Reporting the limits of detection and quantification for environmental DNA assays

Environmental DNA, Journal Year: 2019, Volume and Issue: 2(3), P. 271 - 282

Published: Sept. 16, 2019

Abstract Background Environmental DNA (eDNA) analysis is increasingly being used to detect the presence and relative abundance of rare species, especially invasive or imperiled aquatic species. The rapid progress in eDNA field has resulted numerous studies impacting conservation management actions. However, standardization methods reporting across yet be fully established, with one area calculation interpretation assay limit detection (LOD) quantification (LOQ). Aims Here, we propose establishing consistent for determining LOD LOQ single‐species quantitative PCR (qPCR) studies. Materials & Methods/ Results We utilize datasets from multiple cooperating laboratories demonstrate both a discrete threshold approach curve‐fitting modeling LODs LOQs qPCR assays. also provide details an R script developed applied method. Discussion/Conclusions Ultimately, how are determined, interpreted, reported assays will allow more informed results, meaningful interlaboratory comparisons experiments, enhanced capacity assessing technical quality performance different

Language: Английский

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Persistence of environmental DNA in marine systems

Communications Biology, Journal Year: 2018, Volume and Issue: 1(1)

Published: Oct. 29, 2018

As environmental DNA (eDNA) becomes an increasingly valuable resource for marine ecosystem monitoring, understanding variation in its persistence across contrasting environments is critical. Here, we quantify the breakdown of macrobial eDNA over a spatio-temporal axis locally extreme conditions, varying from ocean-influenced offshore to urban-inshore, and between winter summer. We report that degrades 1.6 times faster inshore environment than environment, but contrary expectation find no difference season. Analysis covariables show spatial gradient salinity temporal pH, with salinity-or biotic correlates thereof-most important. Based on our estimated half-life naturally occurring concentrations, estimate may be detected around 48 h, offering potential collect ecological community data high local fidelity. conclude by placing these results context previously published decay rates.

Language: Английский

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Uses and Misuses of Environmental DNA in Biodiversity Science and Conservation

Annual Review of Ecology Evolution and Systematics, Journal Year: 2018, Volume and Issue: 49(1), P. 209 - 230

Published: Aug. 3, 2018

The study of environmental DNA (eDNA) has the potential to revolutionize biodiversity science and conservation action by enabling census species on a global scale in near real time. To achieve this promise, technical challenges must be resolved. In review, we explore main uses eDNA as well complexities introduced its misuse. Current methods require refinement improved calibration validation along entire workflow lessen false positives/negatives. Moreover, there is great need for better understanding “natural history” eDNA—its origins, state, lifetime, transportation—and more detailed insights concerning physical ecological limitations use. Although analysis can provide powerful information, particularly freshwater marine environments, impact likely less significant terrestrial settings. broad adoption tools will largely depend addressing current uncertainties data interpretation.

Language: Английский

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The detection of aquatic macroorganisms using environmental DNA analysis—A review of methods for collection, extraction, and detection

Environmental DNA, Journal Year: 2019, Volume and Issue: 1(2), P. 99 - 108

Published: June 20, 2019

Abstract The field of environmental DNA (eDNA) analysis has rapidly developed over the past decade and technique become widely used for detecting aquatic macroorganisms in a variety habitats. However, measurement protocols have been individually different eDNA studies this may lead to confusion others who wish incorporate their research. It is important therefore synthesize current status of—and future challenges to—the methodology analysis. We here synthesized from total 438 published were calculate frequency using each method steps. found that methods converged one or two any step. Furthermore, although procedure with highest not always best, it was shown collection by filtration subsequent extraction/purification DNeasy Blood Tissue extraction kit (Qiagen, Hilden, Germany) PowerWater Extraction Kit (Qiagen) most common procedure. An understanding characteristics commonly can help those newly engaged understand basic outline Our review will be useful improvement development analytical techniques sharing recognition methodological characteristic including advantages disadvantages major techniques.

Language: Английский

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Environmental DNA Time Series in Ecology

Trends in Ecology & Evolution, Journal Year: 2018, Volume and Issue: 33(12), P. 945 - 957

Published: Oct. 9, 2018

Language: Английский

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Beyond Biodiversity: Can Environmental DNA (eDNA) Cut It as a Population Genetics Tool?

