Multi-habitat distribution and coalescence of resistomes at the watershed scale based on metagenomics

The characteristics of the resistome distribution in rivers have been extensively studied. However, the distribution patterns of resistomes in multiple habitats and contributions of upstream habitats to the resistome profile in water bodies remains unclear. The current study explored the distribution and coalescence of antibiotic resistance genes (ARGs), metal resistance genes (MRGs), and mobile genetic elements (MGEs) in four habitats (including water bodies, sediments, biofilms, and riparian soils) within the Shichuan River watershed. The results revealed significant variations in the abundances and diversity of resistomes across the four habitats and two seasons. Assembly processes of resistomes were predominated by stochastic processes in summer but deterministic processes in winter. The main source of the resistome in summer water bodies was the movement of genes from upstream water bodies. However, the main sources of resistome in downstream water bodies in winter were the movement of resistomes in upstream sediments and the input of external pollution. The physicochemical properties of winter water bodies significantly influenced the movement of the resistomes across habitats. The current study elucidated the multi-habitat distribution pattern and migration mechanism of the resistome in the river system, providing new insights for effectively monitoring and controlling bacterial resistance.