Metaprobes associated with demersal longline surveys allow monitoring of deep sea fish communities

Monitoring the status of marine resources is a key activity in biodiversity conservation and fisheries science. However, scientific surveys still largely rely on costly and time-consuming traditional visual and capture-based methods. Recent advances in DNA sequencing allow species identification from trace DNA in the environment - environmental DNA (eDNA), which is becoming a primary source of biodiversity information in various environments. Here we collected samples through a low-cost and low-effort eDNA passive sampler - a hollow perforated spherical probe (the ‘metaprobe’) filled with gauze rolls - during a deep sea demersal longline survey in the southern Adriatic Sea (depth 900-1147 m). Samples were metabarcoded using an elasmobranch-specific marker (elas02-12S) and data analysis was performed through the OBITools metabarcoding pipeline, assigning taxonomy against a custom-made 12S vertebrate reference database. We were able to molecularly identify 6 elasmobranchs (Galeus melastomus, Mustelus mustelus, Etmopterus sp., Raja sp., Dipturus oxyrinchus, and Centrophorus cf uyato) and 20 bony fish taxa at genus/species level. Comparisons with catch data revealed that eDNA metabarcoding correctly reported all the species captured in each of the six hauls and provided an additional biodiversity ‘bonus’ of species not otherwise catchable, allowing for an overall better qualitative estimation of fish species composition of the deep pelagic environment (e.g., passing swordfish, the layer of myctophids). Further investigation is needed to overcome challenges inherent to the eDNA passive samplers' interaction with longline fishing gears, with the aim of expanding the range of fishing operations that can contribute to next-generation marine ecosystem monitoring.