Multi-trophic microbial communities drive nitrogen cycling in river ecosystems: Synergistic control of hydrological regime and nutrient input

Abstract

Urbanization and agricultural activities drive nutrient enrichment in riverine systems through land-use modification and hydrological alteration, resulting in microbial community restructuring and reprogramming of nitrogen cycling. Using multi-omics analyses, multi-trophic microbial communities were characterized across river sections with distinct land use types (woodland, cropland, and urbanized) during wet and dry seasons. Anthropogenically impacted sections exhibited 20–40% increases in the relative abundances of Bacteroidetes, Diatomea, and Dinoflagellata, along with 20–30% increases in predators, leading to cross-trophic metabolic coupling. Built-up river sections developed simplified networks dominated by r-strategist algal and bacterial colonization, in contrast to cooperative networks in woodland sections. These interactions produced seasonal oscillations between metabolic activation in the wet season and metabolic slowdown in the dry season. During the wet season, the relative abundance of nitrogen fixation genes in built-up sections was three times higher than in woodland sections, whereas hao and nrfA gene relative abundances in cropland sections increased by 1.5-fold compared with woodland sections. Denitrification genes (nirS, nirK, and nosZ) peaked during the wet season but declined by more than 60% during the dry season. Algal-derived dissolved organic carbon promoted denitrification, and nrfA-mediated nitrate ammonification enhanced nitrogen removal in cropland and built-up sections. In the wet season, high turbulence intensified carbon–energy coupling and algal–bacterial synergy, driving more than 50% nitrate removal in cropland sections, albeit with increased risks of N₂O emissions due to algal bloom–induced fluctuations in dissolved oxygen. In the dry season, hydro-stress imposed carbon limitation and metabolic competition, disrupted C–N coupling, and led to total nitrogen accumulation above 18 mg/L; nitrification declined by more than 90% under top-down predator control. Nutrient overload triggered “overload co-amplification” among both lower trophic levels and predators in cropland and built-up sections. This study proposes multi-dimensional watershed nitrogen management strategies to restore stoichiometric balance by optimizing energy flows across trophic levels through environmental flow management, integrating external nutrient reduction, and regulating food web interactions for multi-trophic control in river ecosystems.