Sustainable monitoring of commercial fish in the Belgian part of the North Sea through eDNA ddPCR analyses

Traditional monitoring of fish in the North Sea mainly occurs via trawling, yet this method is invasive and destructive to the environment as it disturbs the seafloor and causes bycatch of non-target species. Furthermore, due to regulations it is not allowed to monitor via trawling in certain important regions, such as windfarms. Recent advancements in environmental DNA (eDNA) applications offer opportunities for more sustainable alternatives for fish monitoring. eDNA comprises all intra- as well as extracellular genetic material present in an environmental sample. In the case of fish, this DNA can come from the shedding of scales and mucus or the release of gametes for example. A great advantage of using eDNA, is that only a small amount of water is required to analyse it. Therefore, samples can be taken from smaller vessels or even automated samplers, without having to catch any fish or disturb the environment. By analysing the eDNA, species presence/absence and community composition can be inferred. This method is very sensitive and often detects rare and elusive species that traditional methods tend to miss. In this study, we wanted to take this one step further and investigate whether species specific eDNA concentrations in marine water samples correlate with local fish abundance estimates obtained via traditional beam trawling. eDNA concentrations were determined through droplet digital PCR (ddPCR), which is a very sensitive technique that can detect and quantify even a few molecules of DNA in a sample. We tested whether eDNA concentrations of three of Belgians most economically important species, being common sole (Solea solea), plaice (Pleuronectes platessa) and whiting (Merlangius merlangus) correlate with their abundances based on beam trawling data. To this end, water samples were collected in tandem with beam trawl 1 km transects in March 2020 at 12 sites in the Belgian part of the North Sea (BPNS). These sites were selected based on the absence, low or high abundances of the three fishes as indicated by monitoring data of epibenthos from previous years. Species specific ddPCR primer/probe assays were developed for sole and whiting and an existing one was implemented for plaice. Results indicate promising correlations for all three species but with some “false” positives. Yet, these may actually be true positive detections that the trawling transects missed and therefor warrant further investigation to see how far eDNA signals can be detected. Next, 50 water samples were collected in Autumn 2020, involving more locations with or without the three fishes. This time samples were taken at the beginning, middle and end of the 1 km transects to assure that the eDNA better represents the trawling transect and to investigate local variation in concentrations. The autumn samples are currently being processed, and results will be able to further fine tune these correlations for the BPNS. As a next step, species specific DNA shedding rates will be investigated as well as the local eDNA patterns which are likely to be more complex in the marine environment compared to freshwater systems. The combined results of these experiments will show if the correlations can become strong enough to allow accurate abundance estimations, and will allow a thorough evaluation off eDNA as a potentially efficient and sustainable alternative/addition to traditional abundance estimation methods.

Jaar van publicatie:2021