Strain identifier

BacDive ID: 13842

Type strain: Yes

Species: Tropicibacter naphthalenivorans

Strain Designation: C02

Strain history: Y. Kasai C02.

NCBI tax ID(s): 441103 (species)

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General

@ref: 8176

BacDive-ID: 13842

DSM-Number: 19561

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

description: Tropicibacter naphthalenivorans C02 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from Seawater.

NCBI tax id

  • NCBI tax id: 441103
  • Matching level: species

strain history

@refhistory
8176<- Y. Kasai, Marine Biotechnol. Inst., Kamaishi, Japan; C02 <- T. U. Harwati
67770Y. Kasai C02.

doi: 10.13145/bacdive13842.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Tropicibacter
  • species: Tropicibacter naphthalenivorans
  • full scientific name: Tropicibacter naphthalenivorans Harwati et al. 2009

@ref: 8176

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Tropicibacter

species: Tropicibacter naphthalenivorans

full scientific name: Tropicibacter naphthalenivorans Harwati et al. 2009

strain designation: C02

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32634negative2.25 µm0.4 µmrod-shapedyes
69480negative99.998

pigmentation

  • @ref: 32634
  • production: no

Culture and growth conditions

culture medium

  • @ref: 8176
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
8176positivegrowth37mesophilic
32634positivegrowth10-43
32634positiveoptimum37mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
32634positivegrowth6.5-8.5alkaliphile
32634positiveoptimum7.6

Physiology and metabolism

oxygen tolerance

  • @ref: 32634
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.957

halophily

@refsaltgrowthtested relationconcentration
32634NaClpositivegrowth01-15 %
32634NaClpositiveoptimum5 %

observation

@refobservation
32634aggregates in clumps
67770quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3263430089acetate+carbon source
3263416449alanine+carbon source
3263422599arabinose+carbon source
3263435391aspartate+carbon source
3263417057cellobiose+carbon source
3263423652dextrin+carbon source
3263428757fructose+carbon source
3263417234glucose+carbon source
3263417596inosine+carbon source
3263417716lactose+carbon source
3263417306maltose+carbon source
3263437684mannose+carbon source
3263428053melibiose+carbon source
3263426271proline+carbon source
3263426546rhamnose+carbon source
3263417822serine+carbon source
3263430911sorbitol+carbon source
3263430031succinate+carbon source
3263417992sucrose+carbon source
3263427082trehalose+carbon source
3263453426tween 80+carbon source
3263416704uridine+carbon source
3263417151xylitol+carbon source
3263417632nitrate+reduction

metabolite production

  • @ref: 32634
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

  • @ref: 32634
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
32634acid phosphatase+3.1.3.2
32634alpha-galactosidase+3.2.1.22
32634cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8176SeawaterJava, Semarang PortIndonesiaIDNAsia
67770Seawater in Semarang PortJavaIndonesiaIDNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_6756.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_3192;97_3916;98_4983;99_6756&stattab=map
  • Last taxonomy: Tropicibacter naphthalenivorans subclade
  • 16S sequence: AB302370
  • Sequence Identity:
  • Total samples: 53
  • soil counts: 2
  • aquatic counts: 51

Safety information

risk assessment

  • @ref: 8176
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8176
  • description: Tropicibacter naphthalenivorans gene for 16S rRNA, partial sequence
  • accession: AB302370
  • length: 1363
  • database: ena
  • NCBI tax ID: 441103

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Tropicibacter naphthalenivorans strain CECT 7648441103.7wgspatric441103
66792Tropicibacter naphthalenivorans strain DSM 19561441103.4wgspatric441103
66792Tropicibacter naphthalenivorans DSM 195612622736506draftimg441103
66792Tropicibacter naphthalenivorans CECT 76482713896963draftimg441103
67770Tropicibacter naphthalenivorans CECT 7648GCA_001458375scaffoldncbi441103
67770Tropicibacter naphthalenivorans DSM 19561GCA_900176475scaffoldncbi441103

GC content

@refGC-contentmethod
817664.6high performance liquid chromatography (HPLC)
3263464.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.767no
anaerobicno95.664yes
halophileyes72.7no
spore-formingno96.842no
glucose-utilyes80.217no
aerobicyes85.839yes
flagellatedno77.76no
thermophileno94.965yes
motileyes70.382yes
glucose-fermentno91.794no

External links

@ref: 8176

culture collection no.: DSM 19561, CECT 7648, JCM 14838

straininfo link

  • @ref: 83018
  • straininfo: 360723

literature

  • topic: Phylogeny
  • Pubmed-ID: 19196784
  • title: Tropicibacter naphthalenivorans gen. nov., sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from Semarang Port in Indonesia.
  • authors: Harwati TU, Kasai Y, Kodama Y, Susilaningsih D, Watanabe K
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65821-0
  • year: 2009
  • mesh: Fatty Acids/analysis, Indonesia, Molecular Sequence Data, Phenotype, Phylogeny, Polycyclic Aromatic Hydrocarbons/*metabolism, RNA, Ribosomal, 16S, Rhodobacteraceae/chemistry/*classification/genetics/metabolism/ultrastructure, Seawater/*microbiology, Species Specificity
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
8176Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19561)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19561
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
32634Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2884528776041
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
83018Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID360723.1StrainInfo: A central database for resolving microbial strain identifiers