Environmental DNA metabarcoding links eutrophication to small-scale changes in biotic community structure: The importance of taxon mobility

Environmental DNA (eDNA) metabarcoding has been used for monitoring community shifts, but its resolution in detecting small-scale biotic gradients remains largely untested. In this study, we applied eDNA metabarcoding to detect alterations in marine communities using 12S-V5 (vertebrates) and 18S-uni (other eukaryotes) primer sets along a ~ 20 km harbour in Hong Kong. Analysis of water quality data from 2018 to 2022 revealed a eutrophication gradient, characterised by increasing concentrations of chlorophyll-a and biochemical oxygen demand (BOD5), from the harbour to the open ocean. We observed a rise in vertebrate taxa richness, from 16 in the harbour to 27 in the open ocean. The richness of other eukaryotes was significantly lower at the harbour site. Community analyses revealed substantial differences in biotic assemblages. High-trophic consumers increased from 26 to 54 along the sites. Sampling sites and environmental variables significantly explained the dissimilarities in the relatively stationary other eukaryotes, and explained the dissimilarities of the relatively mobile vertebrate communities to a lesser extent. Non-metric multidimensional scaling further supported the importance of environmental factors in shaping the assemblages. We discovered that the BIOENV-selected variables and eutrophication index effectively predicted the abundance of several taxa, particularly for the other eukaryotes. The concentration of phaeo-pigments was the most significant negative predictor of the trophic levels. We identified several polychaetes and dinoflagellates as indicator species of eutrophic waters. This study highlights the effectiveness of eDNA-based biomonitoring in linking community composition to eutrophication and the importance of considering animal mobility in understanding small-scale changes in community structure.