Strain identifier

BacDive ID: 2080

Type strain: Yes

Species: Polynucleobacter rarus

Strain Designation: MT-CBb6A5

Strain history: CIP <- 2009, DSMZ <- M.W. Hahn, Limnology, Academy of Science, Mondsee, Austria: strain MT-CBb6A5

NCBI tax ID(s): 556055 (species)

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General

@ref: 15865

BacDive-ID: 2080

DSM-Number: 21648

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

description: Polynucleobacter rarus MT-CBb6A5 is an aerobe, chemoorganotroph, mesophilic bacterium that was isolated from water from the pelagic zone of an acidic lake.

NCBI tax id

  • NCBI tax id: 556055
  • Matching level: species

strain history

@refhistory
15865<- M. W. Hahn, Austrian Academy of Sciences, Inst. Limnology; MWH-MT-CBb6A5 <- M. Tarao
122139CIP <- 2009, DSMZ <- M.W. Hahn, Limnology, Academy of Science, Mondsee, Austria: strain MT-CBb6A5

doi: 10.13145/bacdive2080.20230509.8.1

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 rarus
  • full scientific name: Polynucleobacter rarus Hahn et al. 2011

@ref: 15865

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Polynucleobacter

species: Polynucleobacter rarus

full scientific name: Polynucleobacter rarus Hahn et al. 2011

strain designation: MT-CBb6A5

type strain: yes

Morphology

cell morphology

@refcell lengthcell widthcell shapemotilityconfidencegram stain
231650.8-1.8 µm0.6-0.8 µmrod-shapedno
69480no93.027
6948099.969negative
122139rod-shapednonegative

colony morphology

@refincubation periodcolony shapemedium used
158658-14 days
23165circularNSY and R2A

pigmentation

  • @ref: 23165
  • production: no
  • name: no pigments

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15865R2A 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
23165NSY and R2Ayes
37883MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
122139CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
15865positivegrowth28mesophilic
23165nogrowth5psychrophilic
23165nogrowth35mesophilic
37883positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23165aerobe
23165facultative anaerobe

nutrition type

  • @ref: 23165
  • type: chemoorganotroph

spore formation

@refspore formationconfidence
69481no100
69480no99.997

halophily

@refsaltgrowthtested relationconcentration
23165NaClpositivemaximum0.3 %(w/v)
23165NaClpositivemaximum0 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2316517750betaine-carbon source
2316516947citrate-carbon source
2316512936D-galactose-carbon source
2316517634D-glucose-carbon source
2316517924D-sorbitol-carbon source
2316515740formate-carbon source
2316516977L-alanine-carbon source
2316517196L-asparagine-carbon source
2316529991L-aspartate-carbon source
2316529985L-glutamate-carbon source
2316517115L-serine-carbon source
2316515792malonate-carbon source
2316516452oxaloacetate-carbon source
2316517272propionate-carbon source
2316517750betaine-growth
2316516947citrate-growth
2316512936D-galactose-growth
2316517634D-glucose-growth
2316517924D-sorbitol-growth
2316515740formate-growth
2316516977L-alanine-growth
2316517196L-asparagine-growth
2316529991L-aspartate-growth
2316529985L-glutamate-growth
2316515792malonate-growth
2316530623oxalate-growth
2316516452oxaloacetate-growth
2316517272propionate-growth
2316516094thiosulfate-growth
2316516199urea-growth
2316530089acetate+carbon source
2316515824D-fructose+carbon source
2316528847D-fucose+carbon source
2316518024D-galacturonic acid+carbon source
2316562318D-lyxose+carbon source
2316516024D-mannose+carbon source
2316529806fumarate+carbon source
2316529805glycolate+carbon source
2316536655glyoxylate+carbon source
2316517561L-cysteine+carbon source
23165391504-oxopentanoate+carbon source
2316525115malate+carbon source
2316530623oxalate+carbon source
2316515361pyruvate+carbon source
2316530031succinate+carbon source
23165391504-oxopentanoate+growth
2316530089acetate+growth
2316515824D-fructose+growth
2316528847D-fucose+growth
2316518024D-galacturonic acid+growth
2316562318D-lyxose+growth
2316516024D-mannose+growth
2316529806fumarate+growth
2316529805glycolate+growth
2316536655glyoxylate+growth
2316517561L-cysteine+growth
2316525115malate+growth
2316530031succinate+growth

enzymes

@refvalueactivityec
23165catalase+1.11.1.6
23165cytochrome oxidase+1.9.3.1
122139oxidase+
122139catalase+1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15865water from the pelagic zone of an acidic lakeCrystal Bog Lake, WisconsinUSAUSANorth America
122139Environment, Freshwater lakeCrystal Bog lake, WisconsinUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Lake (large)
#Condition#Acidic

taxonmaps

  • @ref: 69479
  • File name: preview.99_8038.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_3713;97_4565;98_5858;99_8038&stattab=map
  • Last taxonomy: Polynucleobacter rarus subclade
  • 16S sequence: FM208182
  • Sequence Identity:
  • Total samples: 1177
  • soil counts: 65
  • aquatic counts: 1074
  • animal counts: 35
  • plant counts: 3

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
158651Risk group (German classification)
1221391Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15865
  • description: Polynucleobacter rarus 16S rRNA gene (partial), IGS and 23S rRNA gene (partial), strain MT-CBb6A5
  • accession: FM208182
  • length: 2134
  • database: ena
  • NCBI tax ID: 556055

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Polynucleobacter rarus MT-CBb6A5GCA_003072505scaffoldncbi556055
66792Polynucleobacter rarus strain MT-CBb6A5556055.3wgspatric556055
66792Polynucleobacter rarus MT-CBb6A52645728114draftimg556055

GC content

  • @ref: 15865
  • GC-content: 40.3
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno94.891no
gram-positiveno98.103no
anaerobicno97.767yes
halophileno91.87yes
spore-formingno95.776no
glucose-utilno89.402yes
aerobicyes85.556no
thermophileno98.433yes
motileno92.794yes
glucose-fermentno91.593no

External links

@ref: 15865

culture collection no.: DSM 21648, CIP 109928

straininfo link

  • @ref: 71727
  • straininfo: 371503

literature

  • topic: Phylogeny
  • Pubmed-ID: 20435748
  • title: Polynucleobacter rarus sp. nov., a free-living planktonic bacterium isolated from an acidic lake.
  • authors: Hahn MW, Lang E, Tarao M, Brandt U
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.017350-0
  • year: 2010
  • mesh: Aerobiosis, Anaerobiosis, Base Composition, Burkholderiaceae/*classification/genetics/*isolation & purification/physiology, Cluster Analysis, Culture Media/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Oxidoreductases/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature, *Water Microbiology, Wisconsin
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
15865Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21648)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21648
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
23165Martin W. Hahn, Elke Lang, Mitsunori Tarao, Ulrike Brandt10.1099/ijs.0.017350-0Polynucleobacter rarus sp. nov., a free-living planktonic bacterium isolated from an acidic lakeIJSEM 61: 781-787 201120435748
37883Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7727
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)
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
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
71727Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID371503.1StrainInfo: A central database for resolving microbial strain identifiers
122139Curators of the CIPCollection of Institut Pasteur (CIP 109928)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109928