Zoom into a twilight zone: a biodiversity survey of the Dohrn Canyon (Mediterranean sea) through environmental DNA metabarcoding

The deep sea represents the largest ecosystem on Earth, and the mesopelagic zone, particularly submarine canyons, provides fundamental ecosystem services. Despite their importance, deep sea habitats remain one of the least explored ecosystems due to their remoteness, inaccessibility, and high costs for exploration. In this study, we used environmental DNA (eDNA) metabarcoding to investigate the biodiversity of the Dohrn Canyon in the Gulf of Naples (ca. 800 m; Mediterranean Sea), using two gene markers (V9-18S rRNA Euk1391F and EukBr and 12S rRNA MiFish_U primers) to detect eukaryotes, both protozoans and metazoans, including fish. We report on the biodiversity of this deep environment, including 41 planktonic phyla and 5 mesopelagic fish. The copepod genus Clausocalanus was dominant among planktonic metazoa, while Radiolaria and the parasitic dinoflagellate Syndiniales were the most representative protist taxa. Most fishes detected belong to mesopelagic fauna. Our study reports a snapshot of the biodiversity of a poorly explored deep ecosystem and provides the base for future ecological investigations, highlighting the need to expand knowledge of the deep sea in the Gulf of Naples by integrating eDNA data and visual surveys.