Strain identifier

BacDive ID: 13841

Type strain: Yes

Species: Tropicimonas isoalkanivorans

Strain Designation: B51

Strain history: Y. Kasai B51.

NCBI tax ID(s): 441112 (species)

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General

@ref: 8166

BacDive-ID: 13841

DSM-Number: 19548

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

description: Tropicimonas isoalkanivorans B51 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from Seawater.

NCBI tax id

  • NCBI tax id: 441112
  • Matching level: species

strain history

@refhistory
8166<- Y. Kasai, Marine Biotechnol. Inst., Kamaishi, Japan; B51 <- T. U. Harwati
67770Y. Kasai B51.

doi: 10.13145/bacdive13841.20230509.8.1

Name and taxonomic classification

LPSN

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

@ref: 8166

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Tropicimonas

species: Tropicimonas isoalkanivorans

full scientific name: Tropicimonas isoalkanivorans Harwati et al. 2009

strain designation: B51

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32635negative0.75 µm0.4 µmrod-shapedyes
69480negative99.999

Culture and growth conditions

culture medium

  • @ref: 8166
  • 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
8166positivegrowth37mesophilic
32635positivegrowth10-46
32635positiveoptimum37mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepH
32635positivegrowth5.5-8.0
32635positiveoptimum7.6

Physiology and metabolism

oxygen tolerance

  • @ref: 32635
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no93
69480no99.994

halophily

@refsaltgrowthtested relationconcentration
32635NaClpositivegrowth01-06 %
32635NaClpositiveoptimum3 %

observation

@refobservation
32635aggregates in clumps
67770quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3263515963ribitol+carbon source
3263516449alanine+carbon source
3263522599arabinose+carbon source
3263517057cellobiose+carbon source
3263523652dextrin+carbon source
3263528757fructose+carbon source
3263528260galactose+carbon source
3263517234glucose+carbon source
3263529987glutamate+carbon source
3263517754glycerol+carbon source
3263517306maltose+carbon source
3263529864mannitol+carbon source
3263537684mannose+carbon source
3263528053melibiose+carbon source
3263526271proline+carbon source
3263517822serine+carbon source
3263530911sorbitol+carbon source
3263517992sucrose+carbon source
3263517748thymidine+carbon source
3263527082trehalose+carbon source
3263516704uridine+carbon source
3263517151xylitol+carbon source

enzymes

  • @ref: 32635
  • value: cytochrome oxidase
  • activity: +
  • ec: 1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8166SeawaterJava, Semarang PortIndonesiaIDNAsia
67770Seawater in Semarang PortJavaIndonesiaIDNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_143230.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_5771;97_6945;98_95103;99_143230&stattab=map
  • Last taxonomy: Tropicimonas isoalkanivorans subclade
  • 16S sequence: AB302379
  • Sequence Identity:
  • Total samples: 4
  • soil counts: 1
  • aquatic counts: 3

Safety information

risk assessment

  • @ref: 8166
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8166
  • description: Tropicimonas isoalkanivorans gene for 16S rRNA, partial sequence
  • accession: AB302379
  • length: 1335
  • database: ena
  • NCBI tax ID: 441112

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Tropicimonas isoalkanivorans strain DSM 19548441112.6wgspatric441112
66792Tropicimonas isoalkanivorans DSM 195482615840715draftimg441112
67770Tropicimonas isoalkanivorans DSM 19548GCA_900112335scaffoldncbi441112

GC content

@refGC-contentmethod
816666.5high performance liquid chromatography (HPLC)
3263566.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno93no
gram-positiveno98.133yes
anaerobicno93.331yes
halophileno54.655no
spore-formingno96.95no
glucose-utilyes89.107yes
aerobicyes68.958yes
flagellatedno81.949no
thermophileno98.068no
motileyes52.449yes
glucose-fermentno90.676no

External links

@ref: 8166

culture collection no.: DSM 19548, JCM 14837

straininfo link

  • @ref: 83017
  • straininfo: 402760

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19196783Tropicimonas isoalkanivorans gen. nov., sp. nov., a branched-alkane-degrading bacterium isolated from Semarang Port in Indonesia.Harwati TU, Kasai Y, Kodama Y, Susilaningsih D, Watanabe KInt J Syst Evol Microbiol10.1099/ijs.0.65822-02009Alkanes/*metabolism, Microscopy, Electron, Transmission, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/metabolism/ultrastructure, Seawater/*microbiology, Species SpecificityMetabolism
Phylogeny21551334Tropicimonas aquimaris sp. nov., isolated from seawater, and emended description of the genus Tropicimonas Harwati et al. 2009.Oh KH, Choi WC, Jung YT, Kang SJ, Oh TK, Yoon JHInt J Syst Evol Microbiol10.1099/ijs.0.029371-02011Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature, Ubiquinone/analysisGenetics
Phylogeny28866994Psychromarinibacter halotolerans gen. nov., sp. nov., isolated from seawater of the Yellow Sea.Qiao Y, Wang Y, Yang X, Liu J, Wu Y, Zhang XHInt J Syst Evol Microbiol10.1099/ijsem.0.0021592017Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Oceans and Seas, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
8166Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19548)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19548
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
32635Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2884628776041
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
83017Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402760.1StrainInfo: A central database for resolving microbial strain identifiers