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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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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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.</description><identifier>ISSN: 2073-4441</identifier><identifier>EISSN: 2073-4441</identifier><identifier>DOI: 10.3390/w16050631</identifier><language>eng</language><publisher>Basel: MDPI AG</publisher><subject>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</subject><ispartof>Water (Basel), 2024-03, Vol.16 (5), p.631</ispartof><rights>COPYRIGHT 2024 MDPI AG</rights><rights>2024 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c352t-3fa99f002b88bde1d4f34d2e200a9038d9a7f1a7d8c07ec31f31e7929234723e3</cites><orcidid>0000-0002-3594-7988 ; 0009-0000-8827-8709</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780,27903,27904</link.rule.ids></links><search><creatorcontrib>Li, Yiwen</creatorcontrib><creatorcontrib>Tang, Minzhe</creatorcontrib><creatorcontrib>Lu, Suxiang</creatorcontrib><creatorcontrib>Zhang, Xiaochun</creatorcontrib><creatorcontrib>Fang, Chengchi</creatorcontrib><creatorcontrib>Tan, Li</creatorcontrib><creatorcontrib>Xiong, Fan</creatorcontrib><creatorcontrib>Zeng, Honghui</creatorcontrib><creatorcontrib>He, Shunping</creatorcontrib><title>A Comparative Evaluation of eDNA Metabarcoding Primers in Fish Community Monitoring in the East Lake</title><title>Water (Basel)</title><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.</description><subject>Bar codes</subject><subject>Biodiversity</subject><subject>biodiversity conservation</subject><subject>Biological diversity</subject><subject>China</subject><subject>Climate change</subject><subject>community structure</subject><subject>Comparative analysis</subject><subject>Cytochrome</subject><subject>DNA barcoding</subject><subject>Ecosystems</subject><subject>environmental DNA</subject><subject>Environmental quality</subject><subject>Fish</subject><subject>fish communities</subject><subject>Fishes</subject><subject>Fresh water</subject><subject>freshwater</subject><subject>freshwater fish</subject><subject>Genes</subject><subject>Genetic markers</subject><subject>lakes</subject><subject>oligodeoxyribonucleotides</subject><subject>Protection and preservation</subject><subject>River ecology</subject><subject>RNA</subject><subject>species diversity</subject><subject>Surveys</subject><subject>Taxonomy</subject><subject>Wildlife conservation</subject><issn>2073-4441</issn><issn>2073-4441</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>BENPR</sourceid><recordid>eNptkU9PGzEQxVeolYggB76BJS7tIWHs8f7xMUqhICWUA5wtZ3ccTHfXqb1LlW9fRyBoK-zDPNm_9zSaybIzDnNEBRe_eQE5FMiPsomAEmdSSv7pL32cTWN8gnSkqqocJlmzYEvf7Uwwg3smdvls2jFJ3zNvGX27XbA1DWZjQu0b12_ZXXAdhchcz65cfDyYu7F3w56tfSo-HKD0OTymMBMHtjI_6TT7bE0bafpaT7KHq8v75fVs9eP7zXKxmtWYi2GG1ihlAcSmqjYN8UZalI0gAWAUYNUoU1puyqaqoaQauUVOpRJKoCwFEp5kX15yd8H_GikOunOxprY1PfkxauQ58kIgioSe_4c--TH0qTstVJ4rKHKQ79TWtKRdb_0QTH0I1YuyKqQEzlWi5h9Q6TbUudr3ZF16_8fw9cVQBx9jIKt3aawm7DUHfdikftsk_gEl-YyC</recordid><startdate>20240301</startdate><enddate>20240301</enddate><creator>Li, Yiwen</creator><creator>Tang, Minzhe</creator><creator>Lu, Suxiang</creator><creator>Zhang, Xiaochun</creator><creator>Fang, Chengchi</creator><creator>Tan, Li</creator><creator>Xiong, Fan</creator><creator>Zeng, Honghui</creator><creator>He, Shunping</creator><general>MDPI AG</general><scope>AAYXX</scope><scope>CITATION</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BENPR</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>7S9</scope><scope>L.6</scope><orcidid>https://orcid.org/0000-0002-3594-7988</orcidid><orcidid>https://orcid.org/0009-0000-8827-8709</orcidid></search><sort><creationdate>20240301</creationdate><title>A Comparative Evaluation of eDNA Metabarcoding Primers in Fish Community Monitoring in the East Lake</title><author>Li, Yiwen ; 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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.</abstract><cop>Basel</cop><pub>MDPI AG</pub><doi>10.3390/w16050631</doi><orcidid>https://orcid.org/0000-0002-3594-7988</orcidid><orcidid>https://orcid.org/0009-0000-8827-8709</orcidid><oa>free_for_read</oa></addata></record> |
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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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