Marine ecosystems are increasingly threatened by human-induced pressures such as overfishing, pollution, climate change, and habitat degradation. These disturbances lead to biodiversity loss, shifts in species composition, and the spread of non-indigenous species, underscoring the urgent need for effective conservation and monitoring strategies. Environmental DNA (eDNA) metabarcoding has emerged as a powerful, non-invasive approach for assessing biodiversity by detecting organisms through genetic material present in environmental samples. This study explores the application of eDNA metabarcoding to monitor metazoan biodiversity across multiple benthic habitats within the Tremiti Islands Marine Protected Area (MPA) in the southern Adriatic Sea. By comparing community composition among distinct marine environments, the research highlights the potential of eDNA-based methods to reveal ecological patterns and detect invasive species, even in the absence of visual records. These findings reinforce the value of molecular tools for marine biodiversity assessments and call for further efforts to expand reference databases and integrate complementary sampling strategies to enhance monitoring accuracy in Mediterranean MPAs.
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