Mobilome dominates fomesafen-responsive dissemination of antibiotic resistome in manure-amended agricultural soils

Pesticides are increasingly perceived as emerging drivers in the spread of antibiotic resistance genes (ARGs) within agroecosystems. Pesticides with longer half-lives tend to impose persistent stresses on soil microbiomes, yet the selection for ARG dissemination remains overlooked. Focusing on a widely used long residual herbicide fomesafen, we examined recommended dose-based selection on the dissemination of ARGs in agricultural soils with or without manure amendment. The degradation half-lives of fomesafen in the blank soils and manure-amended soils were 35.77–124.00 and 20.00–73.27 d, respectively. After 42-d exposure, the total abundances of ARGs in the fomesafen-treated manure-amended soils at exposure concentrations of 1 and 5 mg/kg were 1.20- and 1.36-fold higher than that in the controls, with the changes of mobile genetic elements (MGEs) reaching 1.24–2.22 folds; while no significant change was observed in the blank soils. Furthermore, no significant change was observed in either bacterial communities or ARG-carrying metagenome-assembled genomes in both manure-amended soils and blank soils under fomesafen selection. Variation partition analysis suggested that 24.42%–25.41% of the variations in ARGs could be individually explained by MGEs, while only 13.47%–13.75% by bacterial communities. Overall, these findings demonstrate that MGE-mediated horizontal transfer predominates fomesafen-responsive dissemination of ARGs in manure-amended agriculture soils and underscores the urgency of re-evaluating agricultural practices involving co-application of manures and long residual herbicides.