Strain identifier

BacDive ID: 133074

Type strain: Yes

Species: Polynucleobacter wuianus

Strain Designation: QLW-P1FAT50C-4

Strain history: CIP <- 2016, DSMZ <- M.W. Hahn, Innsbruck Univ., Mondsee, Austria: strain QLW-P1FAT50C-4

NCBI tax ID(s): 1743168 (species)

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General

@ref: 24862

BacDive-ID: 133074

DSM-Number: 24008

keywords: genome sequence, 16S sequence, Bacteria, aerobe, chemoorganotroph, mesophilic, rod-shaped, colony-forming

description: Polynucleobacter wuianus QLW-P1FAT50C-4 is an aerobe, chemoorganotroph, mesophilic bacterium that forms circular colonies and was isolated from shallow acidic freshwater pond.

NCBI tax id

  • NCBI tax id: 1743168
  • Matching level: species

strain history

@refhistory
24862<- M. W. Hahn, Austrian Academy of Science, Inst. Limnology, Mondsee; QLW-P1FAT50C-4 <- Q. L. Wu, Austrian Academy of Sci., Inst. Limnology
123963CIP <- 2016, DSMZ <- M.W. Hahn, Innsbruck Univ., Mondsee, Austria: strain QLW-P1FAT50C-4

doi: 10.13145/bacdive133074.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Burkholderiaceae
  • genus: Polynucleobacter
  • species: Polynucleobacter wuianus
  • full scientific name: Polynucleobacter wuianus Hahn et al. 2017

@ref: 24862

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Polynucleobacter

species: Polynucleobacter wuianus

full scientific name: Polynucleobacter wuianus Hahn et al. 2017

strain designation: QLW-P1FAT50C-4

type strain: yes

Morphology

cell morphology

@refcell lengthcell widthcell shapemotilitygram stainconfidence
252030.6-1.7 µm0.3-0.6 µmrod-shapedno
69480negative99.992
69480no94.074
123963rod-shapednonegative

colony morphology

  • @ref: 25203
  • colony color: non-pigmented
  • colony shape: circular
  • medium used: nutrient broth soyotone yeast extract (NSY) medium

multimedia

  • @ref: 24862
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_24008.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
25203nutrient broth soyotone yeast extract (NSY) mediumyes
24862R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
24862NSY-MEDIUM FOR POLYNUCLEOBACTER (DSMZ Medium 1167)yeshttps://mediadive.dsmz.de/medium/1167Name: NSY-MEDIUM FOR POLYNUCLEOBACTER (DSMZ Medium 1167) Composition: Soy peptone 1.0 g/l Nutrient broth 1.0 g/l Yeast extract 1.0 g/l MgSO4 x 7 H2O 0.075 g/l Ca(NO3)2 x 4 H2O 0.043 g/l NaHCO3 0.016 g/l KCl 0.005 g/l K2HPO4 x 3 H2O 0.0037 g/l Na2-EDTA 5e-05 g/l H3BO3 3e-05 g/l CoCl2 x 6 H2O 2e-05 g/l FeSO4 x 7 H2O 2e-05 g/l ZnSO4 x 7 H2O 1e-05 g/l MnCl2 x 4 H2O 3e-06 g/l Na2MoO4 x 2 H2O 3e-06 g/l NiCl2 x 6 H2O 2e-06 g/l CuCl2 x 2 H2O 1e-06 g/l Tap water Distilled water
123963CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@reftypetemperaturerangegrowth
25203maximum34mesophilic
25203growth5.0-34.0positive
24862growth22psychrophilicpositive

Physiology and metabolism

oxygen tolerance

  • @ref: 25203
  • oxygen tolerance: aerobe

nutrition type

  • @ref: 25203
  • type: chemoorganotroph

spore formation

@refspore formationconfidence
69481no100
69480no99.999

halophily

  • @ref: 25203
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0.0-0.5 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2520317750betaine-assimilation
2520316947citrate-assimilation
2520312936D-galactose-assimilation
2520317634D-glucose-assimilation
2520362318D-lyxose-assimilation
2520316024D-mannose-assimilation
2520317924D-sorbitol-assimilation
2520329805glycolate-assimilation
2520318287L-fucose-assimilation
2520315603L-leucine-assimilation
2520317115L-serine-assimilation
2520330623oxalate-assimilation
25203391504-oxopentanoate+assimilation
2520330089acetate+assimilation
2520335391aspartate+assimilation
2520373706bromosuccinate+assimilation
2520315824D-fructose+assimilation
2520318024D-galacturonic acid+assimilation
2520329806fumarate+assimilation
2520336655glyoxylate+assimilation
2520316977L-alanine+assimilation
2520317196L-asparagine+assimilation
2520317561L-cysteine+assimilation
2520329985L-glutamate+assimilation
2520315971L-histidine+assimilation
2520325115malate+assimilation
2520315792malonate+assimilation
2520316452oxaloacetate+assimilation
2520317272propionate+assimilation
2520315361pyruvate+assimilation
2520330031succinate+assimilation

