Synergistic Regulation of Plankton Communities by Polyculture of Grass Carp and Crucian Carp: Seasonal Dynamics and Interaction Networks Based on eDNA.

Large-water fisheries are central to China's freshwater aquaculture, but their sustainability is threatened by eutrophication from traditional high-density stocking. Polyculture of grass carp and crucian carp offers an ecologically sound alternative; nevertheless, its direct effects on plankton communities require further study. We conducted monthly sampling from July to December 2023 (over two seasons within a single aquaculture cycle) in polyculture ponds and used eDNA metabarcoding (18S V9) with high-throughput sequencing. We detected 288 planktonic taxa across 28 phyla and 290 genera based on eDNA sequence assignment. Alpha diversity (Chao1, Shannon, Simpson) peaked in autumn and was lowest in winter, with Chao1 showing greater seasonal variation. Beta diversity revealed season as the dominant factor (R2 = 0.287, p = 0.012), with significant summer-winter divergence. Null-model analysis indicated stochastic processes (56.3%) slightly exceeded deterministic filtering (43.7%), and stochasticity was higher in summer (67.2%), suggesting fish bioturbation and grazing create heterogeneous microhabitats. Co-occurrence networks were dominated by positive links (87.3%), with Cryptomonas as a central hub, implying mutualism and niche complementarity. This study is the first to integrate eDNA metabarcoding with community assembly theory to elucidate seasonal succession and interactions in this polyculture. Our findings confirm that polyculture sustains diversity and stability via top-down (grazing) and bottom-up (nutrient release) effects, providing eDNA-based taxonomic evidence for management of large-water aquaculture.