Nutrient loading induces bistability in microeukaryotes of pump station forebay sediments with interdomain regulation of nitrogen cycling

Excessive nutrient inputs significantly alter the stability and functioning of aquatic ecosystems. However, a systematic understanding of how benthic microbial communities respond to nutrient loading through nonlinear regime shifts remains limited. This study investigated the multi-stability characteristics and functional feedback mechanisms of microbial communities under varying nutrient loads in sediments from pump station forebays, by using 16S rRNA and 18S rRNA amplicon sequencing. Results revealed a distinct bistable distribution in microeukaryotic communities, while bacterial communities exhibited a continuous, monostable response. Stability landscape analysis identified a hysteresis window (0.958–1.741) in the microeukaryotic response to nutrient loading. When nutrient levels exceeded this threshold, the microeukaryotic community shifted from State B (active nitrogen metabolism) to State A (reduced nitrogen metabolic potential). Under bistable conditions, State B exhibited higher network complexity between microeukaryotes and bacteria, suggesting stronger inter-domain associations and greater functional redundancy. Partial least squares path modeling (PLS-PM) revealed significant associations among nutrient loading, microeukaryotic community bistability, bacterial community structure, and nitrogen metabolic potential. The results support a conceptual framework in which microeukaryotic community states are closely linked to cross-trophic community organization and benthic nitrogen cycling potential. This study provides new insights into nutrient load management and microbial-based strategies aimed at enhancing ecosystem resilience and restoration. • Microeukaryotic not bacterial communities were proved to exist bistability. • Microeukaryotes exhibit a hysteretic response to nutrient loading. • State B shows more complex networks and higher nitrogen-cycling potential. • Microeukaryotic bistability mediates cross-trophic nutrient-function associations.