Sediment and bottom water eDNA metabarcoding to support coastal management

Ocean sprawl and climate change exacerbate coastal erosion and flooding, resulting in habitat loss and decreasing biodiversity. To counteract these threats, different coastal defence tools have been developed, with an increasing emphasis on nature-based solutions. However, tracking the impacts of these interventions on marine benthic organisms requires appropriate sampling designs and timely investigation methods due to the dynamic nature of coastal environments. Environmental DNA metabarcoding is a promising, non-invasive, and quick technique to monitor community changes. Here, environmental DNA COI-based metabarcoding data from sediment and bottom water samples were used to characterize benthic communities at three sites along the Emilia-Romagna coast differing in the topology of coastal defence actions (from no defences to groynes and low-crested barriers) and to evaluate the effectiveness of the two sampling matrices in detecting local biodiversity. The findings revealed significant differences in the structure of the benthic communities depending on site, sample type (i.e., sediment versus bottom water), and their interaction. The three sites differ in abiotic characteristic affecting the community composition. Lido di Dante and Riccione showed higher species diversity due to the new type of substrata provided by the hard defence structure, while Foce del Bevano showed the presence of species typical of low impacted areas. Bottom water, hosting more traces of pelagic and nektonic species, showed significantly different species composition compared to sediment samples, suggesting the need to consider both matrices in coastal monitoring.