Pesticide Type Distinctly Shapes Soil Resistomes: A Comparative Analysis of Antibiotic and Non-Antibiotic Agro-Chemicals

Agricultural pesticides are significant drivers of antibiotic resistance in soil. However, the differential impacts of antibiotic versus non-antibiotic pesticides on the soil resistome are poorly characterized. Here, we analyzed sequencing data from soils exposed to either antibiotic or non-antibiotic pesticides to compare differences in antibiotic resistance gene (ARG) burden, diversity, assembly processes, network topology, and host taxonomy. Soils exposed to antibiotic pesticides exhibited a significantly higher ARG burden (0.52% vs. 0.27% of total genes), whereas soils exposed to non-antibiotic pesticides showed significantly higher alpha diversity (p < 0.05). ARG community compositions also differed significantly between antibiotic and non-antibiotic exposures (PERMANOVA, R2 = 0.215, p < 0.001). Assembly analysis using the modified stochasticity ratio indicated that deterministic processes governed ARG community assembly in both groups, with stronger influence observed in non-antibiotic soils. Co-occurrence network analysis revealed contrasting patterns. A compact, highly centralized network emerged in antibiotic-exposed soils, while a larger, more dispersed network characterized non-antibiotic soils. In both networks, aminoglycoside ARGs served as keystone nodes, accompanied by the β-lactam ARG in antibiotic soils and the macrolide ARG in non-antibiotic soils. Pseudomonadota was the predominant ARG host (>60% contribution) across both exposures, though many other phyla exhibited significance (p < 0.05) between group differences in their ARG contributions. Non-pathogenic bacteria comprised the majority of ARG hosts in all samples. When examining ARG contributions from pathogenic hosts, zoonotic and animal-associated pathogens contributed significantly (p < 0.01) more in non-antibiotic soils than in antibiotic soils, whereas the ARG contribution from plant pathogens was comparable between the two pesticide groups. Overall, our study suggests that antibiotic and non-antibiotic pesticides shape distinct ARG network patterns and host–pathogen profiles, posing distinct risks to public health and agricultural ecosystems.