Inter-laboratory ring test for environmental DNA extraction protocols: implications for marine megafauna detection using three novel qPCR assays
The comparability of methods applied to environmental DNA (eDNA) samples across laboratories remains a significant challenge for biodiversity monitoring on a global scale. Performance differences between protocols can jeopardize effective conservation strategies across regions and focal species. To...
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| Format: | Article |
| Language: | English |
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Pensoft Publishers
2025-01-01
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| Series: | Metabarcoding and Metagenomics |
| Online Access: | https://mbmg.pensoft.net/article/128235/download/pdf/ |
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| author | Lauren Kelly Rodriguez Lorenzo De Bonis Jack McKee James A. McKenna Teddy Urvois Eleonora Barbaccia Eileen Dillane Caterina Lanfredi Helene Hjellnes Armelle Jung Enrico Villa Arianna Azzellino Jon-Ivar Westgaard Erwan Quéméré Bettina Thalinger |
| author_facet | Lauren Kelly Rodriguez Lorenzo De Bonis Jack McKee James A. McKenna Teddy Urvois Eleonora Barbaccia Eileen Dillane Caterina Lanfredi Helene Hjellnes Armelle Jung Enrico Villa Arianna Azzellino Jon-Ivar Westgaard Erwan Quéméré Bettina Thalinger |
| author_sort | Lauren Kelly Rodriguez |
| collection | DOAJ |
| description | The comparability of methods applied to environmental DNA (eDNA) samples across laboratories remains a significant challenge for biodiversity monitoring on a global scale. Performance differences between protocols can jeopardize effective conservation strategies across regions and focal species. To address potential discrepancies amongst four international partners within a collaborative eDNA initiative, an inter-laboratory comparison (i.e., ring test) was conducted to compare efficiencies of established DNA extraction methodologies based on 39 eDNA samples. Each laboratory contributed eight to eleven samples collected throughout the North-East Atlantic and the Mediterranean Sea near sperm whales, porbeagle sharks, basking sharks, bottlenose dolphins and common dolphins. After lysis, aliquots were exchanged between laboratories before subsequent DNA extraction using each facility’s preferred method. Extracts were returned to the lysates’ respective laboratories of origin for measurements of total DNA concentration, as well as quantitative PCR using three novel species-specific assays for marine megafauna. Our findings revealed similar concentrations of total DNA, yet a significant reduction in extraction performance for targeted qPCR reactions by one laboratory, who has therefore modified their extraction method to be used for the remainder of this project. Overall, detection success differed based on the target taxa with sharks being less often detected (and at lower concentrations) than marine mammals. Significant interaction effects were found between combinations of laboratories and species, suggesting a link between extraction protocols and variable environmental conditions. Our study serves as a foundational step towards establishing reproducible practices that are crucial for the success of multinational eDNA projects to enable comparable results. |
| format | Article |
| id | doaj-art-47cbd2a2826b48d0a98c71eb17f0af14 |
| institution | Kabale University |
| issn | 2534-9708 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Pensoft Publishers |
| record_format | Article |
| series | Metabarcoding and Metagenomics |
| spelling | doaj-art-47cbd2a2826b48d0a98c71eb17f0af142025-01-09T08:30:39ZengPensoft PublishersMetabarcoding and Metagenomics2534-97082025-01-01913410.3897/mbmg.9.128235128235Inter-laboratory ring test for environmental DNA extraction protocols: implications for marine megafauna detection using three novel qPCR assaysLauren Kelly Rodriguez0Lorenzo De Bonis1Jack McKee2James A. McKenna3Teddy Urvois4Eleonora Barbaccia5Eileen Dillane6Caterina Lanfredi7Helene Hjellnes8Armelle Jung9Enrico Villa10Arianna Azzellino11Jon-Ivar Westgaard12Erwan Quéméré13Bettina Thalinger14University of InnsbruckUniversity College CorkUniversity College CorkInstitute of Marine ResearchEcosystem Dynamics and SustainabilityPolitecnico di Milano DICA Civil and Environmental Engineering DepartmentUniversity College CorkTethys Research InstituteInstitute of Marine ResearchDes Requins et Des HommesCetacean Watching LdaPolitecnico di Milano DICA Civil and Environmental Engineering DepartmentInstitute of Marine ResearchEcosystem Dynamics and SustainabilityUniversity of InnsbruckThe comparability of methods applied to environmental DNA (eDNA) samples across laboratories remains a significant challenge for biodiversity monitoring on a global scale. Performance differences between protocols can jeopardize effective conservation strategies across regions and focal species. To address potential discrepancies amongst four international partners within a collaborative eDNA initiative, an inter-laboratory comparison (i.e., ring test) was conducted to compare efficiencies of established DNA extraction methodologies based on 39 eDNA samples. Each laboratory contributed eight to eleven samples collected throughout the North-East Atlantic and the Mediterranean Sea near sperm whales, porbeagle sharks, basking sharks, bottlenose dolphins and common dolphins. After lysis, aliquots were exchanged between laboratories before subsequent DNA extraction using each facility’s preferred method. Extracts were returned to the lysates’ respective laboratories of origin for measurements of total DNA concentration, as well as quantitative PCR using three novel species-specific assays for marine megafauna. Our findings revealed similar concentrations of total DNA, yet a significant reduction in extraction performance for targeted qPCR reactions by one laboratory, who has therefore modified their extraction method to be used for the remainder of this project. Overall, detection success differed based on the target taxa with sharks being less often detected (and at lower concentrations) than marine mammals. Significant interaction effects were found between combinations of laboratories and species, suggesting a link between extraction protocols and variable environmental conditions. Our study serves as a foundational step towards establishing reproducible practices that are crucial for the success of multinational eDNA projects to enable comparable results.https://mbmg.pensoft.net/article/128235/download/pdf/ |
| spellingShingle | Lauren Kelly Rodriguez Lorenzo De Bonis Jack McKee James A. McKenna Teddy Urvois Eleonora Barbaccia Eileen Dillane Caterina Lanfredi Helene Hjellnes Armelle Jung Enrico Villa Arianna Azzellino Jon-Ivar Westgaard Erwan Quéméré Bettina Thalinger Inter-laboratory ring test for environmental DNA extraction protocols: implications for marine megafauna detection using three novel qPCR assays Metabarcoding and Metagenomics |
| title | Inter-laboratory ring test for environmental DNA extraction protocols: implications for marine megafauna detection using three novel qPCR assays |
| title_full | Inter-laboratory ring test for environmental DNA extraction protocols: implications for marine megafauna detection using three novel qPCR assays |
| title_fullStr | Inter-laboratory ring test for environmental DNA extraction protocols: implications for marine megafauna detection using three novel qPCR assays |
| title_full_unstemmed | Inter-laboratory ring test for environmental DNA extraction protocols: implications for marine megafauna detection using three novel qPCR assays |
| title_short | Inter-laboratory ring test for environmental DNA extraction protocols: implications for marine megafauna detection using three novel qPCR assays |
| title_sort | inter laboratory ring test for environmental dna extraction protocols implications for marine megafauna detection using three novel qpcr assays |
| url | https://mbmg.pensoft.net/article/128235/download/pdf/ |
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