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Combining ddPCR and environmental DNA to improve detection capabilities of a critically endangered freshwater invertebrate

Research output: Contribution to journalA1: Web of Science-article

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Combining ddPCR and environmental DNA to improve detection capabilities of a critically endangered freshwater invertebrate. / Mauvisseau, Quentin; Davy-Bowker, John; Bulling, Mark; Brys, Rein; Neyrinck, Sabrina; Troth, Christopher; Sweet, Michael.

In: Scientific Reports, Vol. 9, No. 1, 2019.

Research output: Contribution to journalA1: Web of Science-article

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Mauvisseau, Quentin ; Davy-Bowker, John ; Bulling, Mark ; Brys, Rein ; Neyrinck, Sabrina ; Troth, Christopher ; Sweet, Michael. / Combining ddPCR and environmental DNA to improve detection capabilities of a critically endangered freshwater invertebrate. In: Scientific Reports. 2019 ; Vol. 9, No. 1.

Bibtex

@article{43d0a2eff3794d67b98bf189759d02be,
title = "Combining ddPCR and environmental DNA to improve detection capabilities of a critically endangered freshwater invertebrate",
abstract = "Isogenus nubecula is a critically endangered Plecoptera species. Considered extinct in the UK, I. nubecula was recently rediscovered (in one location of the River Dee, Wales), after 22 years of absence. In a similar way to many other species of Perlodidae, I. nubecula could be utilised as a bio-indicator, for assessing water quality and health status of a given freshwater system. However, conventional monitoring of invertebrates via kick-sampling, is invasive and expensive (time consuming). Further, such methods require a high level of taxonomic expertise. Here, we compared the traditional kick-sampling method with the use of eDNA detection using qPCR and ddPCR-analyses. In spring 2018, we sampled eDNA from twelve locations on the River Dee. I. nubecula was detected using kick-sampling in five of these locations, three locations using both eDNA detection and kick-sampling and one location using eDNA detection alone – resulting in a total of six known and distinct populations of this critically endangered species. Interestingly, despite the eDNA assay being validated in vitro and in silico, and results indicating high sensitivity, qPCR analysis of the eDNA samples proved to be ineffective. In contrast, ddPCR analyses resulted in a clear detection of I. nubecula at four locations suggesting that inhibition most likely explains the large discrepancy between the obtained qPCR and ddPCR results. It is therefore important to explore inhibition effects on any new eDNA assay. We also highlight that ddPCR may well be the best option for the detection of aquatic organisms which are either rare or likely to shed low levels of eDNA into their environment.",
author = "Quentin Mauvisseau and John Davy-Bowker and Mark Bulling and Rein Brys and Sabrina Neyrinck and Christopher Troth and Michael Sweet",
year = "2019",
doi = "10.1038/s41598-019-50571-9",
language = "English",
volume = "9",
journal = "Scientific Reports",
issn = "2045-2322",
publisher = "Nature Publishing Group",
number = "1",

}

RIS

TY - JOUR

T1 - Combining ddPCR and environmental DNA to improve detection capabilities of a critically endangered freshwater invertebrate

AU - Mauvisseau, Quentin

AU - Davy-Bowker, John

AU - Bulling, Mark

AU - Brys, Rein

AU - Neyrinck, Sabrina

AU - Troth, Christopher

AU - Sweet, Michael

PY - 2019

Y1 - 2019

N2 - Isogenus nubecula is a critically endangered Plecoptera species. Considered extinct in the UK, I. nubecula was recently rediscovered (in one location of the River Dee, Wales), after 22 years of absence. In a similar way to many other species of Perlodidae, I. nubecula could be utilised as a bio-indicator, for assessing water quality and health status of a given freshwater system. However, conventional monitoring of invertebrates via kick-sampling, is invasive and expensive (time consuming). Further, such methods require a high level of taxonomic expertise. Here, we compared the traditional kick-sampling method with the use of eDNA detection using qPCR and ddPCR-analyses. In spring 2018, we sampled eDNA from twelve locations on the River Dee. I. nubecula was detected using kick-sampling in five of these locations, three locations using both eDNA detection and kick-sampling and one location using eDNA detection alone – resulting in a total of six known and distinct populations of this critically endangered species. Interestingly, despite the eDNA assay being validated in vitro and in silico, and results indicating high sensitivity, qPCR analysis of the eDNA samples proved to be ineffective. In contrast, ddPCR analyses resulted in a clear detection of I. nubecula at four locations suggesting that inhibition most likely explains the large discrepancy between the obtained qPCR and ddPCR results. It is therefore important to explore inhibition effects on any new eDNA assay. We also highlight that ddPCR may well be the best option for the detection of aquatic organisms which are either rare or likely to shed low levels of eDNA into their environment.

AB - Isogenus nubecula is a critically endangered Plecoptera species. Considered extinct in the UK, I. nubecula was recently rediscovered (in one location of the River Dee, Wales), after 22 years of absence. In a similar way to many other species of Perlodidae, I. nubecula could be utilised as a bio-indicator, for assessing water quality and health status of a given freshwater system. However, conventional monitoring of invertebrates via kick-sampling, is invasive and expensive (time consuming). Further, such methods require a high level of taxonomic expertise. Here, we compared the traditional kick-sampling method with the use of eDNA detection using qPCR and ddPCR-analyses. In spring 2018, we sampled eDNA from twelve locations on the River Dee. I. nubecula was detected using kick-sampling in five of these locations, three locations using both eDNA detection and kick-sampling and one location using eDNA detection alone – resulting in a total of six known and distinct populations of this critically endangered species. Interestingly, despite the eDNA assay being validated in vitro and in silico, and results indicating high sensitivity, qPCR analysis of the eDNA samples proved to be ineffective. In contrast, ddPCR analyses resulted in a clear detection of I. nubecula at four locations suggesting that inhibition most likely explains the large discrepancy between the obtained qPCR and ddPCR results. It is therefore important to explore inhibition effects on any new eDNA assay. We also highlight that ddPCR may well be the best option for the detection of aquatic organisms which are either rare or likely to shed low levels of eDNA into their environment.

U2 - 10.1038/s41598-019-50571-9

DO - 10.1038/s41598-019-50571-9

M3 - A1: Web of Science-article

VL - 9

JO - Scientific Reports

JF - Scientific Reports

SN - 2045-2322

IS - 1

ER -

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