02009DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Sphingomonadaceae/*classification/genetics/*isolation & purification/metabolismMetabolism
Phylogeny25336722Parablastomonas 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 FInt J Syst Evol Microbiol10.1099/ijs.0.067231-02014Arctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Ice Cover, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/chemistry, Sphingomonadaceae/*classification/genetics/isolation & purification, Svalbard, Ubiquinone/chemistryGenetics
Phylogeny30570478Sphingosinicella 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 GInt J Syst Evol Microbiol10.1099/ijsem.0.0031862018*Arsenic, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Environmental Pollution, Farms, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Soil Pollutants, Sphingomonadaceae/*classification/isolation & purification, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6896Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17328)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17328
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
32275Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2851528776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
69479João 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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
83448Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID401686.1StrainInfo: A central database for resolving microbial strain identifiers