Effects of preservation strategies on environmental DNA detection and quantification using ddPCR
Molecular-based monitoring relying on environmental DNA (eDNA) detection became routinely used around the world in the last few years, especially in aquatic environments. The large potential and increasing applications of this technique calls for technical improvements to optimize the reliability of...
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ftoslouniv:oai:www.duo.uio.no:10852/91462 2023-05-15T17:08:53+02:00 Effects of preservation strategies on environmental DNA detection and quantification using ddPCR Mauvisseau, Quentin Halfmaerten, David Neyrinck, Sabrina Burian, Alfred Brys, Rein 2021-11-17T16:09:51Z http://hdl.handle.net/10852/91462 http://urn.nb.no/URN:NBN:no-94065 https://doi.org/10.1002/edn3.188 EN eng http://urn.nb.no/URN:NBN:no-94065 Mauvisseau, Quentin Halfmaerten, David Neyrinck, Sabrina Burian, Alfred Brys, Rein . Effects of preservation strategies on environmental DNA detection and quantification using ddPCR. Environmental DNA. 2021 http://hdl.handle.net/10852/91462 1955665 info:ofi/fmt:kev:mtx:ctx&ctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Environmental DNA&rft.volume=&rft.spage=&rft.date=2021 Environmental DNA 3 4 815 822 https://doi.org/10.1002/edn3.188 URN:NBN:no-94065 Fulltext https://www.duo.uio.no/bitstream/handle/10852/91462/1/Environmental%2BDNA%2B-%2B2021%2B-%2BMauvisseau%2B-%2BEffects%2Bof%2Bpreservation%2Bstrategies%2Bon%2Benvironmental%2BDNA%2Bdetection%2Band.pdf Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/ CC-BY 2637-4943 Journal article Tidsskriftartikkel Peer reviewed PublishedVersion 2021 ftoslouniv https://doi.org/10.1002/edn3.188 2022-03-02T23:33:45Z Molecular-based monitoring relying on environmental DNA (eDNA) detection became routinely used around the world in the last few years, especially in aquatic environments. The large potential and increasing applications of this technique calls for technical improvements to optimize the reliability of these surveys. An important technical aspect in the eDNA workflow is the appropriate preservation of samples taken in the field, as it can significantly affect eDNA recovery and ultimately false negative rates. In this study, we explored the efficiency of five different preservation strategies by using a controlled mesocosm experiment in which we included three fish communities of different composition. Specifically, we compared eDNA recovery in DNA extractions (a) performed immediately following collection, or after eight months storage from (b) frozen filters, (c) unfiltered water samples stored at −20°C, and filters preserved at room temperature with (d) Longmire and (e) Sarkosyl buffer. Effects of different preservation strategies were quantified using ddPCR measurements of three fish species (Neogobius melanostomus, Rutilus rutilus, and Lota lota) and total fish DNA content using group-specific primers for Teleostei. Samples extracted immediately following collection without any further preservation yielded significantly less DNA compared to the other approaches. Overall, Longmire's buffer facilitated the best eDNA recovery across all fish species although approaches such as filter freezing or the use of Sarkosyl buffer yielded similar recovery results. Relative measurement variability, an important indicator for reliable eDNA quantification, was lowest when using Longmire's and Sarkosyl buffers and generally decreased when increasing eDNA quantity. Overall, our results clearly highlight the significant impact of sample preservation and how this can substantially affect the performance and reliability of eDNA-based approaches. Article in Journal/Newspaper Lota lota lota Universitet i Oslo: Digitale utgivelser ved UiO (DUO) Environmental DNA 3 4 815 822 |
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Open Polar |
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Universitet i Oslo: Digitale utgivelser ved UiO (DUO) |
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ftoslouniv |
language |
English |
description |
