Horizontal gene transfer and shifts in linked bacterial community composition are associated with maintenance of antibiotic resistance genes during food waste composting

Abstract About 1.3 billion tons of food waste (FW) is annually produced at a global scale. A major fraction of FW is deposited into landfills thereby contributing to environmental pollution and emission of greenhouse gasses. While increasing amounts of FW are recycled more sustainably into fertilizers in industrial-scale composting, very little is known about the antibiotic resistance genes (ARGs) present in FW and how their abundance is affected by composting. To study this, we quantified the diversity and abundance of ARGs, mobile genetic elements (MGEs) and bacterial communities in the beginning, during and at the end of the FW composting. All targeted 27 ARGs and 5 MGEs were detected in every sample suggesting that composted FW remains a reservoir of ARGs and MGEs. While the composting drastically changed the abundance, composition and diversity of bacterial communities, an increase in total ARG and MGE abundances was observed. Changes in ARGs were linked with shifts in the composition of bacterial communities as revealed by a Procrustes analysis ( P 3 − and moisture. Together our findings suggest that traditional composting is not efficient at removing ARGs and MGEs from FW. More effective composting strategies are thus needed to minimize ARG release from composted FW into agricultural environments.