A line with no hook: longline-associated passive eDNA samplers for deep-sea fish monitoring

Monitoring the status of marine biological resources is a key activity in biodiversity conservation and fisheries science. While scientific surveys still largely rely on costly and labour-intensive visual and capture-based methods, sequencing DNA traces from the environment has emerged as a promising alternative and integrative tool for biodiversity assessments. The environmental DNA (eDNA) approach has recently been further boosted by the development of a variety of passive collection methods, which can considerably reduce costs and upscale sampling reach. We adopted a 3D-printed, low-cost passive eDNA sampler (the ‘metaprobe’) to collect data during a deep-sea demersal longline survey in the southern Adriatic Sea (depth range: 900–1147 m). eDNA samples from 12 metaprobes were metabarcoded using 12S rDNA primers targeting elasmobranchs, and taxonomic assignment was performed against an improved custom 12S Mediterranean fish reference database. eDNA detected all four cartilaginous and three of the five bony fish species captured, and additionally 11 species (three cartilaginous and eight bony fish) not caught by the gear. These taxa not caught by the longline produced a more comprehensive picture of the deep pelagic fish assemblages (e.g., large pelagic species such as tuna and swordfish, and mesopelagic lanternfishes) and the diel variation related to these species' behaviours, highlighting the potential benefit of integrating this simple sampling tool with cooperating longline fisheries operations. Further investigation should refine sampling methodologies to optimize metaprobes interaction with longlines, to expand the types of fishing activity that can contribute to next-generation marine ecosystem monitoring.