Strain identifier

BacDive ID: 22944

Type strain: Yes

Species: Cupriavidus pampae

Strain Designation: CCM-A-29:1289, CPDB6

Strain history: CIP <- 2014, CCUG <- 2008 V. Cuadrado, Buenos Aires Univ., Buenos Aires, Argentina: strain CPDB6

NCBI tax ID(s): 659251 (species)

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General

@ref: 19108

BacDive-ID: 22944

DSM-Number: 26888

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

description: Cupriavidus pampae CCM-A-29:1289 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from agricultural soil subject to a long-period application of chlorinated phenoxy herbicides.

NCBI tax id

  • NCBI tax id: 659251
  • Matching level: species

strain history

@refhistory
19108<- CCUG <- V. Cuadrado, Cátedra de Microbiología Industrial y Biotecnología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires
121523CIP <- 2014, CCUG <- 2008 V. Cuadrado, Buenos Aires Univ., Buenos Aires, Argentina: strain CPDB6

doi: 10.13145/bacdive22944.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Burkholderiaceae
  • genus: Cupriavidus
  • species: Cupriavidus pampae
  • full scientific name: Cupriavidus pampae Cuadrado et al. 2010

@ref: 19108

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Cupriavidus

species: Cupriavidus pampae

full scientific name: Cupriavidus pampae Cuadrado et al. 2010

strain designation: CCM-A-29:1289, CPDB6

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
29668negativerod-shapedyes
121523negativerod-shapedyes

colony morphology

  • @ref: 60802
  • incubation period: <1 day

pigmentation

  • @ref: 29668
  • production: yes

multimedia

  • @ref: 19108
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_26888.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
19108NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
19108MINERAL MEDIUM WITH VITAMINS (DSMZ Medium 462)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium462.pdf
41611MEDIUM 45 - for Columbia agar with sheep bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Sheepblood (100.000 ml)
121523CIP Medium 45yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=45

culture temp

@refgrowthtypetemperaturerange
19108positivegrowth28mesophilic
29668positivegrowth10-30
29668positiveoptimum30mesophilic
41611positivegrowth30mesophilic
60802positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29668aerobe
60802aerobe

spore formation

  • @ref: 29668
  • spore formation: no

observation

  • @ref: 29668
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2966817128adipate+carbon source
2966827689decanoate+carbon source
2966816947citrate+carbon source
2966824265gluconate+carbon source
2966817234glucose+carbon source
2966824996lactate+carbon source
2966825115malate+carbon source
6836925115malate+assimilation
6836917128adipate+assimilation
6836927689decanoate+assimilation
6836924265gluconate+assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea+hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
19108----+---------++++--+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
19108agricultural soil subject to a long-period application of chlorinated phenoxy herbicidesHumid PampaArgentinaARGMiddle and South America
60802Soil,CPDB,history of phenoxy herbicides useArgentinaARGMiddle and South America
121523Environment, SoilHumid PampaArgentinaARGMiddle and South America

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture
#Environmental#Terrestrial#Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
191081Risk group (German classification)
1215231Risk group (French classification)

Sequence information

16S sequences

  • @ref: 19108
  • description: Cupriavidus pampae partial 16S rRNA gene, strain CPDB6
  • accession: FN430567
  • length: 1504
  • database: ena
  • NCBI tax ID: 659251

External links

@ref: 19108

culture collection no.: DSM 26888, CCUG 55948, CIP 110847, CCM A-29:1289

straininfo link

  • @ref: 87192
  • straininfo: 353992

literature

  • topic: Phylogeny
  • Pubmed-ID: 20023053
  • title: Cupriavidus pampae sp. nov., a novel herbicide-degrading bacterium isolated from agricultural soil.
  • authors: Cuadrado V, Gomila M, Merini L, Giulietti AM, Moore ERB
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.018341-0
  • year: 2009
  • mesh: 2,4-Dichlorophenoxyacetic Acid/*analogs & derivatives/metabolism, Cupriavidus/classification/genetics/*isolation & purification/*metabolism, DNA, Bacterial/genetics, Fatty Acids/metabolism, Herbicides/*metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Soil/analysis, *Soil Microbiology
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
19108Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26888)https://www.dsmz.de/collection/catalogue/details/culture/DSM-26888
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
29668Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2605528776041
41611Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/34401
60802Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 55948)https://www.ccug.se/strain?id=55948
68369Automatically annotated from API 20NE
87192Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID353992.1StrainInfo: A central database for resolving microbial strain identifiers
121523Curators of the CIPCollection of Institut Pasteur (CIP 110847)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110847