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

The ongoing urbanisation of coastlines around the globe greatly impacts biodiversity, including coastal marine fishes. In many places, baseline data on fish communities are inadequate for understanding and managing the ecological 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 % of 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. Visual estimates of fish generic richness were reduced by 1.6- to 3-fold under the highly turbid estuarine conditions found around Lantau compared to other regions. However, there were only moderate changes in the fish community regionally overall. Seasonal variations in fish generic 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 fish richness from eDNA in the semienclosed Port Shelter might reflect limited exchange of water and genetic materials. Eleven species not previously reported from Hong Kong were detected. The potential new records, together with other regionally understudied species of ecological and economic value, highlight the need for more comprehensive biodiversity baselines and monitoring to inform marine resource management plans that more effectively safeguard the region's coastal marine biodiversity.