Strain identifier

BacDive ID: 140982

Type strain: Yes

Species: Pseudomonas wadenswilerensis

Strain Designation: ID2

Strain history: CIP <- 2017, CCOS <- M. Opoku, ZHAW, Wädenswil, Switzerland: strain ID2

NCBI tax ID(s): 1785161 (species)

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General

@ref: 43871

BacDive-ID: 140982

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

description: Pseudomonas wadenswilerensis ID2 is an aerobe, chemoorganotroph, Gram-negative bacterium that was isolated from soil sample of Reidholz forest between the cities Wädenswil and Richterswil, Switzerland.

NCBI tax id

  • NCBI tax id: 1785161
  • Matching level: species

strain history

  • @ref: 123898
  • history: CIP <- 2017, CCOS <- M. Opoku, ZHAW, Wädenswil, Switzerland: strain ID2

doi: 10.13145/bacdive140982.20230509.8.1

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 wadenswilerensis
  • full scientific name: Pseudomonas wadenswilerensis Frasson et al. 2017

@ref: 43871

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas wadenswilerensis

strain designation: ID2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43871negative1.0-2.2 µm0.5-0.9 µmrod-shapedyes
69480yes96.898
69480negative99.993
123898negativerod-shaped

pigmentation

  • @ref: 43871
  • production: no
  • name: Fluorescent pigment

Culture and growth conditions

culture medium

@refnamegrowthlink
43871King's medium Byes
43871LB (Luria-Bertani) MEDIUMyes
43871Reasoner's 2A agar (R2A)yes
123898CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
43871positivegrowth4-37
43871positiveoptimum25-30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 43871
  • oxygen tolerance: aerobe

nutrition type

  • @ref: 43871
  • type: chemoorganotroph

spore formation

@refspore formationconfidence
43871no
69481no100
69480no99.997

halophily

  • @ref: 43871
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-6 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4387118401phenylacetate-assimilation
4387127689decanoate-carbon source
4387118333D-arabitol-carbon source
4387118024D-galacturonic acid-carbon source
4387115748D-glucuronate-carbon source
4387116899D-mannitol-carbon source
4387133801D-saccharate-carbon source
4387117234glucose-carbon source
4387130849L-arabinose-carbon source
4387125115malate-carbon source
4387130860methylmalonic acid-carbon source
4387153258sodium citrate-carbon source
4387117992sucrose-carbon source
43871309162-oxoglutarate+carbon source
43871182404-hydroxy-L-proline+carbon source
43871181014-hydroxyphenylacetic acid+carbon source
4387130089acetate+carbon source
4387117925alpha-D-glucose+carbon source
438718295beta-hydroxybutyrate+carbon source
4387173706bromosuccinate+carbon source
4387116383cis-aconitate+carbon source
4387116947citrate+carbon source
4387115570D-alanine+carbon source
4387115824D-fructose+carbon source
438718391D-gluconate+carbon source
4387116523D-serine+carbon source
4387117126DL-carnitine+carbon source
4387124996lactate+carbon source
4387116000ethanolamine+carbon source
4387116865gamma-aminobutyric acid+carbon source
4387132323glucuronamide+carbon source
4387117754glycerol+carbon source
4387117596inosine+carbon source
4387116977L-alanine+carbon source
4387173786L-alanylglycine+carbon source
4387117196L-asparagine+carbon source
4387129991L-aspartate+carbon source
4387129985L-glutamate+carbon source
4387115971L-histidine+carbon source
4387115603L-leucine+carbon source
4387117203L-proline+carbon source
4387118183L-pyroglutamic acid+carbon source
4387117115L-serine+carbon source
4387151850methyl pyruvate+carbon source
43871506227N-acetylglucosamine+carbon source
4387173784glycyl-l-glutamate+carbon source
4387117272propionate+carbon source
4387117148putrescine+carbon source
4387126490quinate+carbon source
4387130031succinate+carbon source
4387153423tween 40+carbon source
4387153426tween 80+carbon source
4387127248urocanic acid+carbon source
43871skimmed milk+hydrolysis
4387117234glucose+oxidation
4387128053melibiose+oxidation
4387117632nitrate+reduction

metabolite production

  • @ref: 43871
  • Chebi-ID: 31624
  • metabolite: fluorescein
  • production: no

enzymes

@refvalueactivityec
43871cytochrome oxidase+1.9.3.1
43871catalase+1.11.1.6
43871gelatinase+
43871arginine dihydrolase+3.5.3.6
43871tryptophan deaminase+4.1.99.1
43871esterase Lipase (C 8)+
43871leucine arylamidase+3.4.11.1
43871acid phosphatase+3.1.3.2
43871naphthol-AS-BI-phosphohydrolase+

