Environmental DNA as a method to reconstruct food webs and assess ecosystem health

• A food web was constructed with taxa identified using environmental DNA (eDNA). • Ecological Network Analysis (ENA) indices help us to define ecosystem properties. • ENA indicators were adapted to be calculated from eDNA-based food webs. • eDNA-based indicators appear to be powerful to assess ecosystem health. • Further research is needed to facilitate the implementation of such analyses. Food web indicators have been developed to describe ecosystem structure and dynamics. Their potential to inform ecosystem management and conservation is undeniable (e.g., Marine Strategy Framework Directive / Descriptor 4). Here, a method was developed to obtain a set of indicators of ecosystem structure and functioning (e.g., mean trophic level, connectivity, redundancy) based on food webs reconstructed using environmental DNA (eDNA). Indeed, eDNA metabarcoding datasets were used to identify the trophic groups and their predator–prey interactions were assessed from the literature. Traditional methods generally require collecting extensive data on biomasses and diets. Such methods are robust but time-consuming, expensive, subject to bias and they require lethal sampling. eDNA-based food web reconstructions are more exhaustive (due to the high detectability of species using eDNA), rapid and non-invasive. In 2023, a study was conducted in Normandy (France) to compare this innovative approach to a more commonly used method (Ecopath with Ecosim), based on the same set of indicators. Correlations were observed, especially on response patterns. With eDNA, ‘complete’ snapshots of food webs can be obtained to monitor the effects of natural and anthropogenic changes (e.g. development projects) as well as the effects of conservation or restoration actions on ecosystem properties.