Increasing marine trophic web knowledge through DNA analyses of fish stomach content: a step towards an ecosystem-based approach to fisheries research.

Multispecies and ecosystem models, which are key for the implementation of ecosystem-based approaches to fisheries management, require extensive data on the trophic interactions between marine organisms, including changes over time. DNA metabarcoding, by allowing the simultaneous taxonomic identification of the community present in hundreds of samples, could be used for speeding up large-scale stomach content data collection. Yet, for DNA metabarcoding to be routinely implemented, technical challenges should be addressed, such as the potentially complicated sampling logistics, the detection of a high proportion of predator DNA, and the inability to provide reliable abundance estimations. Here, we present a DNA metabarcoding assay developed to examine the diet of five commercially important fish, which can be feasibly incorporated into routinary samplings. The method is devised to speed up the analysis process by avoiding the stomach dissection and content extraction steps, while preventing the amplification of predator DNA by using blocking primers. Tested in mock samples and in real stomach samples, the method has proven effective and shows great effectiveness discerning diet variations due to predator ecology or prey availability. Additionally, by applying our protocol to mackerel stomachs previously analyzed by visual inspection, we showcase how DNA metabarcoding could complement visually based data by detecting overlooked prey by the visual approach. We finally discuss how DNA metabarcoding-based data can contribute to trophic data collection. Our work reinforces the potential of DNA metabarcoding for the study and monitoring of fish trophic interactions and provides a basis for its incorporation into routine monitoring programs, which will be critical for the implementation of ecosystem-based approaches to fisheries management.

Analysis of potential drivers of spatial and temporal changes in anisakid larvae infection levels in European hake, Merluccius merluccius (L.), from the North-East Atlantic fishing grounds.

We analysed the spatial and temporal variability of Anisakis larvae infection in hake (Merluccius merluccius) from the North-East Atlantic from 1998 to 2020 and the potential drivers (i.e., environmental and host abundance) of such variation. The results showed that hake from separate sea areas in the North Atlantic have marked differences in temporal abundance levels. Hake larger than 60 cm were all parasitized in all ICES (International Council for the Exploration of the Sea) subareas 6, 7, and 8. The belly flaps were the most parasitized parts of the flesh, accounting for 92% of the total. Individuals of Anisakis simplex, Anisakis pegreffii, Anisakis spp. and a hybrid of Anisakis simplex × pegreffii were genetically identified, and Anisakis simplex as the most abundant (88-100%). An ecological niche model of Anisakis occurrence in fishes in the NE Atlantic was built to define the thermal optimum and environmental ranges for salinity, depth, chlorophyll concentration, and diffuse attenuation. The temporal variability of anisakid infection in fishes in the last two decades indicated an increase in the NE Atlantic at an annual rate of 31.7 nematodes per total number of specimens examined per year. This rise in infection levels could be triggered by the increase in intermediate host fish stocks, especially hake in the area.