Characterisation of coastal reef fish assemblages across an estuarine-urbanisation gradient using underwater visual survey and environmental DNA metabarcoding

Abstract

The ongoing urbanisation of coastlines around the globe jeopardises biodiversity, including coastal marine fishes. In many places, baseline data on fish communities are inadequate for understanding the ecological and conservation impacts of this urbanisation. Here, we document spatiotemporal patterns in fish diversity (at genus level) across an estuarine gradient around Hong Kong, a highly urbanised coastal megacity bordering the estuary of the Pearl River, the second largest river in the People’s Republic of China. We combined underwater visual census (UVC) with eDNA metabarcoding (eDNA) to overcome challenges associated with the high turbidity of Hong Kong’s aquatic environment that limits the capacity for visual observations. Similar to previous studies, UVC and eDNA captured different components of the fish community, sharing only 36.5 % fish genera in common. Nevertheless, we recorded 17 % of the known fish diversity and provided a comprehensive picture of patterns in fish diversity across the gradient, despite limited sampling effort. Fish richness was reduced by 1.6-to 3-fold under the highly turbid estuarine conditions found around Lantau compared to other regions. However, overall, there were only moderate changes in the fish community regionally. Seasonal variations in fish richness and assemblage structure were observed using both approaches, taken to reflect changes in fish behaviour, physiology, and naturally occurring events (i.e., spawning and recruitment) between seasons. A notable, consistent reduction in eDNA richness in the semi-enclosed Port Shelter might reflect limited exchange of water and genetic materials. A total of eleven species that had not been previously reported from Hong Kong were detected. These potentially novel species, as well as other ecologically and economically important species in Hong Kong, might be insufficiently protected from unregulated fishing activities due to the limited spatial coverage of marine protected areas.