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Effects of sampling strategies and DNA extraction methods on eDNA metabarcoding: A case study of estuarine fish diversity monitoring

文献类型： 外文期刊

作者： Ruan, Hui-Ting 1 ; Wang, Rui-Li 1 ; Li, Hong-Ting 2 ; Liu, Li 1 ; Kuang, Tian-Xu 1 ; Li, Min 2 ; Zou, Ke-Shu 1 ;

作者机构： 1.South China Agr Univ, Univ Joint Lab Guangdong Prov Hong Kong & Macao R, Coll Marine Sci, Guangzhou 510642, Guangdong, Peoples R China

2.Chinese Acad Fishery Sci, South China Sea Fisheries Res Inst, Key Lab Sustainable Utilizat Open Sea Fishery, Minist Agr & Rural Affairs, Guangzhou 510300, Guangdong, Peoples R China

3.Southern Marine Sci & Engn Guangdong Lab Guangzho, Guangzhou 511458, Guangdong, Peoples R China

4.Guangzhou CAOMUFAN Ecol Res Ltd Co, Guangzhou 510520, Guangdong, Peoples R China

5.Shanghai Ocean Univ, Coll Marine Sci, Shanghai 201306, Peoples R China

关键词： eDNA metabarcoding; Fish diversity; Sampling strategies; DNA extraction; Estuarine ecosystem

期刊名称：ZOOLOGICAL RESEARCH （ 影响因子：6.975； 五年影响因子：4.811 ）

ISSN： 2095-8137

年卷期： 2022 年 43 卷 2 期

页码：

收录情况： SCI

摘要： Environmental DNA (eDNA) integrated with metabarcoding is a promising and powerful tool for species composition and biodiversity assessment in aquatic ecosystems and is increasingly applied to evaluate fish diversity. To date, however, no standardized eDNA-based protocol has been established to monitor fish diversity. In this study, we investigated and compared two filtration methods and three DNA extraction methods using three filtration water volumes to determine a suitable approach for eDNA-based fish diversity monitoring in the Pearl River Estuary (PRE), a highly anthropogenically disturbed estuarine ecosystem. Compared to filtration-based precipitation, direct filtration was a more suitable method for eDNA metabarcoding in the PRE. The combined use of DNeasy Blood and Tissue Kit (BT) and traditional phenol/chloroform (PC) extraction produced higher DNA yields, amplicon sequence variants (ASVs), and Shannon diversity indices, and generated more homogeneous and consistent community composition among replicates. Compared to the other combined protocols, the PC and BT methods obtained better species detection, higher fish diversity, and greater consistency for the filtration water volumes of 1 000 and 2 000 mL, respectively. All eDNA metabarcoding protocols were more sensitive than bottom trawling in the PRE fish surveys and combining two techniques yielded greater taxonomic diversity. Furthermore, combining traditional methods with eDNA analysis enhanced accuracy. These results indicate that methodological decisions related to eDNA metabarcoding should be made with caution for fish community monitoring in estuarine ecosystems.

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