Strain identifier

BacDive ID: 13154

Type strain: Yes

Species: Pseudomonas protegens

Strain Designation: CHA0

Strain history: <- G. Défago, ETH Zuerich; CHA0

NCBI tax ID(s): 380021 (species)

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General

@ref: 7886

BacDive-ID: 13154

DSM-Number: 19095

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Pseudomonas protegens CHA0 is a mesophilic bacterium that was isolated from soil suppressing black root rot of tobacco .

NCBI tax id

  • NCBI tax id: 380021
  • Matching level: species

strain history

  • @ref: 7886
  • history: <- G. Défago, ETH Zuerich; CHA0

doi: 10.13145/bacdive13154.20230509.8.1

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 protegens
  • full scientific name: Pseudomonas protegens Ramette et al. 2012

@ref: 7886

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas protegens

full scientific name: Pseudomonas protegens Ramette et al. 2012

strain designation: CHA0

type strain: yes

Culture and growth conditions

culture medium

@refnamegrowthlink
7886LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium381.pdf
7886NUTRIENT AGAR (DSMZ Medium 1)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1.pdf
7886TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf
7886TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium545.pdf

culture temp

  • @ref: 7886
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

compound production

@refcompound
78862,4 diacetylphloroglucinol
7886pyoluteorin

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate+assimilation
6836924265gluconate+assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose+assimilation
683695291gelatin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine+hydrolysis
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase+
68369urease-3.5.1.5
68369arginine dihydrolase+3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7886--++-+/-+-+-+++-++-++++
7886---+--+-+-+++-++-++++
7886---+--+-+-+++-++-++++
7886--++--+-+-+++-++-++++

Isolation, sampling and environmental information

isolation

  • @ref: 7886
  • sample type: soil suppressing black root rot of tobacco (Nicotiana glutinosa)
  • host species: Nicotiana glutinosa
  • geographic location: Morens
  • country: Switzerland
  • origin.country: CHE
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_926.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_61;97_89;98_365;99_926&stattab=map
  • Last taxonomy: Pseudomonas
  • 16S sequence: AJ278812
  • Sequence Identity:
  • Total samples: 28709
  • soil counts: 5812
  • aquatic counts: 6618
  • animal counts: 11260
  • plant counts: 5019

Safety information

risk assessment

  • @ref: 7886
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7886
  • description: Pseudomonas protegens 16S rRNA gene, type strain CHA0T
  • accession: AJ278812
  • length: 1531
  • database: ena
  • NCBI tax ID: 380021

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas protegens CHA0GCA_900560965completencbi1124983
66792Pseudomonas protegens CHA0GCA_000397205completencbi1124983
66792Pseudomonas protegens CHA01124983.3completepatric1124983
66792Pseudomonas protegens CHA01124983.33completepatric1124983
66792Pseudomonas protegens CHA02554235341completeimg1124983
66792Pseudomonas protegens CHA02917070673completeimg1124983

GC content

  • @ref: 7886
  • GC-content: 60.1
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes87.417no
gram-positiveno98.367no
anaerobicno98.462no
aerobicyes93.681no
halophileno91.079no
spore-formingno94.42no
thermophileno99.878yes
glucose-utilyes94.388yes
motileyes91.908no
glucose-fermentno88.791no

External links

@ref: 7886

culture collection no.: DSM 19095, CCOS 2, CFBP 6595

straininfo link

  • @ref: 82362
  • straininfo: 380598

literature

  • topic: Phylogeny
  • Pubmed-ID: 21392918
  • title: Pseudomonas protegens sp. nov., widespread plant-protecting bacteria producing the biocontrol compounds 2,4-diacetylphloroglucinol and pyoluteorin.
  • authors: Ramette A, Frapolli M, Fischer-Le Saux M, Gruffaz C, Meyer JM, Defago G, Sutra L, Moenne-Loccoz Y
  • journal: Syst Appl Microbiol
  • DOI: 10.1016/j.syapm.2010.10.005
  • year: 2011
  • mesh: Anti-Bacterial Agents/*metabolism, Bacterial Proteins/genetics, Base Sequence, DNA Fingerprinting, DNA Gyrase/genetics, DNA, Bacterial/genetics, Genes, Bacterial/genetics, Gossypium/microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Pest Control, Biological, Phenols/*metabolism, Phenotype, Phloroglucinol/analogs & derivatives/metabolism, Phylogeny, Plant Diseases/microbiology/*prevention & control, Plant Roots/microbiology, Pseudomonas/*classification/genetics/metabolism, Pyrroles/*metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Siderophores/classification, Soil Microbiology, Tobacco/microbiology, Triticum/microbiology
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitle
7886Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19095)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19095
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
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)
68369Automatically annotated from API 20NE
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
82362Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID380598.1StrainInfo: A central database for resolving microbial strain identifiers