Enriched multifunctional microbes coupling antibiotic resistance risk and nitrogen metabolic potential in eutrophic lakes.

Lakes are facing increasing threats from the dual challenges of eutrophication and antibiotic contamination, yet how microorganisms respond to these concurrent threats remains poorly understood. Here, we conducted a metagenomic binning investigation into the co-occurrence patterns of antibiotic resistance genes (ARGs) and nitrogen cycling functional genes (NFGs) within resistant microbes across three lakes with distinct eutrophic levels. We found a significant increase in the abundance and diversity of ARGs along the trophic gradient. Meanwhile, ARG hosts tended to show a transition pattern from carrying combinations of ARGs, virulence factor genes (VFGs), and NFGs to possessing highly integrated complexes encompassing ARGs, mobile genetic elements (MGEs), VFGs, and NFGs. This reflected the coupling between antibiotic resistance and nitrogen metabolism, and contributed to the survival of resistant microbes that cope with environmental stress. Furthermore, multifunctional hosts (accounting for 57.55%), dominated by Limnohabitans_A, CAISIP01, and RFTU01, could play important roles in linking ecological functions and biosafety risks under highly eutrophic conditions. These findings present a framework centered on multifunctional microbes for elucidating resistome evolution across varying trophic levels, thus guiding host-based strategies to inform ARG risk assessment and eutrophication management in lakes.