Genes, Journal Year: 2019, Volume and Issue: 10(3), P. 192 - 192

Published: March 1, 2019

Population genetic data underpin many studies of behavioral, ecological, and evolutionary processes in wild populations contribute to effective conservation management. However, collecting samples can be challenging when working with endangered, invasive, or cryptic species. Environmental DNA (eDNA) offers a way sample material non-invasively without requiring visual observation. While eDNA has been trialed extensively as biodiversity biosecurity monitoring tool strong taxonomic focus, it yet fully explored means for obtaining population information. Here, we review current research that employs approaches the study populations. We outline challenges facing eDNA-based methodologies, suggest avenues future developments. advocate further optimizations, this emergent field holds great potential part genetics toolkit.

Language: Английский

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A validation scale to determine the readiness of environmental DNA assays for routine species monitoring

Environmental DNA, Journal Year: 2021, Volume and Issue: 3(4), P. 823 - 836

Published: March 16, 2021

Abstract The use of environmental DNA (eDNA) analysis for species monitoring requires rigorous validation—from field sampling to the PCR‐based results—for meaningful application and interpretation. Assays targeting eDNA released by individual are typically validated with no predefined criteria answer specific research questions in one ecosystem. Hence, general applicability assays, as well associated uncertainties limitations, often remain undetermined. absence clear guidelines assay validation prevents targeted assays from being incorporated into policy; thus, their establishment is essential realizing potential eDNA‐based surveys. We describe measures tests necessary successful pitfalls form basis guidelines. A list 122 variables was compiled, consolidated 14 thematic blocks (e.g., “in silico analysis”), arranged on a 5‐level scale “incomplete” “operational” defined minimum each level. These were evaluated 546 published single‐species assays. resulting dataset used provide an overview current practices test future rating. Of variables, 20% 76% reported; majority (30%) investigated classified Level 1 (incomplete), 15% did not achieve this first characterized minimal vitro testing, but share annually has declined since 2014. meta‐analysis demonstrates suitability assessing It user‐friendly tool evaluate previously routine monitoring, while also enabling appropriate interpretation results. Finally, it provides guidance reporting standards newly developed

Language: Английский

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Methodology of fish eDNA and its applications in ecology and environment

The Science of The Total Environment, Journal Year: 2020, Volume and Issue: 755, P. 142622 - 142622

Published: Oct. 1, 2020

Language: Английский

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Environmental DNA (eDNA) From the Wake of the Whales: Droplet Digital PCR for Detection and Species Identification

Frontiers in Marine Science, Journal Year: 2018, Volume and Issue: 5

Published: April 19, 2018

Genetic sampling for identification of species, subspecies or stock whales, dolphins and porpoises at sea remains challenging. Most samples have been collected with some form a biopsy dart requiring close approach vessel while the individual is surface. Here we adopted droplet digital (dd)PCR technology detection species cetaceans using environmental (e)DNA from seawater. We conducted series eDNA experiments during 25 encounters killer Orcinus orca, in Puget Sound (the Salish Sea). The regular habits whales these inshore waters allowed us to locate pods collect seawater, an initial distance 200 m 15-minute intervals, up two hours after passage whales. To optimize detection, designed set oligonucleotide primers probes target short fragments mitochondrial (mt)DNA control region, focus on known whale ecotypes. confirmed potential detect wake hours, despite movement water mass by several kilometers due tidal currents. Re-amplification sequencing barcode that ddPCR included 'southern resident community' consistent calls hydrophone recordings visual observations.

Language: Английский

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Improving eDNA yield and inhibitor reduction through increased water volumes and multi-filter isolation techniques

Scientific Reports, Journal Year: 2019, Volume and Issue: 9(1)

Published: March 27, 2019

Abstract To inform management and conservation decisions, environmental DNA (eDNA) methods are used to detect genetic material shed into the water by imperiled invasive species. Methodological enhancements needed reduce filter clogging, PCR inhibition, false-negative detections when eDNA is at low concentrations. In first of three simple experiments, we sought ameliorate clogging from particulates organic through a scaled-up, multi-filter protocol. We combined four filters in 5 mL Phenol-Chloroform-Isoamyl (PCI) procedure allow for larger volumes (~1 L) be filtered rapidly. Increasing volume times resulted 4.4X yield target DNA. Next, inhibition can or block PCR-based assays. remove inhibitory compounds retained during isolation, tested chemically strip inhibitors molecules. The use CTAB as short-term (5–8 day) storage buffer, followed PCI highest yields. Finally, opposed linear relationship among increasing concentrations genomic eDNA, observed sharp change between lower (70–280 ng) higher (420–560 amounts. This may important effectively precipitating protocol testing.

Language: Английский

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