Strain identifier

BacDive ID: 141166

Type strain: Yes

Species: Sphingomonas difficilis

Strain Designation: 1PNM-26

Strain history: <- Guangda Feng, South China Agricultural Univ.

NCBI tax ID(s): 1141888 (species)

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General

@ref: 64988

BacDive-ID: 141166

DSM-Number: 27573

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

description: Sphingomonas difficilis 1PNM-26 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from From abandoned lead-zinc ore in Meizhou.

NCBI tax id

  • NCBI tax id: 1141888
  • Matching level: species

strain history

@refhistory
64988<- G. Feng, Guangdong Inst. Microbiology, Guangdong Academy Sci., China; 1PNM-26
67771<- Guangda Feng, South China Agricultural Univ.

doi: 10.13145/bacdive141166.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Sphingomonas
  • species: Sphingomonas difficilis
  • full scientific name: Sphingomonas difficilis Feng et al. 2017

@ref: 64988

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas difficilis

full scientific name: Sphingomonas difficilis Feng et al. 2017

strain designation: 1PNM-26

type strain: yes

Morphology

cell morphology

  • @ref: 44085
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 44085
  • colony size: 1-2 mm
  • colony color: orange
  • incubation period: 4 days
  • medium used: R2A agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
44085Liquid mediano
44085Nutrient agar (NA)no
44085PYEyes
44085Reasoner's 2A agar (R2A)yes
44085Trypticase Soy Agar (TSA)no
64988R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
44085positivegrowth20-35
44085positiveoptimum28-30mesophilic
64988positivegrowth28mesophilic
67771positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
44085aerobe
67771aerobe

spore formation

  • @ref: 44085
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentrationhalophily level
44085NaClpositivegrowth0-1 %(w/v)
44085NaClpositiveoptimum0 %(w/v)non-halophilic

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4408517128adipate-assimilation
4408527689decanoate-assimilation
4408516947citrate-assimilation
4408516899D-mannitol-assimilation
4408516024D-mannose-assimilation
4408524265gluconate-assimilation
4408517234glucose-assimilation
4408530849L-arabinose-assimilation
4408525115malate-assimilation
4408517306maltose-assimilation
44085506227N-acetylglucosamine-assimilation
4408518401phenylacetate-assimilation
4408517234glucose-fermentation
440855291gelatin-hydrolysis
4408528017starch-hydrolysis
4408553426tween 80-hydrolysis
4408517632nitrate-reduction
440854853esculin+hydrolysis
4408553423tween 40+hydrolysis

metabolite production

  • @ref: 44085
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
44085cytochrome oxidase+1.9.3.1
44085catalase+1.11.1.6
44085beta-galactosidase+3.2.1.23
44085arginine dihydrolase-3.5.3.6
44085urease-3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment culture
67771From abandoned lead-zinc ore in MeizhouGuangdong ProvinceChinaCHNAsia
44085abandoned lead-zinc mineMeizhou, Guangdong ProvinceChinaCHNAsia24.3622116.276R2A
64988abandoned lead-zinc oreGuangdong Province, Meizhou (24° 21' 44'' N 116° 16' 34'' E)ChinaCHNAsia24.3622116.276

isolation source categories

Cat1Cat2Cat3
#Engineered#Other#Mine
#Engineered#Contamination#Heavy metal

Safety information

risk assessment

  • @ref: 64988
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 64988
  • description: Sphingomonas difficilis strain 1PNM-26 16S ribosomal RNA gene, partial sequence
  • accession: JQ608334
  • length: 1434
  • database: ena
  • NCBI tax ID: 1141888

GC content

  • @ref: 64988
  • GC-content: 66.3
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 64988

culture collection no.: GDMCC 1.664, KCTC 42758, DSM 27573

straininfo link

  • @ref: 96876
  • straininfo: 402663

literature

  • topic: Phylogeny
  • Pubmed-ID: 29091024
  • title: Sphingomonas difficilis sp. nov., a difficultly cultivable bacterium that grows on solid but not in liquid medium, isolated from an abandoned lead-zinc mine.
  • authors: Feng GD, Xiong X, Zhu HH, Li HP
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002461
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, *Mining, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistry, *Zinc
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
44085Guang-Da Feng, Xiong Xiong, Hong-Hui Zhu and Hua-Ping LiSphingomonas difficilis sp. nov., a difficultly cultivable bacterium that grows on solid but not in liquid medium, isolated from an abandoned lead–zinc mine10.1099/ijsem.0.002461IJSEM 67: 5273-5278 201729091024
64988Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-27573Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27573)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
96876Reimer, 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 identifiers10.60712/SI-ID402663.1