An optimized eDNA protocol for fish tracking in estuarine environments
Abstract Environmental DNA (eDNA) is revolutionizing how we investigate biodiversity in aquatic and terrestrial environments. It is increasingly used for detecting rare and invasive species, assessing biodiversity loss and monitoring fish communities, as it is considered a cost-effective and noninva...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-01-01
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| Series: | Scientific Reports |
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| Online Access: | https://doi.org/10.1038/s41598-025-85176-y |
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| author | Fouad El Baidouri Alison W. Watts Jeffrey T. Miller Muriel Kelly Joseph L. Sevigny Heather Gilbert W. Kelley Thomas |
| author_facet | Fouad El Baidouri Alison W. Watts Jeffrey T. Miller Muriel Kelly Joseph L. Sevigny Heather Gilbert W. Kelley Thomas |
| author_sort | Fouad El Baidouri |
| collection | DOAJ |
| description | Abstract Environmental DNA (eDNA) is revolutionizing how we investigate biodiversity in aquatic and terrestrial environments. It is increasingly used for detecting rare and invasive species, assessing biodiversity loss and monitoring fish communities, as it is considered a cost-effective and noninvasive approach. Some environments, however, can be challenging for eDNA analyses. Estuarine systems are highly productive, complex environments, but samples collected from these settings may exhibit PCR inhibition and a low fish read recovery. Here we present an approach for detecting fish in turbid, highly productive estuarine systems. The workflow includes bead-based extraction, inhibition removal, high fidelity and specificity DNA polymerase (Platinum SuperFi II) and multiplexing the universal MiFish primers. By applying this hybrid method to a variety of complex estuarine samples with known inhibition, we have more than doubled the number of recovered fish species while removing most of the off-target amplification. |
| format | Article |
| id | doaj-art-64a415a35fb5468f95fcf5ac9083905c |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj-art-64a415a35fb5468f95fcf5ac9083905c2025-01-12T12:17:36ZengNature PortfolioScientific Reports2045-23222025-01-0115111310.1038/s41598-025-85176-yAn optimized eDNA protocol for fish tracking in estuarine environmentsFouad El Baidouri0Alison W. Watts1Jeffrey T. Miller2Muriel Kelly3Joseph L. Sevigny4Heather Gilbert5W. Kelley Thomas6Department of Civil & Environmental Engineering, University of New HampshireDepartment of Civil & Environmental Engineering, University of New HampshireDepartment of Molecular, Cellular, and Biomedical Sciences, University of New HampshireHubbard Center for Genome Studies, University of New HampshireHubbard Center for Genome Studies, University of New HampshireDepartment of Civil & Environmental Engineering, University of New HampshireHubbard Center for Genome Studies, University of New HampshireAbstract Environmental DNA (eDNA) is revolutionizing how we investigate biodiversity in aquatic and terrestrial environments. It is increasingly used for detecting rare and invasive species, assessing biodiversity loss and monitoring fish communities, as it is considered a cost-effective and noninvasive approach. Some environments, however, can be challenging for eDNA analyses. Estuarine systems are highly productive, complex environments, but samples collected from these settings may exhibit PCR inhibition and a low fish read recovery. Here we present an approach for detecting fish in turbid, highly productive estuarine systems. The workflow includes bead-based extraction, inhibition removal, high fidelity and specificity DNA polymerase (Platinum SuperFi II) and multiplexing the universal MiFish primers. By applying this hybrid method to a variety of complex estuarine samples with known inhibition, we have more than doubled the number of recovered fish species while removing most of the off-target amplification.https://doi.org/10.1038/s41598-025-85176-yeDNAMiFishPlatinum SuperFi IIPCR inhibitionEstuarineFish species |
| spellingShingle | Fouad El Baidouri Alison W. Watts Jeffrey T. Miller Muriel Kelly Joseph L. Sevigny Heather Gilbert W. Kelley Thomas An optimized eDNA protocol for fish tracking in estuarine environments Scientific Reports eDNA MiFish Platinum SuperFi II PCR inhibition Estuarine Fish species |
| title | An optimized eDNA protocol for fish tracking in estuarine environments |
| title_full | An optimized eDNA protocol for fish tracking in estuarine environments |
| title_fullStr | An optimized eDNA protocol for fish tracking in estuarine environments |
| title_full_unstemmed | An optimized eDNA protocol for fish tracking in estuarine environments |
| title_short | An optimized eDNA protocol for fish tracking in estuarine environments |
| title_sort | optimized edna protocol for fish tracking in estuarine environments |
| topic | eDNA MiFish Platinum SuperFi II PCR inhibition Estuarine Fish species |
| url | https://doi.org/10.1038/s41598-025-85176-y |
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