Longitudinal Multiomics Reveals Core Microbiome Disruption and Potential Keystone-Associated Recovery Following Pesticide Exposure

Abstract Pesticides have become indispensable in modern agriculture, serving as a primary tool to minimize crop loss amid increasing human population pressures. While the negative effects of pesticides on the soil microbiome have been reported, the temporal dynamics of soil microorganisms under pesticide use remain underexplored. Specifically, limited knowledge exists regarding how the soil microbiome responds to pesticides before and after the manufacturer-labeled ‘safe period’ of 21 days after application. We conducted a longitudinal microcosm study to investigate the temporal impacts of herbicide, fungicide, and insecticide on soil microbial diversity, composition, network complexity, and functional pathways across five time points. Our results show that soil microbial communities are negatively impacted by pesticide applications, but there is a trend of recovery after 21 days. We found a significant impact of the temporal persistence of pesticides on both bacterial and fungal community composition, with a stronger effect on fungi. Network analysis revealed that core microbiome networks were negatively impacted by pesticide applications, with the core microbial nodes, raw associations, and modularity declining in pesticide-treated soils, and this negative effect was particularly strong for pyrethroid insecticides. We identified several differentially abundant taxa, including Xanthobacteraceae and Vicinamibacteriales among bacteria, and Mortierella, Mytilinidales among fungi, which could serve as useful biomarkers for pesticide-affected soils. Results from microbial co-occurrence network analysis revealed that one ASV assigned to the Methyloligellaceae family consistently emerged as a keystone taxon in pesticide-treated soils. Using genome-resolved metagenomics, we assembled the genomes (MAGs) of Methyloligellaceae members and found these taxa harbor putative genes associated with pesticide degradation and antimicrobial resistance, suggesting their possible role in community recovery. Given the remarkably dynamic nature of soil microbial communities, our findings bridge an important knowledge gap regarding the short-term dynamics of microbial structures and functional pathways in response to major pesticides.