The overexploitation of marine resources by commercial fisheries poses significant threats to marine biodiversity and ecosystem stability. Vulnerable Marine Ecosystems (VMEs) require urgent protection to mitigate the adverse impacts of fishing activities, especially deep-sea bottom trawling. Given our incomplete knowledge of the marine environment, rapid and precise localization of VMEs is a priority to protect them effectively. Traditional methods for identifying VMEs are often limited by logistical challenges, high costs, and potential sampling biases. In this study, we assess the effectiveness of environmental DNA (eDNA) metabarcoding as an innovative tool for detecting and mapping VMEs in the Mediterranean Sea. eDNA samples were gathered at 19 sampling sites during a scientific fishing campaign in the Eastern Ionian Sea. Through the amplification of the COI mitochondrial gene, we identified a total of 274 unique taxa. A total of seven VME Indicator (VMEI) taxa were detected. A Joint Species Distribution Model (JSDM), using Hierarchical Modelling of Species Communities (HMSC), was used to investigate possible relationships between VMEI taxa and environmental covariates. Predicted distribution patterns of VMEI taxa were used to calculate a richness-weighted VME index. Taxon richness was highest at sites with high VME Index values. These findings demonstrate the potential of eDNA metabarcoding to effectively map the distribution of VMEI taxa, identify key environmental drivers influencing their occurrence and assess overall ecosystem vulnerability. We argue that an integration of eDNA-based approaches with traditional fisheries surveys could significantly enhance biodiversity assessments and improve conservation strategies in data-limited marine environments.
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