16S, ITS and MAGs from pesticide microcosm study

Pesticides have become an indispensable part of modern agriculture as a primary tool for minimizing crop loss under the pressure of the ever-increasing human population. Although the negative effects of pesticides on the soil microbiome have recently been reported, the temporal dynamics of the soil microbiome under pesticide usage are underexplored. Specifically, how the soil microbiome responds to pesticides during and after the manufacturer-labeled safe period of 21 days after application is yet unknown. We conducted a microcosm study using grassland soils without any pesticide history and performed 16S and ITS-based amplicon sequencing and shotgun metagenomics to investigate the temporal impacts of herbicide, fungicide and insecticide on the soil microbiome. Soil microbial abundance declined initially but recovered partially after 14-21 days, and this pattern was reflected in the temporal dynamics of one of the keystone MAGs. We also found this MAG to contain an expansive set of genes involved in pesticide degradation and antimicrobial resistance, suggesting that keystone taxa harboring this MAG are likely to facilitate community recovery through their connectivity, as well as degrade pesticide residues and outcompete others via antimicrobial resistance. Additionally, we identified several differentially responsive microbial taxa which can be used as biomarkers for pesticide-affected soils. Finally, pesticides caused a significant decline in core microbiome co-occurrence network complexity. These results highlight the perils of indiscriminate pesticide application, as well as the need to conserve the crucial microbial players for sustainable agroecosystem management.