TY - JOUR
T1 - Bottom Trawling and Multi-Marker eDNA Metabarcoding Surveys Reveal Highly Diverse Vertebrate and Crustacean Communities
T2 - A Case Study in an Urbanized Subtropical Estuary
AU - Ip, Jack Chi Ho
AU - Loke, Hai Xin
AU - Yiu, Sam King Fung
AU - Zhao, Meihong
AU - Li, Yixuan
AU - Lin, Yitao
AU - How, Chun Ming
AU - Mo, Jiezhang
AU - Yan, Meng
AU - Cheng, Jinping
AU - Lai, Vincent Chi Sing
AU - Chan, Leo Lai
AU - Leung, Kenneth Mei Yee
AU - Qiu, Jian Wen
N1 - Funding Information:
This work was supported by the Lantau Conservation Fund of Hong Kong SAR (RE-2020-22). Environmental and Conservation Fund of Hong Kong SAR (122/2022 and 129/2022), and Marine Conservation Enhancement Fund (MCEF22116 and MCEF22003). JCHI is supported by the Research Grants Council of Hong Kong SAR (GRF12102623 and ECS23100224). Chung-Ming How and Meng Yan, as well as part of the DNA sequencing work, were supported by the State Key Laboratory of Marine Pollution (City University of Hong Kong), which received regularly funding support from the Innovation and Technology Commission (ITC) of the Hong Kong SAR Government (PJ9448002). However, any opinions, findings, conclusions, or recommendations expressed in this publication do not reflect the views of the Hong Kong SAR Government or the ITC.
Publisher Copyright:
© 2024 The Author(s). Environmental DNA published by John Wiley & Sons Ltd.
PY - 2024/11
Y1 - 2024/11
N2 - Estuarine habitats serve as critical feeding and nursery grounds for many aquatic species and support fisheries. However, monitoring these complex ecosystems using conventional trawling methods is destructive, costly, and labor-intensive. This study compared trawling and a multi-marker environmental DNA (eDNA) metabarcoding approach to monitor marine vertebrate and crustacean communities in an estuarine environment in subtropical Hong Kong. We analyzed 16 bottom trawl samples and the eDNA from 32 two-liter water samples using primer sets specific to fishes and mammals (MiFish-U, 12S-V5, and Berry-Fish) and decapod crustaceans (MiDeca). We found that the eDNA approach detected more pelagic and demersal fishes (237 vs. 106 in trawling) and elasmobranchs (6 vs. 3) than trawling. The eDNA approach was also more effective than trawling in detecting threatened vertebrates (16 vs. 4), including the Indo-Pacific Finless Porpoise and the critically endangered Large Yellow Croaker. Among the detected fish at species level, 70 species were detected by both approaches, 32 species were detected by trawling only, and 142 species were detected by the eDNA approach only. Regarding crustaceans, the eDNA approach detected slightly fewer decapods (61 vs. 77) and stomatopods (5 vs. 8) than trawl surveys. However, the eDNA approach could be enhanced through the development of suitable decapod-specific primers and the expansion of the local reference database. In addition, multivariate analyses of the eDNA data revealed spatial patterns of fish and crustacean assemblages that might be associated with sediment loading, oxygen, and nutrient levels. Furthermore, there was a positive correlation between eDNA read counts and trawl catch, but their correlation coefficient was low. We conclude that eDNA metabarcoding can provide high-resolution detection of species, composition, and unravel community–environment relationships in estuarine ecosystems. Overall, integrating the non-destructive eDNA approach can complement the conventional trawling method for better-informed sustainable fishery management and conservation.
AB - Estuarine habitats serve as critical feeding and nursery grounds for many aquatic species and support fisheries. However, monitoring these complex ecosystems using conventional trawling methods is destructive, costly, and labor-intensive. This study compared trawling and a multi-marker environmental DNA (eDNA) metabarcoding approach to monitor marine vertebrate and crustacean communities in an estuarine environment in subtropical Hong Kong. We analyzed 16 bottom trawl samples and the eDNA from 32 two-liter water samples using primer sets specific to fishes and mammals (MiFish-U, 12S-V5, and Berry-Fish) and decapod crustaceans (MiDeca). We found that the eDNA approach detected more pelagic and demersal fishes (237 vs. 106 in trawling) and elasmobranchs (6 vs. 3) than trawling. The eDNA approach was also more effective than trawling in detecting threatened vertebrates (16 vs. 4), including the Indo-Pacific Finless Porpoise and the critically endangered Large Yellow Croaker. Among the detected fish at species level, 70 species were detected by both approaches, 32 species were detected by trawling only, and 142 species were detected by the eDNA approach only. Regarding crustaceans, the eDNA approach detected slightly fewer decapods (61 vs. 77) and stomatopods (5 vs. 8) than trawl surveys. However, the eDNA approach could be enhanced through the development of suitable decapod-specific primers and the expansion of the local reference database. In addition, multivariate analyses of the eDNA data revealed spatial patterns of fish and crustacean assemblages that might be associated with sediment loading, oxygen, and nutrient levels. Furthermore, there was a positive correlation between eDNA read counts and trawl catch, but their correlation coefficient was low. We conclude that eDNA metabarcoding can provide high-resolution detection of species, composition, and unravel community–environment relationships in estuarine ecosystems. Overall, integrating the non-destructive eDNA approach can complement the conventional trawling method for better-informed sustainable fishery management and conservation.
KW - eDNA biomonitoring
KW - environmental drivers
KW - marine biodiversity
KW - Pearl River Estuary
KW - spatial variation
KW - trawling
UR - http://www.scopus.com/inward/record.url?scp=85208570662&partnerID=8YFLogxK
U2 - 10.1002/edn3.70031
DO - 10.1002/edn3.70031
M3 - Journal article
AN - SCOPUS:85208570662
SN - 2637-4943
VL - 6
JO - Environmental DNA
JF - Environmental DNA
IS - 6
M1 - e70031
ER -
