Journal ArticleDOI
Residual eDNA detection sensitivity assessed by quantitative real-time PCR in a river ecosystem.
TLDR
Residual eDNA sampled in surface water can be mapped quantitatively using qRT–PCR, which allows a more accurate spatial identification of the target species location in lotic systems, and relative residual eDNA signal strength may allow the determination of the timing of the presence of target species.Abstract:
Several studies have demonstrated that environmental DNA (eDNA) can be used to detect the presence of aquatic species, days to weeks after the target species has been removed. However, most studies used eDNA analysis in lentic systems (ponds or lakes), or in controlled laboratory experiments. While eDNA degrades rapidly in all aquatic systems, it also undergoes dilution effects and physical destruction in flowing systems, complicating detection in rivers. However, some eDNA (i.e. residual eDNA) can be retained in aquatic systems, even those subject to high flow regimes. Our goal was to determine residual eDNA detection sensitivity using quantitative real-time polymerase chain reaction (qRT-PCR), in a flowing, uncontrolled river after the eDNA source was removed from the system; we repeated the experiment over 2 years. Residual eDNA had the strongest signal strength at the original source site and was detectable there up to 11.5 h after eDNA source removal. Residual eDNA signal strength decreased as sampling distance downstream from the eDNA source site increased, and was no longer detectable at the source site 48 h after the eDNA source water was exhausted in both experiments. This experiment shows that residual eDNA sampled in surface water can be mapped quantitatively using qRT-PCR, which allows a more accurate spatial identification of the target species location in lotic systems, and relative residual eDNA signal strength may allow the determination of the timing of the presence of target species.read more
Citations
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Journal ArticleDOI
Acidity promotes degradation of multi-species environmental DNA in lotic mesocosms
Mathew Seymour,Isabelle Durance,Bernard J. Cosby,Emma Ransom-Jones,Kristy Deiner,Steve J. Ormerod,John K. Colbourne,Gregory Wilgar,Gary R. Carvalho,Mark de Bruyn,Mark de Bruyn,Francois Edwards,Bridget A. Emmett,Holly M. Bik,Simon Creer +14 more
TL;DR: Using four sets of upland stream mesocosms, Mathew Seymour et al. find that eDNA degrades to non-detectable levels within two days and this degradation is accelerated in acidic environments.
Journal ArticleDOI
Applications of environmental DNA (eDNA) in ecology and conservation: opportunities, challenges and prospects
TL;DR: This work reviews and synthesizes eDNA studies published to date to highlight the opportunities and limitations of utilizing eDNA in ecology and conservation, and identifies potential ways of reducing limitations in eDNA analysis.
Journal ArticleDOI
Environmental DNA detection of rare and invasive fish species in two Great Lakes tributaries.
Katherine D. Balasingham,Ryan P. Walter,Ryan P. Walter,Nicholas E. Mandrak,Nicholas E. Mandrak,Daniel D. Heath +5 more
TL;DR: The results demonstrate that eDNA metabarcoding that targets the fish community as well as individual species of interest provides a better understanding of factors affecting the target species spatial distribution in an ecosystem than possible with only target species data.
Journal ArticleDOI
A comprehensive and comparative evaluation of primers for metabarcoding eDNA from fish
Journal ArticleDOI
Early detection of a highly invasive bivalve based on environmental DNA (eDNA)
Zhiqiang Xia,Zhiqiang Xia,Aibin Zhan,Yangchun Gao,Lei Zhang,G. Douglas Haffner,G. Douglas Haffner,Hugh J. MacIsaac,Hugh J. MacIsaac +8 more
TL;DR: An eDNA tool for early detection of the highly invasive golden mussel, Limnoperna fortunei, based on the mitochondrial cytochrome c oxidase subunit I gene (COI) is developed and applied to field samples collected from water bodies in China.
References
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Journal ArticleDOI
The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments
Stephen A. Bustin,Vladimir Benes,Jeremy A. Garson,Jan Hellemans,Jim F. Huggett,Mikael Kubista,Reinhold Mueller,Tania Nolan,Michael W. Pfaffl,Gregory L. Shipley,Jo Vandesompele,Carl T. Wittwer,Carl T. Wittwer +12 more
TL;DR: The Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines target the reliability of results to help ensure the integrity of the scientific literature, promote consistency between laboratories, and increase experimental transparency.
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Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction
TL;DR: A new software tool called Primer-BLAST is presented to alleviate the difficulty in designing target-specific primers and combines BLAST with a global alignment algorithm to ensure a full primer-target alignment and is sensitive enough to detect targets that have a significant number of mismatches to primers.
Limit of blank, limit of detection and limit of quantitation.
David A Armbruster,Terry Pry +1 more
TL;DR: The Limit of Blank, Limit of Detection, and Limit of Quantitation are terms used to describe the smallest concentration of a measurand that can be reliably measured by an analytical procedure.
Journal ArticleDOI
Environmental DNA - An emerging tool in conservation for monitoring past and present biodiversity
TL;DR: The achievements gained through analyses of eDNA from macro-organisms in a conservation context are reviewed, its potential advantages and limitations are discussed, and it is expected the eDNA-based approaches to move from single-marker analyses of species or communities to meta-genomic surveys of entire ecosystems to predict spatial and temporal biodiversity patterns.
Journal ArticleDOI
Species detection using environmental DNA from water samples.
TL;DR: A novel approach, based on the limited persistence of DNA in the environment, to detect the presence of a species in fresh water, using specific primers that amplify short mitochondrial DNA sequences to track the existence of a frog in controlled environments and natural wetlands.
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