enzymes

@refvalueactivityec
25203catalase+1.11.1.6
25203cytochrome oxidase+1.9.3.1

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    2520311-Methyl C18:1ω7c4.6
    25203C12:03.3
    25203C12:0 2OH0.3
    25203C14:00.3
    25203C15:00.2
    25203C16:018.6
    25203C16:0 2OH1.5
    25203C16:1ω5c0.4
    25203C16:1ω7c40.8
    25203C18:00.5
    25203C18:1ω7c20.4
    25203C19:1ω6c / Unknown1.219
    25203C16:1 iso I / C14:0 3OH7.1
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • agar/liquid: agar
  • incubation temperature: 25
  • incubation time: 8
  • treatment: agar surface was kept moist with liquid R2A medium
  • software version: Sherlock 4.5
  • library/peak naming table: TSBA 40
  • system: MIS MIDI
  • method/protocol: Kämpfer & Kroppenstedt 1996

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudesampling dateenrichment cultureisolation procedureisolation date
24862shallow acidic freshwater pondAlps, Pond-1 (47° 44' 23.37'' N 13° 18' 6.03'' E) 1300 meters above sea levelAustriaAUTEurope47.739813.3017
25203acidic Pond-1 (small, shallow (max depth <1 m) natural freshwater pond)October 2003nutrient broth soyotone yeast extract (NSY) mediumfiltration-acclimatization method
123963Environment, Acidic freshwater pondAustriaAUTEurope2003-10-01

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Freshwater
#Environmental#Aquatic#Pond (small)
#Condition#Acidic

taxonmaps

  • @ref: 69479
  • File name: preview.99_93.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_74;97_77;98_84;99_93&stattab=map
  • Last taxonomy: Polynucleobacter
  • 16S sequence: AJ879778
  • Sequence Identity:
  • Total samples: 42849
  • soil counts: 1815
  • aquatic counts: 34169
  • animal counts: 6310
  • plant counts: 555

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
248621Risk group (German classification)
1239631Risk group (French classification)

Sequence information

16S sequences

  • @ref: 24862
  • description: Polynucleobacter necessarius subsp. asymbioticus partial 16S rRNA gene and ITS1, strain QLW-P1FAT50C-4
  • accession: AJ879778
  • length: 2003
  • database: ena
  • NCBI tax ID: 1743168

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Polynucleobacter wuianus QLW-P1FAT50C-4GCA_001659725chromosomencbi1743168
66792Polynucleobacter sp. QLW-P1FAT50C-41743168.3completepatric1743168
66792Polynucleobacter wuianus QLW-P1FAT50C-42687453598completeimg1743168

GC content

@refGC-contentmethod
2520344.9genome sequence analysis
2486244.9sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.689yes
gram-positiveno98.581no
anaerobicno98.622yes
aerobicyes86.65yes
halophileno91.989yes
spore-formingno96.884no
thermophileno97.938no
glucose-utilno82.269no
flagellatedno94.74yes
glucose-fermentno91.087no

External links

@ref: 24862

culture collection no.: DSM 24008, CIP 111100

straininfo link

  • @ref: 91339
  • straininfo: 405368

literature

  • topic: Phylogeny
  • Pubmed-ID: 27902302
  • title: Polynucleobacter wuianus sp. nov., a free-living freshwater bacterium affiliated with the cryptic species complex PnecC.
  • authors: Hahn MW, Huymann LR, Koll U, Schmidt J, Lang E, Hoetzinger M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001637
  • year: 2017
  • mesh: Austria, Bacterial Typing Techniques, Base Composition, Burkholderiaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
24862Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-24008Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24008)
25203M. W. H. Hahn, L. R.,Koll, U.,Schmidt, J.,Lang, E.,Hoetzinger, M.Polynucleobacter wuianus sp. nov., a free-living freshwater bacterium affiliated with the cryptic species complex PnecC10.1099/ijsem.0.001637IJSEM 67: 379-385 201727902302
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
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
91339Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID405368.1
123963Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20111100Collection of Institut Pasteur (CIP 111100)