Strain identifier
BacDive ID: 14163
Type strain:
Species: Novosphingobium panipatense
Strain Designation: SM16
Strain history: <- R. Lal, Univ. Delhi, Dept. Zoology, India; SM16
NCBI tax ID(s): 428991 (species)
General
@ref: 16605
BacDive-ID: 14163
DSM-Number: 22890
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Novosphingobium panipatense SM16 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from oil-contaminated soil.
NCBI tax id
- NCBI tax id: 428991
- Matching level: species
strain history
- @ref: 16605
- history: <- R. Lal, Univ. Delhi, Dept. Zoology, India; SM16
doi: 10.13145/bacdive14163.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Sphingomonadales
- family: Erythrobacteraceae
- genus: Novosphingobium
- species: Novosphingobium panipatense
- full scientific name: Novosphingobium panipatense Gupta et al. 2009
@ref: 16605
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Sphingomonadales
family: Sphingomonadaceae
genus: Novosphingobium
species: Novosphingobium panipatense
full scientific name: Novosphingobium panipatense Gupta et al. 2009
strain designation: SM16
type strain: yes
Morphology
cell morphology
- @ref: 32592
- gram stain: negative
- cell length: 1.5 µm
- cell width: 0.6 µm
- cell shape: rod-shaped
- motility: no
pigmentation
- @ref: 32592
- production: no
Culture and growth conditions
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
32592 | positive | growth | 28-37 | mesophilic |
32592 | positive | optimum | 32.5 | mesophilic |
culture pH
- @ref: 32592
- ability: positive
- type: optimum
- pH: 7.2
Physiology and metabolism
oxygen tolerance
- @ref: 32592
- oxygen tolerance: aerobe
spore formation
- @ref: 32592
- spore formation: no
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32592 | 30089 | acetate | + | carbon source |
32592 | 22599 | arabinose | + | carbon source |
32592 | 28757 | fructose | + | carbon source |
32592 | 28260 | galactose | + | carbon source |
32592 | 17234 | glucose | + | carbon source |
32592 | 17716 | lactose | + | carbon source |
32592 | 17306 | maltose | + | carbon source |
32592 | 37684 | mannose | + | carbon source |
32592 | 15361 | pyruvate | + | carbon source |
32592 | 16634 | raffinose | + | carbon source |
32592 | 30911 | sorbitol | + | carbon source |
32592 | 27082 | trehalose | + | carbon source |
32592 | 53426 | tween 80 | + | carbon source |
32592 | 17632 | nitrate | + | reduction |
Isolation, sampling and environmental information
isolation
- @ref: 16605
- sample type: oil-contaminated soil
- geographic location: Panipat
- country: India
- origin.country: IND
- continent: Asia
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Contamination | #Oil (Fuel) |
#Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_2040.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_795;97_926;98_1256;99_2040&stattab=map
- Last taxonomy: Novosphingobium
- 16S sequence: EF424402
- Sequence Identity:
- Total samples: 4077
- soil counts: 623
- aquatic counts: 1963
- animal counts: 828
- plant counts: 663
Safety information
risk assessment
- @ref: 16605
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16605
- description: Novosphingobium panipatense strain SM16 16S ribosomal RNA gene, partial sequence
- accession: EF424402
- length: 1396
- database: ena
- NCBI tax ID: 428991
Genome sequences
- @ref: 66792
- description: Novosphingobium panipatense SM16
- accession: 2706794921
- assembly level: draft
- database: img
- NCBI tax ID: 428991
External links
@ref: 16605
culture collection no.: DSM 22890, CCM 7472, MTCC 9019
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19126741 | Novosphingobium panipatense sp. nov. and Novosphingobium mathurense sp. nov., from oil-contaminated soil. | Gupta SK, Lal D, Lal R | Int J Syst Evol Microbiol | 10.1099/ijs.0.65743-0 | 2009 | Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Nucleic Acid Hybridization, *Oils, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Soil Pollutants, Species Specificity, Sphingomonadaceae/*classification/genetics/*isolation & purification/metabolism | Phenotype |
Phylogeny | 27664092 | Novosphingobium profundi sp. nov. isolated from a deep-sea seamount. | Zhang DC, Liu YX, Huang HJ | Antonie Van Leeuwenhoek | 10.1007/s10482-016-0769-3 | 2016 | Animals, Anthozoa/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/metabolism, Fatty Acids/chemistry/metabolism, Pacific Ocean, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sphingomonadaceae/classification/genetics/*isolation & purification/metabolism | Metabolism |
Phylogeny | 28840813 | Novosphingobium clariflavum sp. nov., isolated from a household product plant. | Zhang X, Liu Y, Lin Y, Wang L, Yao S, Cao Y, Zhai L, Tang X, Zhang L, Zhang T, Ge Y, Ling K, Liu J, Cheng C | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001803 | 2017 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Household Products, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/chemistry, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
16605 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22890) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22890 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
32592 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28805 | 28776041 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta |