Dataset Information

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.

SUBMITTER: Mauvisseau Q

PROVIDER: S-EPMC6773776 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

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

Mauvisseau Quentin Q Davy-Bowker John J Bulling Mark M Brys Rein R Neyrinck Sabrina S Troth Christopher C Sweet Michael M

Scientific reports 20191001 1

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). Furt ...[more]

PMID: 31575968

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Project description:More freshwater ecosystems are drying in response to global change thereby posing serious threat to freshwater biota and functions. The production of desiccation-resistant forms is an important adaptation that helps maintain biodiversity in temporary freshwaters by buffering communities from drying, but its potential to mitigate the negative effects of drying in freshwater ecosystems could vary greatly across regions and ecosystem types. We explored this context dependency by quantifying the potential contribution of desiccation-resistance forms to invertebrate community recovery across levels of regional drying prevalence (defined as the occurrence of drying events in freshwaters in a given region) and ecosystem types (lentic, lotic) in temporary neotropical freshwaters. We first predicted that regional drying prevalence influences the selection of species with desiccation-resistant forms from the regional species pools and thus increases the ability of communities to recover from drying. Second, we predicted lentic freshwaters harbor higher proportions of species with desiccation-resistant forms compared to lotic, in response to contrasted hydrologic connectivity. To test these predictions, we used natural experiments to quantify the contribution of desiccation-resistant forms to benthic invertebrate community recovery in nine intermittent streams and six geographically isolated temporary wetlands from three Bolivian regions differing in drying prevalence. The contribution of desiccation-resistant forms to community recovery was highest where regional drying prevalence was high, suggesting the species pool was adapted to regional disturbance regimes. The contribution of desiccation-resistant forms to community recovery was lower in streams than in wetlands, emphasizing the importance of hydrologic connectivity and associated recolonization processes from in-stream refuges to recovery in lotic systems. In all regions, the majority of functional traits were present in desiccation-resistant taxa indicating this adaptation may help maintain ecosystem functions by buffering communities from the loss of functional traits. Accounting for regional context and hydrologic connectivity in community recovery processes following drying can help refine predictions of freshwater biodiversity response to global change.

Dataset Information

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

Publications

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

Similar Datasets

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