Strain identifier

BacDive ID: 13114

Type strain: Yes

Species: Pseudomonas lutea

Strain Designation: OK2

Strain history: <- E. Velázquez Pérez <- A. Peix

NCBI tax ID(s): 243924 (species)

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General

@ref: 6858

BacDive-ID: 13114

DSM-Number: 17257

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

description: Pseudomonas lutea OK2 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 243924
  • Matching level: species

strain history

  • @ref: 6858
  • history: <- E. Velázquez Pérez <- A. Peix

doi: 10.13145/bacdive13114.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pseudomonadales
  • family: Pseudomonadaceae
  • genus: Pseudomonas
  • species: Pseudomonas lutea
  • full scientific name: Pseudomonas lutea Peix et al. 2004

@ref: 6858

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas lutea

full scientific name: Pseudomonas lutea Peix et al. 2004

strain designation: OK2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30122negative1.4 µm0.75 µmrod-shapedyes
69480yes98.171
69480negative100

pigmentation

  • @ref: 30122
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6858TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
6858NUTRIENT 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
6858positivegrowth30mesophilic
30122positiveoptimum25mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 30122
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30122yes
69481no100
69480no99.973

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
30122168082-dehydro-D-gluconate+carbon source
3012215963ribitol+carbon source
3012222599arabinose+carbon source
3012218403L-arabitol+carbon source
3012227689decanoate+carbon source
3012216947citrate+carbon source
3012228757fructose+carbon source
3012233984fucose+carbon source
3012228260galactose+carbon source
3012224265gluconate+carbon source
3012217234glucose+carbon source
3012217754glycerol+carbon source
3012225115malate+carbon source
3012229864mannitol+carbon source
3012237684mannose+carbon source
3012228053melibiose+carbon source
3012233942ribose+carbon source
3012217151xylitol+carbon source
3012218222xylose+carbon source
301224853esculin+hydrolysis

enzymes

  • @ref: 30122
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

  • @ref: 6858
  • sample type: soil
  • country: Spain
  • origin.country: ESP
  • continent: Europe

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Safety information

risk assessment

  • @ref: 6858
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6858
  • description: Pseudomonas lutea strain OK2 16S ribosomal RNA gene, partial sequence
  • accession: AY364537
  • length: 1531
  • database: ena
  • NCBI tax ID: 243924

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas lutea LMG 21974GCA_900110795contigncbi243924
66792Pseudomonas lutea DSM 17257243924.3wgspatric243924
66792Pseudomonas lutea DSM 17257GCA_000759445contigncbi243924

GC content

  • @ref: 6858
  • GC-content: 59.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes92.613no
gram-positiveno97.922no
anaerobicno97.483yes
aerobicyes89.514no
halophileno92.906no
spore-formingno94.399no
glucose-utilyes95.273no
flagellatedyes76.941no
thermophileno99.864no
glucose-fermentno90.299no

External links

@ref: 6858

culture collection no.: DSM 17257, CECT 5822, LMG 21974, CCM 8844

straininfo link

  • @ref: 82322
  • straininfo: 100197

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15143034Pseudomonas lutea sp. nov., a novel phosphate-solubilizing bacterium isolated from the rhizosphere of grasses.Peix A, Rivas R, Santa-Regina I, Mateos PF, Martinez-Molina E, Rodriguez-Barrueco C, Velazquez EInt J Syst Evol Microbiol10.1099/ijs.0.02966-02004Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Molecular Sequence Data, Phenotype, Phosphates/metabolism, Phylogeny, Poaceae/microbiology, Pseudomonas/*classification/genetics/*isolation & purification/metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Solubility, SpainGenetics
Genetics27555890High quality draft genome sequence of the type strain of Pseudomonas lutea OK2(T), a phosphate-solubilizing rhizospheric bacterium.Kwak Y, Park GS, Shin JHStand Genomic Sci10.1186/s40793-016-0173-72016
Phylogeny29867824Discovery of Phloeophagus Beetles as a Source of Pseudomonas Strains That Produce Potentially New Bioactive Substances and Description of Pseudomonas bohemica sp. nov.Saati-Santamaria Z, Lopez-Mondejar R, Jimenez-Gomez A, Diez-Mendez A, Vetrovsky T, Igual JM, Velazquez E, Kolarik M, Rivas R, Garcia-Fraile PFront Microbiol10.3389/fmicb.2018.009132018

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
6858Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17257)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17257
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
30122Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2647628776041
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
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
82322Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100197.1StrainInfo: A central database for resolving microbial strain identifiers