Strain identifier

BacDive ID: 14156

Type strain: Yes

Species: Novosphingobium naphthalenivorans

Strain Designation: TUT562

Strain history: A. Hiraishi TUT562.

NCBI tax ID(s): 1219034 (strain), 273168 (species)

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General

@ref: 7571

BacDive-ID: 14156

DSM-Number: 18518

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

description: Novosphingobium naphthalenivorans TUT562 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from polychlorinated-dioxin-contaminated soil.

NCBI tax id

NCBI tax idMatching level
273168species
1219034strain

strain history

@refhistory
7571<- A. Hiraishi; TUT562
67770A. Hiraishi TUT562.

doi: 10.13145/bacdive14156.20230509.8.1

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 naphthalenivorans
  • full scientific name: Novosphingobium naphthalenivorans Suzuki and Hiraishi 2008

@ref: 7571

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Erythrobacteraceae

genus: Novosphingobium

species: Novosphingobium naphthalenivorans

full scientific name: Novosphingobium naphthalenivorans Suzuki and Hiraishi 2008

strain designation: TUT562

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.994

colony morphology

  • @ref: 60912
  • incubation period: 3 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7571R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
7571NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
7571positivegrowth30mesophilic
60912positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 60912
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.97

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7571-----+--++---+------+
7571-----+--++---+------+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
7571polychlorinated-dioxin-contaminated soilJapanJPNAsia
60912Soil,polychlorinated-dioxin-contaminatedJapanJPNAsia
67770PCDD/F- and PAH-contaminated soil and sediment

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_6979.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_795;97_926;98_1256;99_6979&stattab=map
  • Last taxonomy: Novosphingobium naphthalenivorans
  • 16S sequence: AB177883
  • Sequence Identity:
  • Total samples: 136
  • soil counts: 23
  • aquatic counts: 36
  • animal counts: 58
  • plant counts: 19

Safety information

risk assessment

  • @ref: 7571
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7571
  • description: Novosphingobium naphthalenivorans gene for 16S rRNA
  • accession: AB177883
  • length: 1481
  • database: ena
  • NCBI tax ID: 273168

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Novosphingobium naphthalenivorans NBRC 1020511219034.3wgspatric1219034
66792Novosphingobium naphthalenivorans NBRC 1020512731957632draftimg1219034
67770Novosphingobium naphthalenivorans NBRC 102051GCA_001590985contigncbi1219034

GC content

  • @ref: 67770
  • GC-content: 64.6
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileyes52.125no
gram-positiveno97.094no
anaerobicno97.223no
aerobicyes77.397no
halophileno94.636no
spore-formingno94.438no
thermophileno97.146yes
glucose-utilyes91.328yes
flagellatedno88.698no
glucose-fermentno91.707no

External links

@ref: 7571

culture collection no.: CCUG 56309, DSM 18518, JCM 13951, NBRC 10251, NBRC 102051

straininfo link

  • @ref: 83322
  • straininfo: 343461

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17878661Novosphingobium naphthalenivorans sp. nov., a naphthalene-degrading bacterium isolated from polychlorinated-dioxin-contaminated environments.Suzuki S, Hiraishi AJ Gen Appl Microbiol10.2323/jgam.53.2212007Base Sequence, Molecular Sequence Data, Naphthalenes/*metabolism, Phylogeny, Polymerase Chain Reaction, *Soil Microbiology, Soil Pollutants/*metabolism, Sphingomonadaceae/genetics/*isolation & purification/metabolismMetabolism
Phylogeny19605709Novosphingobium indicum sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from a deep-sea environment.Yuan J, Lai Q, Zheng T, Shao ZInt J Syst Evol Microbiol10.1099/ijs.0.002873-02009Bacterial Typing Techniques, Cluster Analysis, DNA Fingerprinting/methods, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Indian Ocean, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Polyamines/analysis, Polycyclic Aromatic Hydrocarbons/*metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sphingomonadaceae/*classification/genetics/isolation & purification/*metabolismGenetics
Phylogeny20207802Novosphingobium soli sp. nov., isolated from soil.Kampfer P, Young CC, Busse HJ, Lin SY, Rekha PD, Arun AB, Chen WM, Shen FT, Wu YHInt J Syst Evol Microbiol10.1099/ijs.0.022178-02010Bacterial Typing Techniques, DNA, Bacterial/genetics, Lipids/analysis, Molecular Sequence Data, *Phylogeny, Pigments, Biological/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonadaceae/*classification/genetics/isolation & purification, Taiwan, Ubiquinone/analogs & derivatives/analysisGenetics
Phylogeny21097643Novosphingobium sediminicola sp. nov. isolated from freshwater sediment.Baek SH, Lim JH, Jin L, Lee HG, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.024307-02010Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fresh Water/*microbiology, Geologic Sediments/*microbiology, Glycosphingolipids/analysis, Molecular Sequence Data, Phylogeny, Pigments, Biological/metabolism, Polyamines/analysis, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sphingomonadaceae/*classification/genetics/*isolation & purification/physiologyGenetics
Phylogeny23104365Novosphingobium lindaniclasticum sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH dumpsite.Saxena A, Anand S, Dua A, Sangwan N, Khan F, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.045443-02012Bacterial 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/analogs & derivatives/analysisGenetics
Phylogeny34328829Novosphingobium aureum sp. nov., a marine bacterium isolated from salt flat sediment.Yoo Y, Kim D, Lee H, Khim JS, Kim B, Yang D, Pathiraja D, Choi IG, Kim JJInt J Syst Evol Microbiol10.1099/ijsem.0.0049302021Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Fatty Acids/chemistry, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, Sphingomonadaceae, UbiquinoneTranscriptome

Reference

@idauthorscataloguedoi/urltitle
7571Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18518)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18518
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
60912Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 56309)https://www.ccug.se/strain?id=56309
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
83322Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID343461.1StrainInfo: A central database for resolving microbial strain identifiers