Strain identifier

BacDive ID: 2081

Type strain: Yes

Species: Polynucleobacter difficilis

Strain Designation: AM-8B5

Strain history: CIP <- 2009, A. Minasyan <- M. Hahn, Austrian Academy of Science, Inst. for Limnology, Mondsee, Austria: strain AM-8B5

NCBI tax ID(s): 556054 (species)

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General

@ref: 16306

BacDive-ID: 2081

DSM-Number: 22349

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

description: Polynucleobacter difficilis AM-8B5 is an aerobe, chemoorganotroph, mesophilic bacterium that was isolated from freshwater taken from a depth of 60 m close to the bottom of a eutrophic lake.

NCBI tax id

  • NCBI tax id: 556054
  • Matching level: species

strain history

@refhistory
16306<- M. W. Hahn, Austrian Academy of Sci., Inst. Limnology; AM-8B5 <- A. Minasyan
118935CIP <- 2009, A. Minasyan <- M. Hahn, Austrian Academy of Science, Inst. for Limnology, Mondsee, Austria: strain AM-8B5

doi: 10.13145/bacdive2081.20230509.8.1

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 difficilis
  • full scientific name: Polynucleobacter difficilis Hahn et al. 2012

@ref: 16306

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Polynucleobacter

species: Polynucleobacter difficilis

full scientific name: Polynucleobacter difficilis Hahn et al. 2012

strain designation: AM-8B5

type strain: yes

Morphology

cell morphology

@refcell lengthcell widthcell shapemotilitygram stainconfidence
231660.6-1.8 µm0.4-0.5 µmrod-shapedno
69480negative100
118935rod-shapednegative

colony morphology

@refincubation periodcolony shapemedium used
16306>14 days
23166circularNSY and R2A

pigmentation

  • @ref: 23166
  • production: no
  • name: no pigments

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16306R2A 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
23166NSY and R2Ayes
37911MEDIUM718 - for Polynucleobacter rarumyes
118935CIP Medium 751Ayeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=751A

culture temp

@refgrowthtypetemperaturerange
16306positivegrowth25mesophilic
23166positivegrowth5psychrophilic
23166nogrowth35mesophilic
37911positivegrowth25mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23166aerobe
23166facultative anaerobe

nutrition type

  • @ref: 23166
  • type: chemoorganotroph

spore formation

@refspore formationconfidence
69481no100
69480no99.994

halophily

@refsaltgrowthtested relationconcentration
23166NaClpositivemaximum0.2 %(w/v)
23166NaClpositivegrowth0 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2316629991L-aspartate-carbon source
23166391504-oxopentanoate-carbon source
2316630089acetate-carbon source
2316617750betaine-carbon source
2316616947citrate-carbon source
2316615824D-fructose-carbon source
2316612936D-galactose-carbon source
2316617634D-glucose-carbon source
2316616024D-mannose-carbon source
2316617924D-sorbitol-carbon source
2316629805glycolate-carbon source
2316636655glyoxylate-carbon source
2316616977L-alanine-carbon source
2316617196L-asparagine-carbon source
2316629985L-glutamate-carbon source
2316617115L-serine-carbon source
2316615792malonate-carbon source
2316630623oxalate-carbon source
2316617272propionate-carbon source
23166391504-oxopentanoate-growth
2316630089acetate-growth
2316617750betaine-growth
2316616947citrate-growth
2316615824D-fructose-growth
2316612936D-galactose-growth
2316617634D-glucose-growth
2316616024D-mannose-growth
2316617924D-sorbitol-growth
2316629805glycolate-growth
2316636655glyoxylate-growth
2316616977L-alanine-growth
2316617196L-asparagine-growth
2316629991L-aspartate-growth
2316629985L-glutamate-growth
2316617115L-serine-growth
2316615792malonate-growth
2316630623oxalate-growth
2316617272propionate-growth
2316628847D-fucose+carbon source
2316618024D-galacturonic acid+carbon source
2316662318D-lyxose+carbon source
2316615740formate+carbon source
2316629806fumarate+carbon source
2316617561L-cysteine+carbon source
2316625115malate+carbon source
2316616452oxaloacetate+carbon source
2316615361pyruvate+carbon source
2316630031succinate+carbon source
2316628847D-fucose+growth
2316618024D-galacturonic acid+growth
2316662318D-lyxose+growth
2316615740formate+growth
2316629806fumarate+growth
2316617561L-cysteine+growth
2316625115malate+growth
2316616452oxaloacetate+growth
2316615361pyruvate+growth
2316630031succinate+growth

enzymes

@refvalueactivityec
23166catalase+1.11.1.6
23166cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeisolation date
16306freshwater taken from a depth of 60 m close to the bottom of a eutrophic lakeLake Sevan (40° 29' 35.50'' N 45° 11' 31.34'' E)ArmeniaARMAsia40.493245.1928
118935Environment, FreshwaterGosh lakeArmeniaARMAsia2006

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Freshwater
#Environmental#Aquatic#Lake (large)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
163061Risk group (German classification)
1189351Risk group (French classification)

Sequence information

16S sequences

  • @ref: 16306
  • description: Polynucleobacter difficilis 16S rRNA gene (partial), IGS and 23S rRNA gene (partial), type strain AM-8B5T
  • accession: FM208181
  • length: 2103
  • database: ena
  • NCBI tax ID: 556054

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Polynucleobacter difficilis AM-8B5GCA_003065365completencbi556054
66792Polynucleobacter difficilis AM-8B52808606694completeimg556054

GC content

@refGC-contentmethod
1630649.4high performance liquid chromatography (HPLC)
2316649.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno67.73yes
gram-positiveno98.771no
anaerobicno95.446yes
halophileno90.688yes
spore-formingno95.017no
glucose-utilno82.081no
aerobicyes72.231no
thermophileno87.43yes
motileyes64.508yes
glucose-fermentno91.794no

External links

@ref: 16306

culture collection no.: DSM 22349, CIP 110078

straininfo link

  • @ref: 71728
  • straininfo: 379267

literature

  • topic: Phylogeny
  • Pubmed-ID: 21441373
  • title: Polynucleobacter difficilis sp. nov., a planktonic freshwater bacterium affiliated with subcluster B1 of the genus Polynucleobacter.
  • authors: Hahn MW, Minasyan A, Lang E, Koll U, Sproer C
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.031393-0
  • year: 2011
  • mesh: Bacterial Typing Techniques, Burkholderiaceae/chemistry/*classification/genetics/*isolation & purification, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Fresh Water/*microbiology, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Plankton/chemistry/*classification/genetics/*isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16306Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22349)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22349
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
23166Martin W. Hahn, Arevik Minasyan, Elke Lang, Ulrike Koll, Catrin Spröer10.1099/ijs.0.031393-0Polynucleobacter difficilis sp. nov., a planktonic freshwater bacterium affiliated with subcluster B1 of the genus PolynucleobacterIJSEM 62: 376-383 201221441373
37911Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7895
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)
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
71728Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID379267.1StrainInfo: A central database for resolving microbial strain identifiers
118935Curators of the CIPCollection of Institut Pasteur (CIP 110078)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110078