Strain identifier
BacDive ID: 24566
Type strain: 
Species: Sphingopyxis indica
Strain Designation: DS15
Strain history: <- R. Lal, Univ. Delhi, Dept. Zoology, India; DS15
NCBI tax ID(s): 436663 (species)
version 8.1 (current version)
General
@ref: 20823
BacDive-ID: 24566
DSM-Number: 27519
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Sphingopyxis indica DS15 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil highly contaminated with hexachlorocyclohexane .
NCBI tax id
- NCBI tax id: 436663
- Matching level: species
strain history
- @ref: 20823
- history: <- R. Lal, Univ. Delhi, Dept. Zoology, India; DS15
doi: 10.13145/bacdive24566.20230509.8.1
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 indica
- full scientific name: Sphingopyxis indica Jindal et al. 2013
@ref: 20823
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Pseudomonadales
family: Sphingomonadaceae
genus: Sphingopyxis
species: Sphingopyxis indica
full scientific name: Sphingopyxis indica Jindal et al. 2013
strain designation: DS15
type strain: yes
Morphology
cell morphology
- @ref: 30636
- gram stain: negative
- cell length: 1.51 µm
- cell width: 0.52 µm
- cell shape: rod-shaped
- motility: no
pigmentation
- @ref: 30636
- production: yes
multimedia
- @ref: 20823
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_27519.jpg
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture temp
- @ref: 30636
- growth: positive
- type: optimum
- temperature: 28
- range: mesophilic
culture pH
- @ref: 30636
- ability: positive
- type: optimum
- pH: 7
Physiology and metabolism
oxygen tolerance
- @ref: 30636
- oxygen tolerance: aerobe
spore formation
- @ref: 30636
- spore formation: no
halophily
- @ref: 30636
- salt: NaCl
- growth: positive
- tested relation: optimum
- concentration: 0.5 %
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30636 | 22599 | arabinose | + | carbon source |
| 30636 | 28757 | fructose | + | carbon source |
| 30636 | 17716 | lactose | + | carbon source |
| 30636 | 18222 | xylose | + | carbon source |
| 30636 | 4853 | esculin | + | hydrolysis |
enzymes
- @ref: 30636
- value: cytochrome oxidase
- activity: +
- ec: 1.9.3.1
Isolation, sampling and environmental information
isolation
- @ref: 20823
- sample type: soil highly contaminated with hexachlorocyclohexane (HCH)
- geographic location: Uttar Pradesh, Lucknow, Ummari Village, 27° 0' N, 81° 09' E
- country: India
- origin.country: IND
- continent: Asia
- latitude: 27
- longitude: 81.15
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Contamination | |
| #Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_44750.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_1020;97_1840;98_2725;99_44750&stattab=map
- Last taxonomy: Sphingopyxis indica
- 16S sequence: EF494193
- Sequence Identity:
- Total samples: 128
- soil counts: 82
- aquatic counts: 30
- animal counts: 15
- plant counts: 1
Safety information
risk assessment
- @ref: 20823
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20823
- description: Sphingopyxis indica strain DS15 16S ribosomal RNA gene, partial sequence
- accession: EF494193
- length: 1401
- database: ena
- NCBI tax ID: 436663
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Sphingopyxis indica DS15 | GCA_900188185 | contig | ncbi | 436663 |
| 66792 | Sphingopyxis indica DS15 | 2706795027 | draft | img | 436663 |
GC content
- @ref: 20823
- GC-content: 67.5
External links
@ref: 20823
culture collection no.: DSM 27519, CCM 7542, MCC 2023, MTCC 9455
literature
- topic: Phylogeny
- Pubmed-ID: 23125320
- title: Sphingopyxis indica sp. nov., isolated from a high dose point hexachlorocyclohexane (HCH)-contaminated dumpsite.
- authors: Jindal S, Dua A, Lal R
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.040840-0
- year: 2012
- mesh: Bacterial 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/analysis
- topic2: Genetics
Reference
| @id | authors | title | doi/url | catalogue | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 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 | 10.1099/ijsem.0.004332 | ||||
| 20823 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-27519 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27519) | ||||
| 30636 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 26967 | 28776041 | ||
| 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) | https://diaspora-project.de/progress.html#genomes | ||||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
| 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 | https://microbeatlas.org/ |