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43871C10:0 3OH0.88
    43871C12:00.21
    43871C12:0 2OH0.49
    43871C12:1 3OH0.26
    43871C14:01.08
    43871C16:038.38
    43871C16:1ω5c0.13
    43871C16:1ω7c / C16:1ω6c20.89
    43871C17:0 cyclo22.85
    43871C18:00.31
    43871C18:1ω7c10.14
    43871C19:0ω8c cyclo0.24
  • type of FA analysis: whole cell analysis
  • incubation medium: Tryptic soy agar
  • agar/liquid: agar
  • incubation temperature: 28
  • incubation time: 2
  • software version: Sherlock 6.1
  • library/peak naming table: ITSA1 1.10
  • system: MIS MIDI
  • instrument: Hewlett Packard HP 6890 gas chromatograph
  • method/protocol: Sasser, 1990
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureisolation date
43871soil sample of Reidholz forest between the cities Wädenswil and Richterswil, SwitzerlandReidholz forestSwitzerlandCHEEurope47.21678.68333King's B medium
123898Environment, Forest soilWädenswilSwitzerlandCHEEurope2014-06-30

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil

Safety information

risk assessment

  • @ref: 123898
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 43871
  • description: 16S rRNA gene sequence
  • accession: LT009706
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas wadenswilerensis CCOS 864GCA_900497695contigncbi1785161
66792Pseudomonas wadenswilerensis strain CCOS 8641785161.3wgspatric1785161

GC content

  • @ref: 43871
  • GC-content: 62.1
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes90.798yes
gram-positiveno98.374yes
anaerobicno98.329yes
aerobicyes95.182yes
halophileno86.635no
spore-formingno95.404yes
thermophileno99.888yes
glucose-utilyes93.892no
flagellatedyes85.24no
glucose-fermentno88.408no

External links

@ref: 43871

culture collection no.: LMG 29327, CCOS 864, CIP 111526

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny28820109Pseudomonas wadenswilerensis sp. nov. and Pseudomonas reidholzensis sp. nov., two novel species within the Pseudomonas putida group isolated from forest soil.Frasson D, Opoku M, Picozzi T, Torossi T, Balada S, Smits THM, Hilber UInt J Syst Evol Microbiol10.1099/ijsem.0.0020352017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Multilocus Sequence Typing, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, Pseudomonas/*classification/genetics/isolation & purification, Pseudomonas putida, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Switzerland, Ubiquinone/chemistryTranscriptome
Genetics30533735High-Quality Draft Genome Sequence of Pseudomonas wadenswilerensis CCOS 864(T).Rutz D, Frasson D, Sievers M, Blom J, Rezzonico F, Pothier JF, Smits THMMicrobiol Resour Announc10.1128/MRA.01059-182018
Phylogeny31483752Pseudomonas tructae sp. nov., novel species isolated from rainbow trout kidney.Oh WT, Jun JW, Giri SS, Yun S, Kim HJ, Kim SG, Kim SW, Kang JW, Han SJ, Kwon J, Kim JH, Smits THM, Park SCInt J Syst Evol Microbiol10.1099/ijsem.0.0036962019Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Kidney/*microbiology, Multilocus Sequence Typing, Oncorhynchus mykiss/*microbiology, Phosphatidylethanolamines/chemistry, *Phylogeny, Pseudomonas/*classification/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
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
43871David Frasson, Michael Opoku, Tara Picozzi, Tanja Torossi, Stefanie Balada, Theo H. M. Smits, Urs HilberPseudomonas wadenswilerensis sp. nov. and Pseudomonas reidholzensis sp. nov., two novel species within the Pseudomonas putida group isolated from forest soil10.1099/ijsem.0.002035IJSEM 67: 2853-2861 201728820109
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
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
123898Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20111526Collection of Institut Pasteur (CIP 111526)