Strain identifier

BacDive ID: 23280

Type strain: Yes

Species: Sphingomonas cynarae

Strain Designation: ITEM-13494, SPC-1

Strain history: G. Mita SPC-1.

NCBI tax ID(s): 930197 (species)

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General

@ref: 19193

BacDive-ID: 23280

DSM-Number: 25525

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

description: Sphingomonas cynarae ITEM-13494 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from phyllosphere of Cynara cardunculus var. sylvestris Fiori .

NCBI tax id

  • NCBI tax id: 930197
  • Matching level: species

strain history

@refhistory
19193<- P. Alifano, University of Salento, DISTEBA, Lecce, Italy; SPC-1 <- G. Mitani
67770G. Mita SPC-1.

doi: 10.13145/bacdive23280.20241212.9.2

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Sphingomonas
  • species: Sphingomonas cynarae
  • full scientific name: Sphingomonas cynarae Talà et al. 2013

@ref: 19193

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas cynarae

full scientific name: Sphingomonas cynarae Talà et al. 2013

strain designation: ITEM-13494, SPC-1

type strain: yes

Morphology

cell morphology

  • @ref: 30267
  • gram stain: negative
  • cell length: 2.25 µm
  • cell width: 0.45 µm
  • cell shape: rod-shaped
  • motility: no

pigmentation

  • @ref: 30267
  • production: yes

multimedia

  • @ref: 19193
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_25525.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

  • @ref: 19193
  • name: NUTRIENT AGAR (DSMZ Medium 1)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1
  • composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperature
19193positivegrowth28
30267positivegrowth05-36
30267positiveoptimum28
67770positivegrowth28

culture pH

@refabilitytypepH
30267positivegrowth6-6.5
30267positiveoptimum6.25

Physiology and metabolism

oxygen tolerance

  • @ref: 30267
  • oxygen tolerance: aerobe

spore formation

  • @ref: 30267
  • spore formation: no

compound production

  • @ref: 19193
  • compound: sphingan

halophily

  • @ref: 30267
  • salt: NaCl
  • growth: positive
  • tested relation: optimum
  • concentration: 0.25 %

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
30267168082-dehydro-D-gluconate+carbon source
30267581435-dehydro-D-gluconate+carbon source
3026722599arabinose+carbon source
3026717057cellobiose+carbon source
3026728757fructose+carbon source
3026728260galactose+carbon source
3026717234glucose+carbon source
3026717716lactose+carbon source
3026717306maltose+carbon source
3026737684mannose+carbon source
3026728053melibiose+carbon source
3026726546rhamnose+carbon source
3026717814salicin+carbon source
3026717992sucrose+carbon source
3026727082trehalose+carbon source
302674853esculin+hydrolysis

enzymes

@refvalueactivityec
30267catalase+1.11.1.6
30267gelatinase+

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
19193phyllosphere of Cynara cardunculus var. sylvestris (Lamk) Fiori (wild cardoon)Cynara cardunculus var. sylvestrisPuglia region, LecceItalyITAEurope
67770Phyllosphere of Cynara cardunculus L. var. sylvestris (Lamk) Fiori (wild carbon), a Mediterranea native plant that is considered to be the wild ancestor of the globe artichoke and cultivated carbonCynara cardunculus L. var. sylvestris

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Leaf (Phyllosphere)

Safety information

risk assessment

  • @ref: 19193
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 19193
  • description: Sphingomonas cynarae strain SPC-1 16S ribosomal RNA gene, partial sequence
  • accession: HQ439186
  • length: 1426
  • database: nuccore
  • NCBI tax ID: 930197

GC content

@refGC-contentmethod
1919366.1high performance liquid chromatography (HPLC)
3026766.1

External links

@ref: 19193

culture collection no.: DSM 25525, JCM 17498, ITEM 13494

straininfo link

  • @ref: 87502
  • straininfo: 401047

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22328613Sphingomonas cynarae sp. nov., a proteobacterium that produces an unusual type of sphingan.Tala A, Lenucci M, Gaballo A, Durante M, Tredici SM, Debowles DA, Pizzolante G, Marcuccio C, Carata E, Piro G, Carpita NC, Mita G, Alifano PInt J Syst Evol Microbiol10.1099/ijs.0.032060-02012Bacterial Typing Techniques, Base Composition, Cynara/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Polyamines/analysis, Polysaccharides, Bacterial/*biosynthesis, RNA, Ribosomal, 16S/genetics, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/analysisGenetics
Phylogeny26155772Sphingomonas panacis sp. nov., isolated from rhizosphere of rusty ginseng.Singh P, Kim YJ, Hoang VA, Farh Mel-A, Yang DCAntonie Van Leeuwenhoek10.1007/s10482-015-0527-y2015Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Locomotion, Nucleic Acid Hybridization, Panax/*microbiology, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analysis, Sphingomonas/*classification/genetics/*isolation & purification/physiology, TemperatureTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
19193Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25525)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25525
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
30267Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2660828776041
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
87502Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID401047.1StrainInfo: A central database for resolving microbial strain identifiers