Fig. 1: Methods summary and hypothesize diagram of this study.

A Methods summary: using sedimentary DNA metabarcoding, we derived an abundance matrix for invertebrates, protozoa, fungi, algae, and bacteria. Species were classified into 13 functional groups based on taxonomy and trophic roles, forming a conceptual network defined by predation, mutualism, and competition. Employing empirical dynamic models with convergent cross mapping, we simulated annual ecological networks, calculating key parameters: connectance and interaction strength. Generalized additive models and structural equation modeling were then applied to assess the impact of environmental factors—lake area, nutrients, and temperature—on network characteristics and to elucidate the pathways through which these factors influence ecological diversity and network structure. B Hypothesize diagram: we hypothesized that species diversity and the connectance and strength of ecological networks would decrease first, then increase, and then decrease again under low–medium–high stress gradients, respectively.