Journal Article

Cultivation-Independent Screening Revealed Hot Spots of IncP-1, IncP-7 and IncP-9 Plasmid Occurrence in Different Environmental Habitats

Gaze, William Hugo, Ding, Guo-Chun, van Elsas, Jan Dirk, Amos, Gregory Charles Auton, Martini, María Carla, Sipkema, Detmer, Heuer, Holger, Smalla, Kornelia, Schlüter, Andreas, Dunon, Vincent, Dealtry, Simone, Papa, María Florencia Del, Weichelt, Viola, Lagares, Antonio, Wellington, Elizabeth Margaret Helen, Sjöling, Sara, Springael, Dirk, Thomas, Christopher

2014

Overview

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.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: adaptation / Agrochemicals / Animals / Bacteria / Base Sequence / biobeds / Biodegradation / Biology / Blotting, Southern / Contaminants / Cultivation / Deoxyribonucleic acid / diversity / DNA / DNA Primers - genetics / DNA, Bacterial - genetics / Ecology / Environmental Pollutants - chemistry / Environmental Studies / Enzymes / Epidemiology / Europe / Farms / Flowers & plants / Gene sequencing / Genes / Genetic Variation / Hybridization / IncP / Life sciences / Medical screening / Microbiology / Miljövetenskapliga studier / Molecular Sequence Data / naphthalene / Nucleotide sequence / Pathogens / pesticide-contaminated / Pesticides / plasmid / Plasmids / Plasmids - genetics / polluted environment / Polluted environments / Pollution sources / Polymerase Chain Reaction / Porifera - microbiology / prevalence / Primers / pseudomonas / Purification / Rep gene / resistance genes / RNA, Ribosomal, 16S - genetics / sediment / Sediments / Sequence Analysis, DNA / soil / Subgroups / transposon / water / Water pollution / Water purification / Water treatment