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.鱼聚集装置（Fish Aggregating Devices, FADs）是人为设计的诱鱼设施，旨在促成海洋物种在空间上的异质性聚集。这类设施会影响中上层渔业的群落结构，进而改变鱼类的分布格局与种间相互作用。利用鱼聚集装置捕捞的标志性大洋上层鱼类之一为鲯鳅（Coryphaena hippurus），该物种在地中海地区拥有较高的商业价值。然而，目前学界对鲯鳅与鱼聚集装置之间的相互作用仍缺乏深入认知，且这类设施所吸引的鱼类群落组成也尚未得到充分表征。环境DNA（environmental DNA, eDNA）宏条形码技术已成为渔业管理领域的强有力工具。本研究于2023年1月的一次鲯鳅捕捞作业期间，在马耳他海域的5个鱼聚集装置周边，采用被动式环境DNA采样器（即元探针采样器）采集鱼类群落相关信息。采样覆盖了不同的昼夜时段：3个站位在日间完成采样，剩余2个站位则在黄昏-夜间时段开展采样。通过扩增线粒体12S基因区域（使用Elas02引物），本研究探究了鲯鳅的捕捞生物量（单位：千克）与标准化读段数之间的关联，并分析了与鱼聚集装置相关的鱼类群落组成。研究结果显示，鲯鳅的环境DNA标准化读段数与其捕捞生物量之间存在显著正相关关系（线性回归模型，R²=0.62，p<0.05）。鱼聚集装置所吸引的鱼类群落组成在日间与黄昏-夜间时段之间存在显著差异。此外，指示物种分析筛选出4个物种作为黄昏-夜间时段的指示类群：D. rafinesquii、H. benoiti、H. hygomii及L. pusillus。相似性百分比（SIMPER）分析识别出7个物种是导致鲯鳅捕捞生物量差异的主要贡献类群。其中，S. pilchardus、T. trachurus、E. encrasicolus及C. labrosus这4个物种的标准化读段数与鲯鳅的捕捞生物量之间存在显著关联。尽管本研究的样本量较小，但仍证实了低成本被动式环境DNA采样技术在评估鱼聚集装置周边中上层鱼类群落组成方面的应用潜力。该研究有助于深化我们对这类捕捞设施周边生态动态的理解，助力优化捕捞效率，进而推动可持续渔业管理策略的制定与实施。