Net gain: Low-cost, trawl-associated eDNA samplers upscale ecological assessment of marine demersal communities

Marine biodiversity stewardship requires costly and time-consuming capture-based monitoring techniques, which limit our understanding of the distribution and status of marine populations. Here, we reconstruct catch and demersal community composition in a set of 24 fishing sites in the central Tyrrhenian Sea by gathering environmental DNA (eDNA) aboard commercial bottom-trawl fishing vessels. We collected genetic material from two sources: the water draining from the net after the end of hauling operations (“slush”), and custom-made rolls of gauze tied to a hollow perforated sphere placed inside the fishing net (“metaprobe”). Species inventories were generated using a combination of fish-specific (Tele02 12S) and universal metazoan (COI) molecular markers. DNA metabarcoding data recovered over 90% of the caught taxa and accurately reconstructed the overall structure of the assemblages of the examined sites, reflecting expected differences linked to major drivers of community structure in Mediterranean demersal ecosystems, such as depth, distance from the coast, and fishing effort. eDNA also returned a “biodiversity bonus” mostly consisting of pelagic species not catchable by bottom trawl but present in the surrounding environment. Overall, the “metaprobe” gauzes showed a greater biodiversity detection power as compared to “slush” water, both qualitatively and quantitatively, strengthening the idea that these low-cost sampling devices can play a major role in upscaling the gathering of data on both catch composition and the broader ecological characteristics of marine communities sustaining trawling activities. This approach has the potential to drastically expand the reach of ecological monitoring, whereby fishing vessels operating across the oceans may serve as opportunistic scientific platforms to increase the strength and granularity of marine biodiversity data.