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

Abstract

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.

Species identification in fish meal from urban fisheries biomass with DNA metabarcoding analysis

“…Besides, DNA metabarcoding method detected almost four species, that is, cod, whiting, haddock, and wolffish from fish silage sample (Hansen et al., 2020). Although 153 fish species were identified from water near the drains of a fish market (Lee, Liao & Hsu, 2021) using the same primers as we used in our study, no quantitative analysis was performed in the earlier study. Furthermore, there have been no studies where more than 100 of fish species detected from processed products directly.…”

Ecotype Origin of an Entangled Killer Whale (Orcinus orca) Identified with Remnant mtDNA

“…Our findings demonstrate both the diagnostic capabilities of genetic sampling and the surprising residency of recoverable mtDNA from anthropogenic debris. mtDNA barcoding has been used in other wildlife forensics applications, from identifying endangered taxa traded in Ecotype entangled killer whale mtDNA markets to shark species from bite wounds (Baker 2008;Lee et al, 2021). Genetic identification of marine mammal carcasses is standard for U.S.-based stranding networks, but we stress there may be added value from genetic analysis of marine debris associated with marine mammal entanglements, particularly in helping to assign an anthropogenic mortality event to ecotypes or Distinct Population Segments (Baulch and Perry, 2014;Carretta et al, 2021).…”