title: Cultivation-independent screening revealed hot spots of IncP-1, IncP-7 and IncP-9 plasmid occurrence in different environmental habitats.
abstract: IncP-1, IncP-7 and IncP-9 plasmids often carry genes encoding enzymes involved in the degradation of man-made and natural contaminants, thus contributing to bacterial survival in polluted environments. However, the lack of suitable molecular tools often limits the detection of these plasmids in the environment. In this study, PCR followed by Southern blot hybridization detected the presence of plasmid-specific sequences in total community (TC-) DNA or fosmid DNA from samples originating from different environments and geographic regions. A novel primer system targeting IncP-9 plasmids was developed and applied along with established primers for IncP-1 and IncP-7. Screening TC-DNA from biopurification systems (BPS) which are used on farms for the purification of pesticide-contaminated water revealed high abundances of IncP-1 plasmids belonging to different subgroups as well as IncP-7 and IncP-9. The novel IncP-9 primer-system targeting the rep gene of nine IncP-9 subgroups allowed the detection of a high diversity of IncP-9 plasmid specific sequences in environments with different sources of pollution. Thus polluted sites are "hot spots" of plasmids potentially carrying catabolic genes.
authors.affiliation: Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany.
authors.forename: Simone
authors.initials: S
authors.lastname: Dealtry
authors.affiliation: Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany.
authors.forename: Guo-Chun
authors.initials: GC
authors.lastname: Ding
authors.affiliation: Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany.
authors.forename: Viola
authors.initials: V
authors.lastname: Weichelt
authors.affiliation: Division of Soil and Water Management, KU Leuven, Heverlee, Belgium.
authors.forename: Vincent
authors.initials: V
authors.lastname: Dunon
authors.affiliation: Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Bielefeld, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Schlüter
authors.affiliation: IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina.
authors.forename: María Carla
authors.initials: MC
authors.lastname: Martini
authors.affiliation: IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina.
authors.forename: María Florencia
authors.initials: MF
authors.lastname: Del Papa
authors.affiliation: IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina.
authors.forename: Antonio
authors.initials: A
authors.lastname: Lagares
authors.affiliation: School of Life Sciences, University of Warwick, Warwick, United Kingdom.
authors.forename: Gregory Charles Auton
authors.initials: GC
authors.lastname: Amos
authors.affiliation: School of Life Sciences, University of Warwick, Warwick, United Kingdom.
authors.forename: Elizabeth Margaret Helen
authors.initials: EM
authors.lastname: Wellington
authors.affiliation: School of Life Sciences, University of Warwick, Warwick, United Kingdom.
authors.forename: William Hugo
authors.initials: WH
authors.lastname: Gaze
authors.affiliation: Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
authors.forename: Detmer
authors.initials: D
authors.lastname: Sipkema
authors.affiliation: Södertörns högskola (Sodertorn University), Inst. för Naturvetenskap, Miljö och medieteknik (School of Natural Sciences, Environmental Studies and media tech), Huddinge, Sweden.
authors.forename: Sara
authors.initials: S
authors.lastname: Sjöling
authors.affiliation: Division of Soil and Water Management, KU Leuven, Heverlee, Belgium.
authors.forename: Dirk
authors.initials: D
authors.lastname: Springael
authors.affiliation: Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany.
authors.forename: Holger
authors.initials: H
authors.lastname: Heuer
authors.affiliation: University of Groningen, Groningen, The Netherlands.
authors.forename: Jan Dirk
authors.initials: JD
authors.lastname: van Elsas
authors.affiliation: School of Biosciences, University of Birmingham, Edgbaston, Birmingham, Warwick, United Kingdom.
authors.forename: Christopher
authors.initials: C
authors.lastname: Thomas
authors.affiliation: Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany.
authors.forename: Kornelia
authors.initials: K
authors.lastname: Smalla
mesh_terms: D000818:Animals; D001483:Base Sequence; D015139:Blotting, Southern; D017931:DNA Primers / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics*; D004785:Environmental Pollutants / Q000737:chemistry*; D005060:Europe; D014644:Genetic Variation; D008969:Molecular Sequence Data; D010957:Plasmids / Q000235:genetics*; D016133:Polymerase Chain Reaction; D011161:Porifera / Q000382:microbiology; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D017931:DNA Primers; D004269:DNA, Bacterial; D004785:Environmental Pollutants; D012336:RNA, Ribosomal, 16S