Strain identifier

BacDive ID: 14163

Type strain: Yes

Species: Novosphingobium panipatense

Strain Designation: SM16

Strain history: <- R. Lal, Univ. Delhi, Dept. Zoology, India; SM16

NCBI tax ID(s): 428991 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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

@refgrowthtypetemperaturerange
32592positivegrowth28-37mesophilic
32592positiveoptimum32.5mesophilic

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

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3259230089acetate+carbon source
3259222599arabinose+carbon source
3259228757fructose+carbon source
3259228260galactose+carbon source
3259217234glucose+carbon source
3259217716lactose+carbon source
3259217306maltose+carbon source
3259237684mannose+carbon source
3259215361pyruvate+carbon source
3259216634raffinose+carbon source
3259230911sorbitol+carbon source
3259227082trehalose+carbon source
3259253426tween 80+carbon source
3259217632nitrate+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

Cat1Cat2Cat3
#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

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19126741Novosphingobium panipatense sp. nov. and Novosphingobium mathurense sp. nov., from oil-contaminated soil.Gupta SK, Lal D, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.65743-02009Bacterial 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/metabolismPhenotype
Phylogeny27664092Novosphingobium profundi sp. nov. isolated from a deep-sea seamount.Zhang DC, Liu YX, Huang HJAntonie Van Leeuwenhoek10.1007/s10482-016-0769-32016Animals, 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/metabolismMetabolism
Phylogeny28840813Novosphingobium 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 CInt J Syst Evol Microbiol10.1099/ijsem.0.0018032017Bacterial 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/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16605Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22890)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22890
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
32592Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2880528776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69479João 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