Biobeds are biological systems designed to mitigate point-source pesticide contamination, yet their long-term performance under high agrochemical loads remains poorly understood. This thesis examines microbial community adaptation in the Denens biobed (Vaud, Switzerland), which has been exposed for nearly two decades to diverse pesticide inputs and heavy metal accumulation, particularly copper. Soil samples from the biobed and nearby control fields were subjected to metagenomic sequencing, metal and pesticide enrichment assays, antibiotic resistance profiling, and functional characterization of isolated strains.

Metagenomic analyses revealed distinct microbial community structures in the biobed compared to controls, with enrichment of taxa such as Lysobacter luteus and Pseudoxanthomonas mexicana, alongside higher abundances of heavy metal resistance genes (HMRGs) and antibiotic resistance genes (ARGs), including those conferring resistance to carbapenems, aminoglycosides, cephalosporins, and penams. Enrichment experiments isolated strains capable of tolerating elevated zinc and copper concentrations, notably Sphingobacterium detergens, which exhibited enhanced metal tolerance. Functional assays further demonstrated partial degradation of pesticides such as penconazole and fluopyram by selected isolates, though overall biodegradation capacity remained limited.

These findings indicate that prolonged agrochemical exposure drives microbial selection with metal tolerance and potential pesticide-degrading traits, but at the cost of fostering environmental reservoirs of antibiotic resistance. The work highlights both the bioremediation potential and ecological risks of biobed systems, emphasizing the need for careful management and microbial monitoring. Ultimately, the study proposes that targeted exploitation of adapted microbial communities could improve biobed remediation efficiency while informing strategies to mitigate the spread of resistance genes.