The structure, factors and analytical frameworks of microbial food webs in aquatic ecosystems

Rivers and lakes are fundamental to global biogeochemical cycles and aquatic ecosystem stability. The health of these systems is largely governed by microbial food web (MFW) dynamics, which regulate energy transfer and nutrient cycling. However, existing methodologies remain largely descriptive, lacking the capacity to quantitatively link MFW structure to ecosystem function—a critical gap that limits predictive understanding of how these systems respond to environmental change. To address this gap, we propose an advanced analytical framework grounded in ecological trophic networks that integrates taxonomic identification, functional annotation, and trophic interaction inference. By explicitly reconstructing trophic architecture and quantifying energy flow pathways, this framework enables mechanistic assessment of material cycling and reveals how MFWs adapt along environmental gradients. This approach thus provides both a robust tool for aquatic ecosystem health assessment and a scientific basis for conservation and sustainable management strategies.