Seasonal wet–dry transitions reveal contrasting microbial stability and nutrient cycling across floodplain lake habitats

Saucer-shaped sub-lakes in floodplains undergo strong seasonal changes in water level and connectivity, but their microbial responses and roles in nutrient cycling remain poorly understood. Here we show, using 28 lake units across Lake Poyang, China, that seasonal hydrological change is associated with distinct patterns of microbial stability and nutrient cycling in water and sediment. Core microbial taxa support both diversity and compositional stability, as their removal reduces both measures of community resistance. Functional shifts are stronger in water, where nitrogen cycling potential increases during the dry season while phosphorus uptake, assimilation, and storage potential declines. Sediment shows weaker seasonal reorganization, with moderate increases in downstream nitrogen reduction and a shift toward phosphorus regeneration and supply. Environmental variation is also associated with changes in core microbial community composition and nutrient cycling potential. Together, these findings show that seasonal hydrological change is accompanied by coordinated but contrasting microbial and nutrient cycling responses in water and sediment.