Environmental DNA (eDNA) Metabarcoding in the Fish Market and Nearby Seafood Restaurants in Taiwan Reveals the Underestimation of Fish Species Diversity in Seafood

Simple Summary: Seafood, especially the traditional one in Taiwan, is rarely sourced from a fixed species and routinely from similar species depending on their availability. Hence, species diversity in seafood could be potentially complicated. While a DNA-based approach has been extensively utilized for species identification, a large scale of seafood species identification in fish markets and nearby seafood restaurants could be challenging (e.g., elevated cost and time-consuming only for a limited number of species identification). Environmental DNA (eDNA) metabarcoding has emerged as a promising tool for the simultaneous identification of multiple species in the environments. In this work, we aimed to identify the majority of fish species potentially consumed in fish markets and nearby seafood restaurants using this novel approach. A total of 153 fish species have been identified. Specifically, 22 chondrichthyan fish, 14 Anguilliformes species, and 15 Serranidae species were potentially linked with smoked sharks, braised moray eels, and grouper fish soups, respectively. This is the first study to examine the feasibility of a large scale of seafood identification using eDNA metabarcoding. Our findings also further imply the species diversity in traditional seafood might be seriously underestimated and crucial for the conservation and management of marine resources. Seafood, especially the traditional one in Taiwan, is rarely sourced from a fixed species and routinely from similar species depending on their availability. Hence, the species composition of seafood can be complicated. While a DNA-based approach has been routinely utilized for species identification, a large scale of seafood identification in fish markets and restaurants could be challenging (e.g., elevated cost and time-consuming only for a limited number of species identification). In the present study, we aimed to identify the majority of fish species potentially consumed in fish markets and nearby seafood restaurants using environmental DNA (eDNA) metabarcoding. Four eDNA samplings from a local fish market and nearby seafood restaurants were conducted using Sterivex cartridges. Nineteen universal primers previously validated for fish species identification were utilized to amplify the fragments of mitochondrial DNA (12S, COI, ND5) of species in eDNA samples and sequenced with NovaSeq 6000 sequencing. A total of 153 fish species have been identified based on 417 fish related operational taxonomic units (OTUs) generated from 50,534,995 reads. Principal Coordinate Analysis (PCoA) further showed the differences in fish species between the sampling times and sampling sites. Of these fish species, 22 chondrichthyan fish, 14 Anguilliformes species, and 15 Serranidae species were respectively associated with smoked sharks, braised moray eels, and grouper fish soups. To our best knowledge, this work represents the first study to demonstrate the feasibility of a large scale of seafood identification using eDNA metabarcoding approach. Our findings also imply the species diversity in traditional seafood might be seriously underestimated and crucial for the conservation and management of marine resources.