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

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 identificatio...

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Autores principales:	Hung-Tai Lee, Cheng-Hsin Liao, Te-Hua Hsu
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	biodiversity DNA barcoding fisheries aquaculture Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/80b3cf0ff3294b6386686ee166c4d7ef
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spelling	oai:doaj.org-article:80b3cf0ff3294b6386686ee166c4d7ef2021-11-25T16:47:21ZEnvironmental DNA (eDNA) Metabarcoding in the Fish Market and Nearby Seafood Restaurants in Taiwan Reveals the Underestimation of Fish Species Diversity in Seafood10.3390/biology101111322079-7737https://doaj.org/article/80b3cf0ff3294b6386686ee166c4d7ef2021-11-01T00:00:00Zhttps://www.mdpi.com/2079-7737/10/11/1132https://doaj.org/toc/2079-7737Seafood, 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.Hung-Tai LeeCheng-Hsin LiaoTe-Hua HsuMDPI AGarticlebiodiversityDNA barcodingfisheriesaquacultureBiology (General)QH301-705.5ENBiology, Vol 10, Iss 1132, p 1132 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	biodiversity DNA barcoding fisheries aquaculture Biology (General) QH301-705.5
spellingShingle	biodiversity DNA barcoding fisheries aquaculture Biology (General) QH301-705.5 Hung-Tai Lee Cheng-Hsin Liao Te-Hua Hsu Environmental DNA (eDNA) Metabarcoding in the Fish Market and Nearby Seafood Restaurants in Taiwan Reveals the Underestimation of Fish Species Diversity in Seafood
description	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.
format	article
author	Hung-Tai Lee Cheng-Hsin Liao Te-Hua Hsu
author_facet	Hung-Tai Lee Cheng-Hsin Liao Te-Hua Hsu
author_sort	Hung-Tai Lee
title	Environmental DNA (eDNA) Metabarcoding in the Fish Market and Nearby Seafood Restaurants in Taiwan Reveals the Underestimation of Fish Species Diversity in Seafood
title_short	Environmental DNA (eDNA) Metabarcoding in the Fish Market and Nearby Seafood Restaurants in Taiwan Reveals the Underestimation of Fish Species Diversity in Seafood
title_full	Environmental DNA (eDNA) Metabarcoding in the Fish Market and Nearby Seafood Restaurants in Taiwan Reveals the Underestimation of Fish Species Diversity in Seafood
title_fullStr	Environmental DNA (eDNA) Metabarcoding in the Fish Market and Nearby Seafood Restaurants in Taiwan Reveals the Underestimation of Fish Species Diversity in Seafood
title_full_unstemmed	Environmental DNA (eDNA) Metabarcoding in the Fish Market and Nearby Seafood Restaurants in Taiwan Reveals the Underestimation of Fish Species Diversity in Seafood
title_sort	environmental dna (edna) metabarcoding in the fish market and nearby seafood restaurants in taiwan reveals the underestimation of fish species diversity in seafood
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/80b3cf0ff3294b6386686ee166c4d7ef
work_keys_str_mv	AT hungtailee environmentaldnaednametabarcodinginthefishmarketandnearbyseafoodrestaurantsintaiwanrevealstheunderestimationoffishspeciesdiversityinseafood AT chenghsinliao environmentaldnaednametabarcodinginthefishmarketandnearbyseafoodrestaurantsintaiwanrevealstheunderestimationoffishspeciesdiversityinseafood AT tehuahsu environmentaldnaednametabarcodinginthefishmarketandnearbyseafoodrestaurantsintaiwanrevealstheunderestimationoffishspeciesdiversityinseafood
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Environmental DNA (eDNA) Metabarcoding in the Fish Market and Nearby Seafood Restaurants in Taiwan Reveals the Underestimation of Fish Species Diversity in Seafood

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