Pesticide-driven bacterial adaptation: biodegradation pathways and co-selection of antibiotic resistance

The intensive use and misuse of pesticides has increased the chemical pressure exerted on soil microbiomes. According to the Food and Agriculture Organization (FAO), the global pesticide used in agriculture in 2023 reached 3.73 million tonnes of active ingredients, highlighting the magnitude of environmental exposure. Soil bacteria can adapt to pesticide contamination through catabolic pathways encoded by chromosomal genes and/or mobile genetic elements (MGEs), enabling pesticide transformation and sometimes supporting bioremediation. In parallel, a growing body of evidence indicates that non-antibiotic chemicals including herbicides and insecticides can contribute to the emergence and persistence of antibiotic resistance through co-selection. Mechanisms include cross-resistance mediated by multidrug efflux pumps and permeability changes, stress-induced responses and enhanced horizontal gene transfer (HGT) that facilitates the dissemination of antibiotic resistance genes (ARGs) and MGEs in environmental ecosystems including soil, water and others. In this review, we summarise current knowledge on biodegradation pathways, genetic determinants and documented evidence linked to antibiotic resistance for five selected pesticide case studies: glyphosate, atrazine, cypermethrin, chlorpyrifos and paraquat. We identify where evidence is strongest (e.g., herbicide-associated AMR outcomes) and where major gaps remain, particularly regarding causal attribution under environmentally realistic concentrations and the frequency of ARG co-localisation with catabolic loci. We further propose an explicit mechanistic framework in which biodegradation and antibiotic resistance are examined as potentially interconnected components of bacterial adaptation, connected by a shared mobilome, a shared efflux and stress-response, the reactive intermediates of incomplete catabolism, and nutrient-driven community restructuring.