Analysis of a Coastal North Sea Fish Community: Comparison of Aquatic Environmental DNA Concentrations to Fish Catches

Abstract Analyses of environmental DNA have the potential to become an integrated tool in fish research and management. We performed a pilot study during the spring migration of fishes from the North Sea into the Wadden Sea and present comparative results from daily fyke catches (20 mm mesh) in the Marsdiep tidal inlet on two locations and results from weekly fish eDNA analyses on three locations, all within 2 km distance. Fish catches did not differ significantly between the two locations, whereas the eDNA composition showed a significant location effect. However, when eDNA analysis was restricted to species that were caught with the fykes, differences among locations became insignificant. Over ten weeks, from late April to early July, presence–absence calls of fishes based on weekly eDNA sampling significantly agreed with calls based on seven days of fyke fishing 1 km westwards. Fish eDNA compositions differed significantly among sample days and months but not between tides. Over the season, patterns in eDNA concentration (12S rRNA gene copies/L) inferred from quantitative PCR and Illumina HiSeq community composition corresponded to patterns in wet mass for the eight most abundant fish species in the fyke (>6 weeks present) despite changes in water temperature and changes in fish size class. Small sandeel and gobies, which are important prey for large fishes and birds, were typically missed with the fyke but contributed up to 25%–40% of the fish eDNA depending on the sample location.