eDNA Metabarcoding Analysis as Tool to Assess the Presence of Non-Indigenous Species (NIS): A Case Study in the Bilge Water

One of the most important causes of biodiversity loss are non-indigenous species (NIS), in particular invasive ones. The dispersion of NIS mainly depends on anthropogenic activities such as maritime traffic, which account for almost half of the total NIS introduction in the European seas, as reported by the European Environmental Agency. For this reason, NIS management measures are mainly focused on commercial ports (i.e., ballast water management and Marine Strategy Framework Directive monitoring), underestimating the role of marinas and tourist harbors; these host small vessels (<20 m), such as recreational, fishery, and sail ones without ballast waters, but are also responsible for NIS arrival and spread through the bilge water as well as from hull fouling. With the aim of paying attention to marinas and tourist harbors and validating an innovative molecular methodology for NIS surveillance and monitoring, in the present work, eDNA metabarcoding of cytochrome oxidase subunit I (COI) was applied to both bilge waters and adjacent ones to assess species composition and particularly NIS presence. A total of 140 OTUs/species with extra-Mediterranean distribution were found in the bilge samples; several of these are most likely ascribed to food contamination (e.g., Salmo salar). Excluding food contamination species, twelve of these found in the bilge waters were already known as NIS in the Mediterranean Sea, belonging to algae, mollusks, crustaceans, annelids, echinoderms, and fishes. Nine of these species are new to Italian waters. The results obtained in the present work support the importance of NIS monitoring in marinas and small harbors, particularly in the bilge waters, through eDNA metabarcoding, having detected several potential NIS that otherwise would not have been discovered.