Decoding Benthic Macroinvertebrate Communities in Freshwater Ecosystems Leveraging Environmental DNA

• eDNA revolutionizes the study of benthic macroinvertebrate community ecology. • eDNA detects how freshwater benthic communities respond to human stressors. • eDNA offers high-resolution biodiversity dynamics in benthic communities. • eDNA enables studying complex multitrophic networks in freshwater ecosystems. • Research must test if morphology-based ecological theories of benthos hold with eDNA. Benthic macroinvertebrates are key indicator groups within freshwater ecosystems, with their community being closely tied to ecosystem functioning. Environmental DNA (eDNA) technology, with its high sensitivity and non-invasive nature, provides a promising tool for studying the spatiotemporal dynamics of benthic macroinvertebrate communities, their responses to anthropogenic disturbances, and the mechanisms governing community assembly. However, current eDNA-based research on freshwater benthic communities largely concentrates on optimizing sampling and detection methods, along with environmental monitoring applications. Broader ecological investigations based on eDNA data remain fragmented and limited in scope. In particular, it remains unresolved whether benthic community ecology theories derived from morphological classification can be reliably reconstructed from eDNA-based molecular signals. We systematically summarize the application of eDNA technology in benthic macroinvertebrate ecology, encompassing diversity assessment, spatiotemporal community dynamics, cascading effects of human-induced disturbances, and multi-trophic interaction networks. Although significant empirical progress has been made, challenges persist, including limited spatiotemporal coverage and methodological constraints. Future developments should prioritize the establishment of long-term monitoring networks, integration of multidimensional data, and deeper engagement with community ecology theories. Such advances will help shift eDNA-based research from descriptive to mechanistic understanding, thereby offering scientific support for the precise management and restoration of river ecosystems.