Strain identifier

BacDive ID: 133856

Type strain: Yes

Species: Dokdonella immobilis

Strain Designation: LM2-5

Strain history: Z.-P. Liu LM2-5.

NCBI tax ID(s): 578942 (species)

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General

@ref: 30686

BacDive-ID: 133856

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

description: Dokdonella immobilis LM2-5 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from bioreactor.

NCBI tax id

  • NCBI tax id: 578942
  • Matching level: species

strain history

  • @ref: 67770
  • history: Z.-P. Liu LM2-5.

doi: 10.13145/bacdive133856.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Lysobacterales
  • family: Rhodanobacteraceae
  • genus: Dokdonella
  • species: Dokdonella immobilis
  • full scientific name: Dokdonella immobilis Liu et al. 2013

@ref: 30686

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Lysobacterales

family: Rhodanobacteraceae

genus: Dokdonella

species: Dokdonella immobilis

strain designation: LM2-5

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotilityconfidence
30686negative4 µmrod-shapedno
69480negative99.997

pigmentation

  • @ref: 30686
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
30686positivegrowth16-37
30686positiveoptimum25mesophilic
67770positivegrowth25mesophilic

culture pH

@refabilitytypepH
30686positivegrowth6.5-7
30686positiveoptimum6.75

Physiology and metabolism

oxygen tolerance

  • @ref: 30686
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30686no
69481no94
69480no99.981

halophily

@refsaltgrowthtested relationconcentration
30686NaClpositivegrowth0-2 %
30686NaClpositiveoptimum1 %

observation

@refobservation
30686aggregates in clumps
67770quinones: Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3068624265gluconate+carbon source
306864853esculin+hydrolysis

enzymes

@refvalueactivityec
30686acid phosphatase+3.1.3.2
30686alkaline phosphatase+3.1.3.1
30686gelatinase+
30686cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample type
30686bioreactor
67770Activated sludge in a sequencing batch reactor use for the treatment of triphenylmethane dye effluent

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Bioreactor

taxonmaps

  • @ref: 69479
  • File name: preview.99_108047.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_13362;97_16251;98_20131;99_108047&stattab=map
  • Last taxonomy: Dokdonella immobilis subclade
  • 16S sequence: FJ455531
  • Sequence Identity:
  • Total samples: 2693
  • soil counts: 620
  • aquatic counts: 1781
  • animal counts: 159
  • plant counts: 133

Sequence information

16S sequences

  • @ref: 30686
  • description: Dokdonella immobilis strain LM2-5 16S ribosomal RNA gene, partial sequence
  • accession: FJ455531
  • length: 1500
  • database: nuccore
  • NCBI tax ID: 578942

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dokdonella immobilis strain CGMCC 1.7659578942.3wgspatric578942
66792Dokdonella immobilis CGMCC 1.76592667527410draftimg578942
67770Dokdonella immobilis CGMCC 1.7659GCA_900115085scaffoldncbi578942

GC content

@refGC-contentmethod
3068666.7
6777066.7thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno94no
gram-positiveno98.099yes
anaerobicno98.705yes
halophileno92.861yes
spore-formingno97.024no
glucose-utilyes78.583no
thermophileno99.549no
flagellatedno97.179no
aerobicyes87.66yes
motileno87.495yes
glucose-fermentno91.332no

External links

@ref: 30686

culture collection no.: CGMCC 1.7659, JCM 15763

literature

  • topic: Phylogeny
  • Pubmed-ID: 22888194
  • title: Dokdonella immobilis sp. nov., isolated from a batch reactor for the treatment of triphenylmethane dye effluent.
  • authors: Liu Y, Jin JH, Liu HC, Liu ZP
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.042002-0
  • year: 2012
  • mesh: Bacterial Typing Techniques, Base Composition, Coloring Agents/metabolism, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Trityl Compounds/*metabolism, *Waste Disposal, Fluid, Xanthomonadaceae/*classification/genetics/isolation & purification/metabolism
  • topic2: Metabolism

Reference

@idauthorstitledoi/urlID_cross_referencepubmedjournal
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
30686Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172701728776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic 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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1