Regular large-scale scientific bottom trawl surveys underpin stock assessments and the monitoring of fishing and environmental change effects on marine shelf communities worldwide and along the French coasts (Figure 1 for surveys in ICES area). They are an essential ingredient for ecosystem-based management. To assess the status of commercial stocks, each year at Ifremer we conduct four bottom trawls surveys, from the North Sea (IBTS) passing through the English Channel (CGFS) to the south of the Bay of Biscay (EVHOE) and in the Mediterranean Sea (MEDIT). These bottom trawl surveys are complemented by acoustic surveys monitoring pelagic species (PELGAS and PELMED). As fish stocks are not limited by country boundaries, all European countries that have access to the sea participate in the global effort of scientific surveys. The information collected during these scientific surveys is centralised and shared between countries. For the Northeast Atlantic, the International Council for the Exploration of the Sea (ICES) organises the harmonisation of data collection, data storage and the provision of scientific advice to the European Union. In turn the European Union co-funds the surveys via the data collection framework (DCF). The data also contribute to fulfil the monitoring obligations of the European Marine Strategy Framework Directive (MFSD). While the ecological impacts of these fish and shellfish bottom trawl surveys are minor in terms of biomass extraction or sea floor impacts compared to commercial fisheries, negative impacts nevertheless exist and raise ethical questions (Trenkel et al. 2019). This project takes up the challenge to develop alternative less impacting monitoring methods, making use of recent progress made in the area of environmental DNA analysis.
Monitoring of fish biodiversity is conventionally based on non-standardized detection methods and dependent on practical and taxonomic expertise (Wheeler et al. 2004). Moreover, each marine species leaves a footprint in the environment via faeces, urine and epidermal cells (Thomsen et al. 2012). All these sources of DNA may persist in the aquatic environment from hours to days and can be detected in water samples or sediments via new methods of DNA analyses called Environmental DNA (eDNA). These methods are non-invasive, demonstrate higher detection capabilities and cost-effectiveness compared to traditional methods (Dejean et al. 2011) and have been suggested to be potentially useful for environmental monitoring (Kelly et al. 2014, Thomsen & Willerslev 2015). Recent aquatic applications demonstrated its use for determining marine species richness (Valentini et al. 2016, Pont et al. 2018,) and seasonal species richness variation (Sigsgaard et al. 2017, Stoeckle et al. 2017), detecting rare endangered species (Simpfendorfer et al. 2016) and for obtaining abundance or biomass proxies (Thomsen et al. 2016, Klobucar et al. 2017). However, there are a range of methodological pitfalls and challenges to turn eDNA into a fully reliable and accurate approach to detect, let alone quantify species present in a given environment/location. These are related to the sampling (false negative due to the sampling protocol and level of detectability of target species, false positive due to contamination…), molecular analyses and bioinformatics (adequacy of the probes used to the taxa targeted, level of taxonomic resolution, sequencing errors, inhibition ...) as well as to the temporal and spatial scales involved (persistence of nucleic acid in the environment) (Thomsen & Willerslev 2015).
The study will be carried out on the French continental shelf of the Bay of Biscay. In this area, the EVHOE bottom trawl survey has been carried out since 1987, providing reliable trawl data for comparison. For a long list of fish and invertebrate species presence/absence information can be compared. For a restricted list of species (see table 1; spatial distributions shown in figure 2) quantified eDNA could be compared to bottom trawl data (numbers or biomass) and possibly related to population size estimates from stock assessment modelling. All the selected species are of commercial interest. For the quantitative eDNA analysis higth species will be selected, the hake (Merluccius merluccius), the blackspot seabream (Pagellus bogaraveo).