Little samplers, big fleet: eDNA metabarcoding from commercial trawlers enhances ocean monitoring

The global need to monitor the status of marine resources is a priority task in marine management, but most ocean surveys still rely on costly and time-consuming capture-based techniques. Here we test a novel, easy-to use device to collect eDNA on board of bottom trawl fishing vessels, during normal fishing operations, quickly and easily: custom-made rolls of gauze tied to a hollow perforated spherical probe (the 'metaprobe') that placed inside the fishing net aims to gather traces of genetic material from the surrounding environment. We collected six samples from three central Tyrrhenian sites. Using an established fish-specific metabarcoding marker, we recovered over 70% of the caught species and accurately reconstructed fish assemblages typical of the different bathymetric layers considered. eDNA metabarcoding data also returned a biodiversity 'bonus' of mostly mesopelagic species, not catchable by bottom trawls. Further investigation is needed to upscale this promising approach as a powerful tool to monitor catch composition, assess the distribution of stocks, and generally record changes in fish communities across the oceans.

Automated summary

This study tests an easy-to-use device for monitoring marine resources, which can quickly collect environmental DNA during normal fishing operations on bottom trawl fishing vessels. Through sample collection and genetic analysis, the study accurately identifies fish assemblages at different depths and discovers mesopelagic species that are not caught by bottom trawls. This promising method has the potential to be a valuable tool for monitoring catch composition, assessing stock distribution, and documenting changes in fish communities in the oceans.