Development of an eDNA-based survey method for urban fish markets

Fish and fishery products are among the most highly traded commodities in the world, and over-exploitation continues to threaten the biodiversity and sustainability of global stocks. The state of knowledge for many fish species is limited by current monitoring techniques, which rely on labour-intensive visual or genetic surveys of individual specimens (often at inconsistent or coarse taxonomic resolution). To address the need for more efficient methods that effectively monitor trade, we developed a novel application of eDNA-based metabarcoding that can identify a broad range of fish taxa from effluent water draining from urban fish markets. Using samples collected at three Hong Kong fish markets over a 5-day period, we tested two DNA capture protocols (filtration vs. precipitation) with the goal of ensuring that methods were relatively easy to implement without sacrificing species coverage relative to each other and to a standard visual survey. eDNA-based survey methods were able to overcome many of the challenges associated with visual identification, such as resolving morphologically similar species and accounting for butchered fish products. However, rare and/or quickly transiting species occasionally went undetected. The two variations of eDNA isolation methods performed almost identically, emphasizing the relative robustness of eDNA metabarcoding, and allowing for user flexibility depending on the turbidity of collected waters. Our results demonstrate the ability of a few spatial and temporal replicates to generate an efficient and accurate market-wide species inventory that can complement visual inspections and guide targeted investigations of illegal trade. This research provides important baseline information on the capabilities of eDNA metabarcoding as a non-invasive survey tool, with the potential to complement conventional surveys. To our knowledge, this study is the first proof of concept using eDNA metabarcoding to monitor wildlife trade and also highlights the potential for eDNA metabarcoding to be applied to investigations of urban ecology.

Automated summary

Fish and fishery products are highly traded commodities, but over-exploitation threatens their sustainability. Current monitoring techniques have limitations in assessing fish species. To address this, researchers developed an eDNA-based method to identify fish taxa from effluent water. Results showed that eDNA methods could overcome challenges of visual identification and provide an efficient and accurate market-wide species inventory.