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

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Veröffentlicht in:Zoological Research vol. 43, no. 2 (Mar 2022), p. 192
1. Verfasser: Ruan, Hui-Ting
Weitere Verfasser: Wang, Rui Li, Li, Hong-Ting, Liu, Li, Kuang, Tian-Xu, Li, Min, Zou, Ke-Shu
Veröffentlicht:
Kunming Institute of Zoology, The Chinese Academy of Sciences
Schlagworte:
China Agricultural University
China
South China Sea
Pearl River Estuary
Community composition
Chloroform
Environmental monitoring
Fish
Estuaries
Species composition
Phenols
Brackishwater environment
Species diversity
Biodiversity
Estuarine dynamics
Water purification
Bottom trawling
Aquatic ecosystems
Ecological monitoring
Decision analysis
Diversity indices
Methods
Composition
Filtration
Ecosystems
Agricultural production
Estuarine fisheries
Anthropogenic factors
Deoxyribonucleic acid > DNA
Surveys
Nucleotide sequence
Trawling
Estuarine ecosystems
River ecology
Taxonomy
Fishing
Brackishwater fishes
Environmental DNA
Commercial fishing
Fisheries
Laboratories
Environmental
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Abstract: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.
ISSN:0254-5853
DOI:10.24272/j.issn.2095-8137.2021.331
Quelle:Science Database