Molecular-based monitoring relying on environmental DNA (eDNA) detection became routinely used around the world in the last few years, especially in aquatic environments. The large potential and increasing applications of this technique calls for technical improvements to optimize the reliability of these surveys. An important technical aspect in the eDNA workflow is the appropriate preservation of samples taken in the field, as it can significantly affect eDNA recovery and ultimately false negative rates. In this study, we explored the efficiency of five different preservation strategies by using a controlled mesocosm experiment in which we included three fish communities of different composition. Specifically, we compared eDNA recovery in DNA extractions (a) performed immediately following collection, or after eight months storage from (b) frozen filters, (c) unfiltered water samples stored at −20°C, and filters preserved at room temperature with (d) Longmire and (e) Sarkosyl buffer. Effects of different preservation strategies were quantified using ddPCR measurements of three fish species (Neogobius melanostomus, Rutilus rutilus, and Lota lota) and total fish DNA content using group-specific primers for Teleostei. Samples extracted immediately following collection without any further preservation yielded significantly less DNA compared to the other approaches. Overall, Longmire's buffer facilitated the best eDNA recovery across all fish species although approaches such as filter freezing or the use of Sarkosyl buffer yielded similar recovery results. Relative measurement variability, an important indicator for reliable eDNA quantification, was lowest when using Longmire's and Sarkosyl buffers and generally decreased when increasing eDNA quantity. Overall, our results clearly highlight the significant impact of sample preservation and how this can substantially affect the performance and reliability of eDNA-based approaches. |
format |
Article in Journal/Newspaper |
author |
Mauvisseau, Quentin Halfmaerten, David Neyrinck, Sabrina Burian, Alfred Brys, Rein |
spellingShingle |
Mauvisseau, Quentin Halfmaerten, David Neyrinck, Sabrina Burian, Alfred Brys, Rein Effects of preservation strategies on environmental DNA detection and quantification using ddPCR |
author_facet |
Mauvisseau, Quentin Halfmaerten, David Neyrinck, Sabrina Burian, Alfred Brys, Rein |
author_sort |
Mauvisseau, Quentin |
title |
Effects of preservation strategies on environmental DNA detection and quantification using ddPCR |
title_short |
Effects of preservation strategies on environmental DNA detection and quantification using ddPCR |
title_full |
Effects of preservation strategies on environmental DNA detection and quantification using ddPCR |
title_fullStr |
Effects of preservation strategies on environmental DNA detection and quantification using ddPCR |
title_full_unstemmed |
Effects of preservation strategies on environmental DNA detection and quantification using ddPCR |
title_sort |
effects of preservation strategies on environmental dna detection and quantification using ddpcr |
publishDate |
2021 |
url |
http://hdl.handle.net/10852/91462 http://urn.nb.no/URN:NBN:no-94065 https://doi.org/10.1002/edn3.188 |
genre |
Lota lota lota |
genre_facet |
Lota lota lota |
op_source |
2637-4943 |
op_relation |
http://urn.nb.no/URN:NBN:no-94065 Mauvisseau, Quentin Halfmaerten, David Neyrinck, Sabrina Burian, Alfred Brys, Rein . Effects of preservation strategies on environmental DNA detection and quantification using ddPCR. Environmental DNA. 2021 http://hdl.handle.net/10852/91462 1955665 info:ofi/fmt:kev:mtx:ctx&ctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Environmental DNA&rft.volume=&rft.spage=&rft.date=2021 Environmental DNA 3 4 815 822 https://doi.org/10.1002/edn3.188 URN:NBN:no-94065 Fulltext https://www.duo.uio.no/bitstream/handle/10852/91462/1/Environmental%2BDNA%2B-%2B2021%2B-%2BMauvisseau%2B-%2BEffects%2Bof%2Bpreservation%2Bstrategies%2Bon%2Benvironmental%2BDNA%2Bdetection%2Band.pdf |
op_rights |
Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/ |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1002/edn3.188 |
container_title |
Environmental DNA |
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3 |
container_issue |
4 |
container_start_page |
815 |
op_container_end_page |
822 |
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1766064809972858880 |