Mediterranean transitional waters are vital ecosystems that provide essential services such as water filtration, carbon sequestration, and habitat support, while also acting as buffers against climate change impacts like sea-level rise and temperature fluctuations. However, these ecosystems face increasing threats from non-indigenous species (NIS), pollution, and human activities, emphasizing the need for effective conservation strategies.

Environmental DNA (eDNA) metabarcoding is increasingly revolutionizing the way large-scale biodiversity monitoring is conducted, offering an innovative and non-invasive approach to assess ecological communities. This method relies on the analysis of genetic material, such as, DNA fragments shed by organisms into their surrounding environment, collected from environmental matrices such as water, soil, or sediment. Bypassing the need for direct observation or physical capture of organisms, eDNA enables the detection of a wide array of taxa, including cryptic, rare, or elusive species, with minimal disturbance to the ecosystem. Within this framework, we applied eDNA-based technologies to explore biodiversity patterns and community structure in transitional aquatic ecosystems of the Mediterranean region.

In particular, the conducted studies implemented eDNA metabarcoding protocols focusing on two widely used genetic markers: the mitochondrial cytochrome c oxidase subunit I (COI) gene, typically employed for the identification of metazoans, and the V4 region of the 18S ribosomal RNA gene, a broad eukaryotic marker suitable for capturing the diversity of microeukaryotic communities like phytoplankton. The obtained results revealed distinct spatial patterns in both phytoplankton and macrozoobenthic communities, closely aligned with the environmental gradients of salinity and temperature characterising transitional waters, suggesting a strong environmental filtering effect on community assembly, where abiotic conditions and localised impacts can influence species occurrence and abundance.

Overall, our research demonstrates the effectiveness of molecular approaches in ecological assessment, emphasizing the need for integrated conservation efforts that combine advanced technologies with traditional monitoring and community engagement to ensure the resilience of Mediterranean lagoon ecosystems in the context of ongoing environmental pressures.