Strain identifier

BacDive ID: 13840

Type strain: Yes

Species: Tranquillimonas alkanivorans

Strain Designation: A34

Strain history: Y. Kasai A34.

NCBI tax ID(s): 441119 (species)

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General

@ref: 8165

BacDive-ID: 13840

DSM-Number: 19547

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

description: Tranquillimonas alkanivorans A34 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from seawater.

NCBI tax id

  • NCBI tax id: 441119
  • Matching level: species

strain history

@refhistory
8165<- Y. Kasai, Marine Biotechnol. Inst., Kamaishi, Japan; A34 <- T. U. Harwati
67770Y. Kasai A34.

doi: 10.13145/bacdive13840.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Tranquillimonas
  • species: Tranquillimonas alkanivorans
  • full scientific name: Tranquillimonas alkanivorans Harwati et al. 2008

@ref: 8165

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Tranquillimonas

species: Tranquillimonas alkanivorans

full scientific name: Tranquillimonas alkanivorans Harwati et al. 2008

strain designation: A34

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32631negative1.7-2.8 µm0.2-0.5 µmrod-shapedno
69480negative99.991

pigmentation

  • @ref: 32631
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 8165
  • 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
8165positivegrowth37mesophilic
32631positivegrowth10-50
32631positiveoptimum43thermophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
32631positivegrowth6.5-9.5alkaliphile
32631positiveoptimum8.5

Physiology and metabolism

oxygen tolerance

  • @ref: 32631
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
32631no
69481no94
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
32631NaClpositivegrowth01-13 %
32631NaClpositiveoptimum2 %

observation

@refobservation
32631aggregates in chains
67770quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3263122599arabinose+carbon source
3263122653asparagine+carbon source
3263135391aspartate+carbon source
3263116947citrate+carbon source
3263115740formate+carbon source
3263128757fructose+carbon source
3263133984fucose+carbon source
3263128260galactose+carbon source
3263124265gluconate+carbon source
3263117234glucose+carbon source
3263129987glutamate+carbon source
3263124996lactate+carbon source
3263117716lactose+carbon source
3263125017leucine+carbon source
3263117306maltose+carbon source
3263129864mannitol+carbon source
3263118257ornithine+carbon source
3263128044phenylalanine+carbon source
3263126271proline+carbon source
3263115361pyruvate+carbon source
3263116634raffinose+carbon source
3263126546rhamnose+carbon source
3263117822serine+carbon source
3263130911sorbitol+carbon source
3263117992sucrose+carbon source
3263126986threonine+carbon source
3263127082trehalose+carbon source
3263153423tween 40+carbon source
3263153426tween 80+carbon source
3263117632nitrate+reduction

enzymes

@refvalueactivityec
32631catalase+1.11.1.6
32631cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8165seawaterJava, Semarang PortIndonesiaIDNAsia
67770Seawater in Semarang PortIndonesiaIDNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_9367.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_4509;97_5480;98_6912;99_9367&stattab=map
  • Last taxonomy: Tranquillimonas alkanivorans subclade
  • 16S sequence: AB302386
  • Sequence Identity:
  • Total samples: 480
  • soil counts: 114
  • aquatic counts: 341
  • animal counts: 19
  • plant counts: 6

Safety information

risk assessment

  • @ref: 8165
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8165
  • description: Tranquillimonas alkanivorans gene for 16S rRNA, partial sequence
  • accession: AB302386
  • length: 1364
  • database: ena
  • NCBI tax ID: 441119

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Tranquillimonas alkanivorans strain DSM 19547441119.6wgspatric441119
66792Tranquillimonas alkanivorans DSM 195472622736594draftimg441119
67770Tranquillimonas alkanivorans DSM 19547GCA_900115595scaffoldncbi441119

GC content

@refGC-contentmethod
816569.1high performance liquid chromatography (HPLC)
3263169.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno94no
gram-positiveno98.523yes
anaerobicno95.398yes
halophileyes80.498no
spore-formingno94.996yes
glucose-utilyes89.827yes
aerobicyes89.623yes
flagellatedno80.078no
thermophileno92.499no
motileyes65.053no
glucose-fermentno92.886no

External links

@ref: 8165

culture collection no.: DSM 19547, JCM 14836

straininfo link

  • @ref: 83016
  • straininfo: 404762

literature

  • topic: Phylogeny
  • Pubmed-ID: 18768615
  • title: Tranquillimonas alkanivorans gen. nov., sp. nov., an alkane-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.0.65817-0
  • year: 2008
  • mesh: Alkanes/*metabolism, Bacterial Typing Techniques, Base Composition, Catalase/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Indonesia, Locomotion, Molecular Sequence Data, Nitrates/metabolism, Nitrites/metabolism, Oxidoreductases/metabolism, Phylogeny, Pigments, Biological/biosynthesis, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/metabolism, Seawater/*microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
8165Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19547)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19547
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
32631Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2884228776041
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
83016Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID404762.1StrainInfo: A central database for resolving microbial strain identifiers