Strain identifier

BacDive ID: 2068

Type strain: Yes

Species: Polynucleobacter asymbioticus

Strain Designation: QLW-P1DMWA-1

Strain history: CIP <- 2008, DSMZ <- M.W. Hahn, Austrian Science Academy, Mondsee, Austria: strain QLW-P1DMWA-1

NCBI tax ID(s): 576611 (species)

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General

@ref: 7372

BacDive-ID: 2068

DSM-Number: 18221

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

description: Polynucleobacter asymbioticus QLW-P1DMWA-1 is a facultative anaerobe, chemoorganotroph, mesophilic bacterium that forms circular colonies and was isolated from acidic freshwater pond.

NCBI tax id

  • NCBI tax id: 576611
  • Matching level: species

strain history

@refhistory
7372<- M. W. Hahn <- M. W. Hahn and Q. L. Wu, Austrian Academy of Sciences, Institute of Limnology; QLW-P1DMWA-1
116533CIP <- 2008, DSMZ <- M.W. Hahn, Austrian Science Academy, Mondsee, Austria: strain QLW-P1DMWA-1

doi: 10.13145/bacdive2068.20230509.8.1

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 asymbioticus
  • full scientific name: Polynucleobacter asymbioticus (Hahn et al. 2009) Hahn et al. 2016

  • synonyms

    • @ref: 20215
    • synonym: Polynucleobacter necessarius subsp. asymbioticus

@ref: 7372

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Polynucleobacter

species: Polynucleobacter asymbioticus

full scientific name: Polynucleobacter asymbioticus (Hahn et al. 2009) Hahn et al. 2016

strain designation: QLW-P1DMWA-1

type strain: yes

Morphology

cell morphology

@refcell lengthcell widthcell shapegram stainmotility
435860.7-1.2 µm0.4-0.5 µmrod-shaped
116533rod-shapednegativeno

colony morphology

  • @ref: 43586
  • colony shape: circular
  • medium used: NSY agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7372R2A 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
41999MEDIUM 706- for Polynucleobacteryes
43586LB (Luria-Bertani) MEDIUMyes
43586NSYyes
43586NSY agaryes
43586Peptone mediumyes
43586Reasoner's 2A agar (R2A)yes
116533CIP Medium 706yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=706

culture temp

@refgrowthtypetemperaturerange
7372positivegrowth28mesophilic
41999positivegrowth30mesophilic
43586positivegrowth34mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 43586
  • oxygen tolerance: facultative anaerobe

nutrition type

  • @ref: 43586
  • type: chemoorganotroph

halophily

@refsaltgrowthtested relationconcentration
43586NaClpositivegrowth0-0.4 %(w/v)
43586NaClnogrowth0.6 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4358616947citrate-assimilation
4358629805glycolate-assimilation
4358617115L-serine-assimilation
4358630623oxalate-assimilation
4358616452oxaloacetate-assimilation
4358630089acetate+assimilation
4358618024D-galacturonic acid+assimilation
4358625115malate+assimilation
4358629806fumarate+assimilation
4358629991L-aspartate+assimilation
4358617561L-cysteine+assimilation
4358629985L-glutamate+assimilation
4358617272propionate+assimilation
4358615361pyruvate+assimilation
4358630031succinate+assimilation
11653317632nitrate-reduction
11653316301nitrite-reduction

metabolite production

  • @ref: 116533
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
116533oxidase-
116533catalase-1.11.1.6
116533urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116533-++--+----++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeisolation date
7372acidic freshwater pondAlps, (47° 44' 27'' N 13° 17' 53'' E at 1300 meters above sea level)AustriaAUTEurope47.740813.2981
43586a small acidic freshwater pond located in the Austrian Alps at an altitude of 1300 mAustrian AlpsAustriaAUTEurope
116533Environment, Freshwater pondAlpesAustriaAUTEurope2003

isolation source categories

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

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: AJ879783
  • 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
73721Risk group (German classification)
1165331Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7372
  • description: Polynucleobacter asymbioticus partial 16S rRNA gene and ITS1, strain QLW-P1DMWA-1
  • accession: AJ879783
  • length: 2000
  • database: ena
  • NCBI tax ID: 312153

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Polynucleobacter asymbioticus QLW-P1DMWA-1GCA_000016345completencbi312153
66792Polynucleobacter asymbioticus QLW-P1DMWA-12639762516completeimg312153

GC content

@refGC-contentmethod
737244.8high performance liquid chromatography (HPLC)
4358644.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno92.586no
flagellatedno93.754no
gram-positiveno98.555no
anaerobicno97.67yes
halophileno91.992yes
spore-formingno96.597no
thermophileno97.913yes
glucose-utilno77.204no
aerobicyes83.728no
glucose-fermentno89.808no

External links

@ref: 7372

culture collection no.: DSM 18221, CIP 109841

straininfo link

  • @ref: 71715
  • straininfo: 364175

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27064460Reclassification of four Polynucleobacter necessarius strains as representatives of Polynucleobacter asymbioticus comb. nov., Polynucleobacter duraquae sp. nov., Polynucleobacter yangtzensis sp. nov. and Polynucleobacter sinensis sp. nov., and emended description of Polynucleobacter necessarius.Hahn MW, Schmidt J, Pitt A, Taipale SJ, Lang EInt J Syst Evol Microbiol10.1099/ijsem.0.0010732016Bacterial Typing Techniques, Base Composition, Burkholderiaceae/*classification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Multilocus Sequence Typing, *Phylogeny, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/genetics, Sequence Analysis, DNATranscriptome
Transcriptome33042055Combined Methylome, Transcriptome and Proteome Analyses Document Rapid Acclimatization of a Bacterium to Environmental Changes.Srivastava A, Murugaiyan J, Garcia JAL, De Corte D, Hoetzinger M, Eravci M, Weise C, Kumar Y, Roesler U, Hahn MW, Grossart HPFront Microbiol10.3389/fmicb.2020.5447852020Proteome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7372Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18221)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18221
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
41999Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7631
43586Martin W. Hahn, Johanna Schmidt, Alexandra Pitt, Sami J. Taipale, Elke Lang10.1099/ijsem.0.001073Reclassification of four Polynucleobacter necessarius strains as representatives of Polynucleobacter asymbioticus comb. nov., Polynucleobacter duraquae sp. nov., Polynucleobacter yangtzensis sp. nov. and Polynucleobacter sinensis sp. nov., and emended description of Polynucleobacter necessariusIJSEM 66: 2883-2892 201627064460
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)
68382Automatically annotated from API zym
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
71715Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID364175.1StrainInfo: A central database for resolving microbial strain identifiers
116533Curators of the CIPCollection of Institut Pasteur (CIP 109841)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109841