Dual differentiation of core and rare antibiotic resistome along lake vertical profiles: Adaptive dynamics and...

Core and rare antibiotic resistance genes (ARGs) have divergent ecological traits and risk potentials; however, their vertical differentiation along the water-sediment profile continua in the lake remains poorly understood. We investigated their stratified patterns spanning surface water and sediments profiles across four paradigmatic lakes in central China. Twelve ARGs, occurred in all samples were defined as core resistome, contributing 10.1-23.5% of richness but 52.2-73.2% of abundance, both proportions rising with depth. By comparison, rare resistome showed declined richness, abundance, and diversity with depth (p < 0.001). Despite this, rare ARGs formed over 80% of nodes and edges in ARG co-occurrence networks. The total profile and community assembly of ARG were also dominated by rare ARGs. Besides, core ARGs exhibited broader niches than the rare at each depth (p < 0.001), mostly encoded by efflux pumps (83.3%), whereas rare ARGs derived from more anthropogenic resistance mechanisms like antibiotic deactivation (46.1%) and cellular protection (8.2%). Notably, rare ARGs in surface water contributed 63.8% of the ARG-MGE-host overlaps along the vertical profile, yet four of five ARGs with cross-media migration potential were core ARGs (multidrug ABC_transporter, multidrug transporter, mexF, and bacA). Interestingly, these two resistome shared 88.5% of the host taxa, accounting for more than 98% of the host abundance. Overall, our findings uncover specific roles of core and rare ARGs in sustaining vertical antibiotic resistance potentials of the lake, providing classified and stratified insights for alleviating antimicrobial resistance.