Strain identifier

BacDive ID: 23265

Type strain: Yes

Species: Novosphingobium barchaimii

Strain Designation: LL02

Strain history: <- R. Lal, Univ. Delhi, Dept. Zoology, India; LL02 <- J. Damborsky, Masaryk Univ., Faculty of Science, Brno, Czech Republic

NCBI tax ID(s): 1420591 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 19229

BacDive-ID: 23265

DSM-Number: 25411

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

description: Novosphingobium barchaimii LL02 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from hexachlorocyclohexane contaminated soil besides lindane producing plant.

NCBI tax id

  • NCBI tax id: 1420591
  • Matching level: species

strain history

  • @ref: 19229
  • history: <- R. Lal, Univ. Delhi, Dept. Zoology, India; LL02 <- J. Damborsky, Masaryk Univ., Faculty of Science, Brno, Czech Republic

doi: 10.13145/bacdive23265.20230509.8.1

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 barchaimii
  • full scientific name: Novosphingobium barchaimii Niharika et al. 2013

@ref: 19229

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Erythrobacteraceae

genus: Novosphingobium

species: Novosphingobium barchaimii

full scientific name: Novosphingobium barchaimii Niharika et al. 2013

strain designation: LL02

type strain: yes

Morphology

cell morphology

  • @ref: 30604
  • gram stain: negative
  • cell length: 1 µm
  • cell width: 1 µm
  • cell shape: rod-shaped
  • motility: no

pigmentation

  • @ref: 30604
  • production: yes

multimedia

  • @ref: 19229
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_25411.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

  • @ref: 19229
  • 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
19229positivegrowth28mesophilic
30604positivegrowth28-37mesophilic
30604positiveoptimum28mesophilic

culture pH

@refabilitytypepH
30604positivegrowth05-07
30604positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 30604
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
30604NaClpositivegrowth0-3 %
30604NaClpositiveoptimum1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3060417234glucose+carbon source
3060426546rhamnose+carbon source
3060417992sucrose+carbon source
3060453424tween 20+carbon source
306044853esculin+hydrolysis
3060417632nitrate+reduction

enzymes

@refvalueactivityec
30604gelatinase+
30604urease+3.5.1.5

Isolation, sampling and environmental information

isolation

  • @ref: 19229
  • sample type: hexachlorocyclohexane contaminated soil besides lindane producing plant
  • country: Czech Republic
  • origin.country: CZE
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Engineered#Industrial#Plant (Factory)
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_1591.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_795;97_926;98_1256;99_1591&stattab=map
  • Last taxonomy: Novosphingobium barchaimii
  • 16S sequence: JN695619
  • Sequence Identity:
  • Total samples: 600
  • soil counts: 125
  • aquatic counts: 120
  • animal counts: 298
  • plant counts: 57

Safety information

risk assessment

  • @ref: 19229
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 19229
  • description: Novosphingobium barchaimii LL02 16S ribosomal RNA gene, partial sequence
  • accession: JN695619
  • length: 1405
  • database: ena
  • NCBI tax ID: 1114963

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Novosphingobium barchaimii LL02GCA_001046635scaffoldncbi1114963
66792Novosphingobium barchaimii LL021114963.3wgspatric1114963
66792Novosphingobium barchaimii LL022654587500draftimg1114963

GC content

@refGC-contentmethod
1922967.72fluorimetric
3060467.72

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno54.652yes
flagellatedno89.61yes
gram-positiveno97.104yes
anaerobicno99.117no
aerobicyes94.745yes
halophileno96.364yes
spore-formingno92.815no
thermophileno99.597no
glucose-utilyes89.736yes
glucose-fermentno93.067no

External links

@ref: 19229

culture collection no.: DSM 25411, CCM 7980

straininfo link

  • @ref: 87488
  • straininfo: 401713

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22544801Novosphingobium barchaimii sp. nov., isolated from hexachlorocyclohexane-contaminated soil.Niharika N, Moskalikova H, Kaur J, Sedlackova M, Hampl A, Damborsky J, Prokop Z, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.039826-02012Bacterial Typing Techniques, Base Composition, Czech Republic, DNA, Bacterial/genetics, Fatty Acids/analysis, *Hexachlorocyclohexane, 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/analogs & derivatives/analysisGenetics
Phylogeny25985829Novosphingobium gossypii sp. nov., isolated from Gossypium hirsutum.Kampfer P, Martin K, McInroy JA, Glaeser SPInt J Syst Evol Microbiol10.1099/ijs.0.0003392015Alabama, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gossypium/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids, *Phylogeny, Pigmentation, Plant Stems/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/chemistry, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistryGenetics
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

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
19229Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25411)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25411
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
30604Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2693528776041
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
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
87488Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID401713.1StrainInfo: A central database for resolving microbial strain identifiers