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

作者：Huiting Ruan, 华南农业大学海洋学院, 粤港澳地区高校海洋生物资源保护与开发联合实验室, 广东 广州 510642, 中国, Ruili Wang, Hongting Li, Li Liu, Tianxu Kuang, Min Li, Keshu Zou, 中国水产科学院南海渔业研究所, 农业农村部公海渔业发展重点实验室, 广东 广州 510300, 中国, 南方海洋科学与工程广东省实验室(广州), 广东 广州 511458, 中国, 广州草木蕃环境科技有限公司, 广东 广州 510520, 中国, 上海海洋大学海洋科学学院, 上海 201306, 中国 · 发表于：动物学研究 · 年份：2022 · DOI：10.24272/j.issn.2095-8137.2021.331 · 被引用次数：47 · 研究领域：Environmental DNA in Biodiversity Studies、Identification and Quantification in Food、Microbial Community Ecology and Physiology

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 res...