Differential decay of multiple environmental nucleic acid components
Abstract Detections of environmental nucleic acids (eNA), such as DNA and RNA, are powerful tools for monitoring biodiversity. Yet, precise interpretation of these indirect detections requires understanding of eNAs persistence. We conducted a decay experiment to track degradation of six eNA componen...
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Nature Portfolio
2025-07-01
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| Online Access: | https://doi.org/10.1038/s41598-025-12916-5 |
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| author | Pedro FP Brandão-Dias Megan Shaffer Gledis Guri Kim M. Parsons Ryan P. Kelly Elizabeth Andruszkiewicz Allan |
| author_facet | Pedro FP Brandão-Dias Megan Shaffer Gledis Guri Kim M. Parsons Ryan P. Kelly Elizabeth Andruszkiewicz Allan |
| author_sort | Pedro FP Brandão-Dias |
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| description | Abstract Detections of environmental nucleic acids (eNA), such as DNA and RNA, are powerful tools for monitoring biodiversity. Yet, precise interpretation of these indirect detections requires understanding of eNAs persistence. We conducted a decay experiment to track degradation of six eNA components derived from the bottlenose dolphin Tursiops truncatus: mitochondrial eDNA of varying lengths, ribosomal eRNA, and messenger eRNA. Target eNAs were quantified over seven days via digital droplet PCR (ddPCR). Decay followed a biphasic exponential model with rapid initial loss (~ 24 h at 15 °C), followed by slower degradation. Mitochondrial messenger eRNA was least stable, disappearing within four hours. Ribosomal eRNA persisted longer but degraded slightly faster than its eDNA counterpart (decay rate λ₁ = 0.236 vs. 0.165 h⁻¹). Longest eDNA fragments decayed more rapidly (λ₁ = 0.190 h−1) than shorter ones (λ₁ = 0.114 h−1). These findings support using eDNA fragment length as a proxy for degradation and reinforce that combining multiple eNA components with distinct stabilities can provide a molecular clock to infer eNA age. This approach improves the spatiotemporal resolution of eNA-based monitoring, particularly for rare cetaceans that act as point sources. We also emphasize the importance of explicitly distinguishing between RNA types (ribosomal vs. messenger) in environmental studies, given their divergent stability and interpretability. |
| format | Article |
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| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-07-01 |
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| spelling | doaj-art-29e21dd9917949659dce209eff34ff392025-08-20T03:45:56ZengNature PortfolioScientific Reports2045-23222025-07-0115111310.1038/s41598-025-12916-5Differential decay of multiple environmental nucleic acid componentsPedro FP Brandão-Dias0Megan Shaffer1Gledis Guri2Kim M. Parsons3Ryan P. Kelly4Elizabeth Andruszkiewicz Allan5School of Marine and Environmental Affairs, University of WashingtonSchool of Marine and Environmental Affairs, University of WashingtonSchool of Marine and Environmental Affairs, University of WashingtonConservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric AdministrationSchool of Marine and Environmental Affairs, University of WashingtonSchool of Marine and Environmental Affairs, University of WashingtonAbstract Detections of environmental nucleic acids (eNA), such as DNA and RNA, are powerful tools for monitoring biodiversity. Yet, precise interpretation of these indirect detections requires understanding of eNAs persistence. We conducted a decay experiment to track degradation of six eNA components derived from the bottlenose dolphin Tursiops truncatus: mitochondrial eDNA of varying lengths, ribosomal eRNA, and messenger eRNA. Target eNAs were quantified over seven days via digital droplet PCR (ddPCR). Decay followed a biphasic exponential model with rapid initial loss (~ 24 h at 15 °C), followed by slower degradation. Mitochondrial messenger eRNA was least stable, disappearing within four hours. Ribosomal eRNA persisted longer but degraded slightly faster than its eDNA counterpart (decay rate λ₁ = 0.236 vs. 0.165 h⁻¹). Longest eDNA fragments decayed more rapidly (λ₁ = 0.190 h−1) than shorter ones (λ₁ = 0.114 h−1). These findings support using eDNA fragment length as a proxy for degradation and reinforce that combining multiple eNA components with distinct stabilities can provide a molecular clock to infer eNA age. This approach improves the spatiotemporal resolution of eNA-based monitoring, particularly for rare cetaceans that act as point sources. We also emphasize the importance of explicitly distinguishing between RNA types (ribosomal vs. messenger) in environmental studies, given their divergent stability and interpretability.https://doi.org/10.1038/s41598-025-12916-5RemovalBayesianMesocosmMarine mammalPuget sound |
| spellingShingle | Pedro FP Brandão-Dias Megan Shaffer Gledis Guri Kim M. Parsons Ryan P. Kelly Elizabeth Andruszkiewicz Allan Differential decay of multiple environmental nucleic acid components Scientific Reports Removal Bayesian Mesocosm Marine mammal Puget sound |
| title | Differential decay of multiple environmental nucleic acid components |
| title_full | Differential decay of multiple environmental nucleic acid components |
| title_fullStr | Differential decay of multiple environmental nucleic acid components |
| title_full_unstemmed | Differential decay of multiple environmental nucleic acid components |
| title_short | Differential decay of multiple environmental nucleic acid components |
| title_sort | differential decay of multiple environmental nucleic acid components |
| topic | Removal Bayesian Mesocosm Marine mammal Puget sound |
| url | https://doi.org/10.1038/s41598-025-12916-5 |
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