Manure fertilization shapes the soil resistome but not the radish crop resistome

Antibiotic resistance is a growing global problem, with agricultural practices and climate change as substantial contributors to the spread of antibiotic resistance genes (ARGs) in the environment. We investigated the effect of drought and fertilization type (organic vs. mineral) on radish crop growth and soil prokaryotic communities, with special emphasis on the radish and soil resistomes, as measured by the relative abundance of ARGs and mobile genetic element (MGE)-linked genes. Manure fertilization significantly increased ARG relative abundances in soil, compared to mineral fertilization. Drought and the presence of radish plants emerged as key variables regulating the association between ARGs and MGE-linked genes. Nonetheless, no connection was observed between the soil and crop resistome, despite radish being a belowground product, suggesting that, under our experimental conditions, the consumption of a belowground crop product does not pose a potential risk of transmission of ARGs from agroecosystems to human bacterial pathogens. Our findings highlight the complex interplay between agricultural practices and climatic factors in shaping the soil and crop resistome.