A Comparative Evaluation of eDNA Metabarcoding Primers in Fish Community Monitoring in the East Lake

East Lake in Wuhan, China, harbors a high number of freshwater fish species of great conservation value, concurrently serving as vital resources for local livelihoods. However, the ecosystem is threatened by an array of anthropogenic activities, thus requiring consistent monitoring of the local fish...

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Veröffentlicht in:Water (Basel) 2024-03, Vol.16 (5), p.631
Hauptverfasser: Li, Yiwen, Tang, Minzhe, Lu, Suxiang, Zhang, Xiaochun, Fang, Chengchi, Tan, Li, Xiong, Fan, Zeng, Honghui, He, Shunping
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container_issue 5
container_start_page 631
container_title Water (Basel)
container_volume 16
creator Li, Yiwen
Tang, Minzhe
Lu, Suxiang
Zhang, Xiaochun
Fang, Chengchi
Tan, Li
Xiong, Fan
Zeng, Honghui
He, Shunping
description East Lake in Wuhan, China, harbors a high number of freshwater fish species of great conservation value, concurrently serving as vital resources for local livelihoods. However, the ecosystem is threatened by an array of anthropogenic activities, thus requiring consistent monitoring of the local fish community to enable more efficacious conservation management. In place of conventional surveying methods, we undertook the first analysis of the fish distribution within East Lake via metabarcoding of environmental DNA (eDNA). The accuracy and efficacy of eDNA metabarcoding rely heavily upon selecting an appropriate primer set for PCR amplification. Given the varying environmental conditions and taxonomic diversity across distinct study systems, it remains a challenge to propose an optimal genetic marker for universal use. Thus, it becomes necessary to select PCR primers suitable for the composition of fish in the East Lake. Here, we evaluated the performance of two primer sets, Mifish-U and Metafish, designed to amplify 12S rRNA barcoding genes in fishes. Our results detected a total of 116 taxonomic units and 51 fish species, with beta diversity analysis indicating significant differences in community structure diversity between the six sampling locations encompassing East Lake. While it was difficult to accurately compare the species-level discriminatory power and amplification bias of the two primers, Mifish outperformed Metafish in terms of taxonomic specificity for fish taxa and reproducibility. These findings will assist with primer selection for eDNA-based fish monitoring and biodiversity conservation in the East Lake and other freshwater ecosystems.
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subjects Bar codes
Biodiversity
biodiversity conservation
Biological diversity
China
Climate change
community structure
Comparative analysis
Cytochrome
DNA barcoding
Ecosystems
environmental DNA
Environmental quality
Fish
fish communities
Fishes
Fresh water
freshwater
freshwater fish
Genes
Genetic markers
lakes
oligodeoxyribonucleotides
Protection and preservation
River ecology
RNA
species diversity
Surveys
Taxonomy
Wildlife conservation
title A Comparative Evaluation of eDNA Metabarcoding Primers in Fish Community Monitoring in the East Lake
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