Effects of sampling strategies and DNA extraction methods on eDNA metabarcoding: A case study of estuarine fish diversity monitoring
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| Publicat a: | Zoological Research vol. 43, no. 2 (Mar 2022), p. 192 |
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| Autor principal: | |
| Altres autors: | , , , , , |
| Publicat: |
Kunming Institute of Zoology, The Chinese Academy of Sciences
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| Matèries: | |
| Accés en línia: | Citation/Abstract Full Text Full Text - PDF |
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| 001 | 2680353544 | ||
| 003 | UK-CbPIL | ||
| 022 | |a 0254-5853 | ||
| 024 | 7 | |a 10.24272/j.issn.2095-8137.2021.331 |2 doi | |
| 035 | |a 2680353544 | ||
| 045 | 2 | |b d20220301 |b d20220331 | |
| 084 | |a 201328 |2 nlm | ||
| 100 | 1 | |a Ruan, Hui-Ting |u University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Science, South China Agricultural University, Guangzhou, Guangdong 510642, China | |
| 245 | 1 | |a Effects of sampling strategies and DNA extraction methods on eDNA metabarcoding: A case study of estuarine fish diversity monitoring | |
| 260 | |b Kunming Institute of Zoology, The Chinese Academy of Sciences |c Mar 2022 | ||
| 513 | |a Case Study Journal Article | ||
| 520 | 3 | |a 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. | |
| 610 | 4 | |a China Agricultural University | |
| 651 | 4 | |a China | |
| 651 | 4 | |a South China Sea | |
| 651 | 4 | |a Pearl River Estuary | |
| 653 | |a Community composition | ||
| 653 | |a Chloroform | ||
| 653 | |a Environmental monitoring | ||
| 653 | |a Fish | ||
| 653 | |a Estuaries | ||
| 653 | |a Species composition | ||
| 653 | |a Phenols | ||
| 653 | |a Brackishwater environment | ||
| 653 | |a Species diversity | ||
| 653 | |a Biodiversity | ||
| 653 | |a Estuarine dynamics | ||
| 653 | |a Water purification | ||
| 653 | |a Bottom trawling | ||
| 653 | |a Aquatic ecosystems | ||
| 653 | |a Ecological monitoring | ||
| 653 | |a Decision analysis | ||
| 653 | |a Diversity indices | ||
| 653 | |a Methods | ||
| 653 | |a Composition | ||
| 653 | |a Filtration | ||
| 653 | |a Ecosystems | ||
| 653 | |a Agricultural production | ||
| 653 | |a Estuarine fisheries | ||
| 653 | |a Anthropogenic factors | ||
| 653 | |a Deoxyribonucleic acid--DNA | ||
| 653 | |a Surveys | ||
| 653 | |a Nucleotide sequence | ||
| 653 | |a Trawling | ||
| 653 | |a Estuarine ecosystems | ||
| 653 | |a River ecology | ||
| 653 | |a Taxonomy | ||
| 653 | |a Fishing | ||
| 653 | |a Brackishwater fishes | ||
| 653 | |a Environmental DNA | ||
| 653 | |a Commercial fishing | ||
| 653 | |a Fisheries | ||
| 653 | |a Laboratories | ||
| 653 | |a Environmental | ||
| 700 | 1 | |a Wang, Rui Li |u University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Science, South China Agricultural University, Guangzhou, Guangdong 510642, China | |
| 700 | 1 | |a Li, Hong-Ting |u Key Laboratory for Sustainable Utilization of Open-sea Fishery, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510300, China | |
| 700 | 1 | |a Liu, Li |u University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Science, South China Agricultural University, Guangzhou, Guangdong 510642, Chinac | |
| 700 | 1 | |a Kuang, Tian-Xu |u University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Science, South China Agricultural University, Guangzhou, Guangdong 510642, China | |
| 700 | 1 | |a Li, Min | |
| 700 | 1 | |a Zou, Ke-Shu | |
| 773 | 0 | |t Zoological Research |g vol. 43, no. 2 (Mar 2022), p. 192 | |
| 786 | 0 | |d ProQuest |t Science Database | |
| 856 | 4 | 1 | |3 Citation/Abstract |u https://www.proquest.com/docview/2680353544/abstract/embedded/J7RWLIQ9I3C9JK51?source=fedsrch |
| 856 | 4 | 0 | |3 Full Text |u https://www.proquest.com/docview/2680353544/fulltext/embedded/J7RWLIQ9I3C9JK51?source=fedsrch |
| 856 | 4 | 0 | |3 Full Text - PDF |u https://www.proquest.com/docview/2680353544/fulltextPDF/embedded/J7RWLIQ9I3C9JK51?source=fedsrch |