The molecularly and visually identified prey of fish in Dutch salt marshes

Coastal marshes are an important habitat for many juvenile and small fishes, providing refuge and feeding opportunities. Understanding their diets can reveal more about the food web and the underlying factors impacting fish in these threatened habitats. We compared the diets of common goby ( Pomatoschistus microps ), three-spined stickleback ( Gasterosteus aculeatus ), Atlantic herring ( Clupea harengus ), European flounder ( Platichthys flesus ), European seabass ( Dicentrarchus labrax ), and European smelt ( Osmerus eperlanus ). These fish were collected seasonally from Dutch Wadden Sea salt marshes using fyke nets set at fixed stations from three locations with varying degrees of habitat modification. Comparing visual identification and DNA metabarcoding (CO1 region) of stomach contents revealed that DNA (relative read abundance) could be used semi-quantitatively for the dominant prey classes, but failed to detect some prey groups identified visually. The dominant prey of most fish species were the harpacticoid copepod Tachidius discipes , the amphipod Corophium volutator , and other crustaceans including Crangon crangon and Neomysis integer. Diets were affected by season, abiotic conditions, predator length, sampling location, and predator species. Gobies and stickleback shared similar diets, while the four other species displayed distinct diets. Flounder diets were characterised by benthic prey, herring diets consisted predominantly of copepods, smelt were generalists, while seabass diets predominantly contained Malacostraca. Fish diets at the least modified sampling location exhibited the greatest prey diversity. Our findings indicate that salt marshes provide a feeding habitat for the resident and migrant fish species studied, where the degree of marsh habitat modification may affect the marine food web. • Salt marshes provide a feeding habitat for resident and migratory fish. • Benthic prey dominated the diets of the six fish species studied. • Fish diets varied according to life history strategy and feeding behaviour. • Cross-referencing DNA and visual methods enhances prey detection in diet analyses. • Results from DNA metabarcoding could be used quantitatively for dominant prey classes.