Comparing the Fate of eDNA by Particle Sizes and Molecule Lengths in Recirculating Streams
ABSTRACT The detection of environmental DNA (eDNA) has revolutionized aquatic species monitoring, yet interpreting eDNA data remains challenging due to gaps in our understanding of eDNA ecology (i.e., origin, state, transport, and fate) and variability in how eDNA methods are applied across the lite...
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| Format: | Article |
| Language: | English |
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Wiley
2025-03-01
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| Series: | Environmental DNA |
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| Online Access: | https://doi.org/10.1002/edn3.70066 |
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| author | Pedro F. P. Brandão‐Dias Elise Snyder Jennifer L. Tank Ursula H. Mahl Brett Peters Arial J. Shogren Diogo Bolster Gary A. Lamberti Kyle Bibby Scott P. Egan |
| author_facet | Pedro F. P. Brandão‐Dias Elise Snyder Jennifer L. Tank Ursula H. Mahl Brett Peters Arial J. Shogren Diogo Bolster Gary A. Lamberti Kyle Bibby Scott P. Egan |
| author_sort | Pedro F. P. Brandão‐Dias |
| collection | DOAJ |
| description | ABSTRACT The detection of environmental DNA (eDNA) has revolutionized aquatic species monitoring, yet interpreting eDNA data remains challenging due to gaps in our understanding of eDNA ecology (i.e., origin, state, transport, and fate) and variability in how eDNA methods are applied across the literature. A crucial aspect of the complexity of eDNA ecology is that eDNA is a heterogeneous mix of components that vary in size and other properties, thereby influencing interactions with the environment in diverse ways. In this study, we explore the interplay between three eDNA particle sizes (the physical dimension of eDNA‐containing particles) and two molecule lengths (DNA size in base pairs) in flowing water systems. Specifically, we elucidated the mechanisms governing the removal of different eDNA components using a set of 24 recirculating mesocosms where we varied light and substrate conditions. Consistent with previous observations, our findings revealed substantial differences in the mechanisms of eDNA removal between small and large eDNA particles. In mesocosms with biofilm‐colonized substrate, we found higher removal rates for smaller particles, but larger eDNA particles were removed more quickly in presence of any substrate. Importantly, we also found that biofilm removes longer eDNA molecules faster, shedding light on a probable mechanism underlying the longstanding association between eDNA removal and the presence of biofilm. Despite the association between biofilm colonization and faster removal of longer molecules, the two eDNA molecule sizes we analyzed (86 and 387 base pairs) exhibited somewhat consistent behavior. In combination, our observations highlight that particle size is an important predictor of eDNA fate, and that eDNA fate shows few differences across varying molecule lengths. Furthermore, our work suggests that conclusions regarding eDNA ecology from studies utilizing short DNA markers are applicable to metabarcoding applications, which typically use longer marker lengths. |
| format | Article |
| id | doaj-art-e4c9288265bf4c59ab119a597754e9f4 |
| institution | DOAJ |
| issn | 2637-4943 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Wiley |
| record_format | Article |
| series | Environmental DNA |
| spelling | doaj-art-e4c9288265bf4c59ab119a597754e9f42025-08-20T03:14:24ZengWileyEnvironmental DNA2637-49432025-03-0172n/an/a10.1002/edn3.70066Comparing the Fate of eDNA by Particle Sizes and Molecule Lengths in Recirculating StreamsPedro F. P. Brandão‐Dias0Elise Snyder1Jennifer L. Tank2Ursula H. Mahl3Brett Peters4Arial J. Shogren5Diogo Bolster6Gary A. Lamberti7Kyle Bibby8Scott P. Egan9Department of Biosciences Rice University Houston Texas USADepartment of Biological Sciences University of Notre Dame Notre Dame Indiana USADepartment of Biological Sciences University of Notre Dame Notre Dame Indiana USADepartment of Biological Sciences University of Notre Dame Notre Dame Indiana USADepartment of Biological Sciences University of Notre Dame Notre Dame Indiana USADepartment of Biological Sciences The University of Alabama Tuscaloosa Alabama USADepartment of Civil and Environmental Engineering University of Notre Dame Notre Dame Indiana USADepartment of Biological Sciences University of Notre Dame Notre Dame Indiana USADepartment of Civil and Environmental Engineering University of Notre Dame Notre Dame Indiana USADepartment of Biosciences Rice University Houston Texas USAABSTRACT The detection of environmental DNA (eDNA) has revolutionized aquatic species monitoring, yet interpreting eDNA data remains challenging due to gaps in our understanding of eDNA ecology (i.e., origin, state, transport, and fate) and variability in how eDNA methods are applied across the literature. A crucial aspect of the complexity of eDNA ecology is that eDNA is a heterogeneous mix of components that vary in size and other properties, thereby influencing interactions with the environment in diverse ways. In this study, we explore the interplay between three eDNA particle sizes (the physical dimension of eDNA‐containing particles) and two molecule lengths (DNA size in base pairs) in flowing water systems. Specifically, we elucidated the mechanisms governing the removal of different eDNA components using a set of 24 recirculating mesocosms where we varied light and substrate conditions. Consistent with previous observations, our findings revealed substantial differences in the mechanisms of eDNA removal between small and large eDNA particles. In mesocosms with biofilm‐colonized substrate, we found higher removal rates for smaller particles, but larger eDNA particles were removed more quickly in presence of any substrate. Importantly, we also found that biofilm removes longer eDNA molecules faster, shedding light on a probable mechanism underlying the longstanding association between eDNA removal and the presence of biofilm. Despite the association between biofilm colonization and faster removal of longer molecules, the two eDNA molecule sizes we analyzed (86 and 387 base pairs) exhibited somewhat consistent behavior. In combination, our observations highlight that particle size is an important predictor of eDNA fate, and that eDNA fate shows few differences across varying molecule lengths. Furthermore, our work suggests that conclusions regarding eDNA ecology from studies utilizing short DNA markers are applicable to metabarcoding applications, which typically use longer marker lengths.https://doi.org/10.1002/edn3.70066ddPCRdecayeDNA ecologynested PCRsequential filtration |
| spellingShingle | Pedro F. P. Brandão‐Dias Elise Snyder Jennifer L. Tank Ursula H. Mahl Brett Peters Arial J. Shogren Diogo Bolster Gary A. Lamberti Kyle Bibby Scott P. Egan Comparing the Fate of eDNA by Particle Sizes and Molecule Lengths in Recirculating Streams Environmental DNA ddPCR decay eDNA ecology nested PCR sequential filtration |
| title | Comparing the Fate of eDNA by Particle Sizes and Molecule Lengths in Recirculating Streams |
| title_full | Comparing the Fate of eDNA by Particle Sizes and Molecule Lengths in Recirculating Streams |
| title_fullStr | Comparing the Fate of eDNA by Particle Sizes and Molecule Lengths in Recirculating Streams |
| title_full_unstemmed | Comparing the Fate of eDNA by Particle Sizes and Molecule Lengths in Recirculating Streams |
| title_short | Comparing the Fate of eDNA by Particle Sizes and Molecule Lengths in Recirculating Streams |
| title_sort | comparing the fate of edna by particle sizes and molecule lengths in recirculating streams |
| topic | ddPCR decay eDNA ecology nested PCR sequential filtration |
| url | https://doi.org/10.1002/edn3.70066 |
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