Monitoring dolphinfish catches and diel assemblage fluctuations using eDNA at Fish Aggregating Devices

Fish Aggregating Devices (FADs) are man-made objects designed to attract fish, with the aim of facilitating spatially heterogeneous aggregations of marine species. These objects influence the structure of pelagic fisheries, consequently affecting fish distributions and interactions. One of the most iconic epipelagic species targeted using FADs is dolphinfish (Coryphaena hippurus), which has high commercial value in the Mediterranean Sea. However, the interactions between dolphinfish and FADs are still poorly understood, and the composition of fish assemblages attracted to these devices remains poorly characterized. Environmental DNA (eDNA) metabarcoding has emerged as a powerful tool for fisheries management. Here, we employed passive eDNA samplers (i.e., metaprobes) to collect information on the fish assemblages around five FADs in Maltese waters during a dolphinfish fishing day in January 2023. Samples were gathered during different diel phases: three stations were sampled in the diurnal phase, while two were sampled during the crepuscular-evening phase. Through the amplification of the mitochondrial 12S gene region (Elas02 primers), we explored the relationship between C. hippurus caught biomass (kg) and transformed read counts, and investigated the composition of fish assemblages associated with FADs. A positive relationship was found between eDNA transformed read counts of dolphinfish and their biomass (linear regression model, R2 = 0.62, p < 0.05). Fish assemblages attracted by FADs were found to significantly change between diurnal and crepuscular-evening phases. Moreover, the Indicator Species Analysis identified four species as being indicative of the crepuscular-evening phase (D. rafinesquii, H. benoiti, H. hygomii and L. pusillus). The SIMPER test identified seven species as the main contributors to variations in dolphinfish caught biomass. Of these, four species (S. pilchardus, T. trachurus, E. encrasicolus and C. labrosus) showed a significant relationship between their transformed read counts and dolphinfish caught biomass. Despite the small number of samples, this study highlighted the potential of low-cost passive eDNA collection to assess the composition of pelagic fish assemblages around FADs. This improves our understanding of the ecological dynamics around these fishing gears and helps to optimise fishing efficiency, thereby promoting sustainable fisheries management strategies.