Strain identifier

BacDive ID: 14286

Type strain: Yes

Species: Sphingopyxis panaciterrulae

Strain history: <- DC Yang, Kyunghee Univ.

NCBI tax ID(s): 462372 (species)

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General

@ref: 17913

BacDive-ID: 14286

DSM-Number: 25122

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

description: Sphingopyxis panaciterrulae DSM 25122 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil of ginseng field.

NCBI tax id

  • NCBI tax id: 462372
  • Matching level: species

strain history

@refhistory
17913<- KCTC <- D.-C. Yang, Korean Ginseng Center, Kyung Hee University, Gyeonggi-do, South Korea
67771<- DC Yang, Kyunghee Univ.

doi: 10.13145/bacdive14286.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Sphingopyxis
  • species: Sphingopyxis panaciterrulae
  • full scientific name: Sphingopyxis panaciterrulae Srinivasan et al. 2010

@ref: 17913

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingopyxis

species: Sphingopyxis panaciterrulae

full scientific name: Sphingopyxis panaciterrulae Srinivasan et al. 2010

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
29718negative0.3-0.9 µm0.2-0.5 µmrod-shapedyes
67771negative

pigmentation

  • @ref: 29718
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 17913
  • name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/535
  • composition: Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
17913positivegrowth28mesophilic
29718positivegrowth25-37mesophilic
29718positiveoptimum25-30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
29718positivegrowth05-10alkaliphile
29718positiveoptimum07-08

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29718aerobe
67771aerobe

observation

@refobservation
29718aggregates in chains
67771quinones: Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2971817234glucose+carbon source
2971825115malate+carbon source
2971817306maltose+carbon source
29718506227N-acetylglucosamine+carbon source
2971826546rhamnose+carbon source
2971817992sucrose+carbon source
297184853esculin+hydrolysis

enzymes

@refvalueactivityec
29718acid phosphatase+3.1.3.2
29718alkaline phosphatase+3.1.3.1
29718catalase+1.11.1.6
29718cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17913soil of ginseng fieldDaejeonRepublic of KoreaKORAsia
67771From soil, ginseng fieldRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)

Safety information

risk assessment

  • @ref: 17913
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17913
  • description: Sphingopyxis panaciterrulae strain DCY34 16S ribosomal RNA gene, partial sequence
  • accession: EU075217
  • length: 1432
  • database: ena
  • NCBI tax ID: 462372

GC content

@refGC-contentmethod
1791362.3high performance liquid chromatography (HPLC)
2971862.3
6777162.32

External links

@ref: 17913

culture collection no.: DSM 25122, JCM 14844, KCTC 22112, DCY 34

straininfo link

  • @ref: 83440
  • straininfo: 370985

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19933588Sphingopyxis panaciterrulae sp. nov., isolated from soil of a ginseng field.Srinivasan S, Kim MK, Sathiyaraj G, Veena V, Mahalakshmi M, Kalaiselvi S, Kim YJ, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.019414-02009Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Korea, Locomotion, Molecular Sequence Data, Panax/*microbiology, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonadaceae/chemistry/*classification/genetics/*isolation & purificationGenetics
Phylogeny23125320Sphingopyxis indica sp. nov., isolated from a high dose point hexachlorocyclohexane (HCH)-contaminated dumpsite.Jindal S, Dua A, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.040840-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, *Hexachlorocyclohexane, India, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Soil Pollutants, Spermidine/analysis, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/analysisGenetics
Phylogeny23264504Sphingopyxis italica sp. nov., isolated from Roman catacombs.Alias-Villegas C, Jurado V, Laiz L, Saiz-Jimenez CInt J Syst Evol Microbiol10.1099/ijs.0.046573-02012Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rome, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/analogs & derivatives/analysisGenetics
Phylogeny26219279Sphingopyxis flava sp. nov., isolated from a hexachlorocyclohexane (HCH)-contaminated soil.Verma H, Rani P, Kumar Singh A, Kumar R, Dwivedi V, Negi V, Lal RInt J Syst Evol Microbiol10.1099/ijsem.0.0004822015Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hexachlorocyclohexane/*analysis, India, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants/analysis, Spermidine/chemistry, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/analogs & derivatives/chemistryGenetics
Phylogeny35672580Sphingopyxis jiangsuensis sp. nov. Isolated From the Surface Water of the Yellow Sea.Gao ZY, Xue HP, Wang L, Yao Y, Zhang DF, Huang J, Liu C, Zhang AHCurr Microbiol10.1007/s00284-022-02895-52022Bacterial Typing Techniques, DNA, Bacterial/genetics, *Fatty Acids/chemistry, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistry, *WaterTranscriptome
Phylogeny35723741Sphingopyxis lutea sp. nov., a novel moderately halotolerant bacterium isolated from pebbles.Chhetri G, Kim I, Seo TArch Microbiol10.1007/s00203-022-03042-12022Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Sphingomonadaceae, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17913Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25122)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25122
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
29718Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2610128776041
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
83440Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID370985.1StrainInfo: A central database for resolving microbial strain identifiers