Field storage of water samples affects measured environmental DNA concentration and detection

Curtis, Amanda N.; Larson, Eric R.; Davis, Mark A.

doi:10.1007/s10201-020-00634-y

Cited by 21 publications

(18 citation statements)

References 16 publications

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“…After sample collection, bottles were sealed in a clean plastic bag, placed on ice in a cooler and filtered <2 hr after collection. During one collection, samples from Copper Slough were refrigerated and filtered the following morning (~12 hr after collection) but this delay does not affect the quantity of eDNA recovered (Curtis et al, 2021). For each sampling event, one field blank of distilled water per site was used to assess potential contamination in collection supplies.…”

Section: Methodsmentioning

confidence: 99%

High stream flows dilute environmental DNA (eDNA) concentrations and reduce detectability

Curtis

Tiemann

Douglass

et al. 2020

Diversity and Distributions

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Aim Environmental DNA (eDNA) is a rapidly emerging methodology with important applications to environmental management and conservation. However, the effects of stream flow or discharge on eDNA have been minimally investigated in lotic (stream and river) environments. In this study, we examined the role of stream flow on eDNA concentrations and detectability of an invasive clam (Corbicula fluminea), while also accounting for other abiotic and biotic variables. Location Illinois, United States of America. Methods We used a longitudinal study over a year in two streams, as well as a seasonal study (summer, autumn) in eight streams, to investigate the effects of variable stream flow on eDNA concentrations and detectability. We used linear mixed‐effects models to assess the influence of various factors on eDNA concentration and occupancy models to make predictions on how seasonality can influence eDNA detection. Results We found higher stream flows decreased eDNA concentrations, and floods produced false negatives or non‐detections at locations where C. fluminea was relatively common. In addition, we found concentrations and detectability of C. fluminea eDNA to be higher in summer than in autumn. Main conclusions We found that stream flow dilutes eDNA concentrations, which may have serious implications for the detection of low abundance organisms. Managers and practitioners applying eDNA for rare species should seek to sample at low or base stream flows when feasible, and future studies should investigate whether our findings here are consistent for other taxa and lotic ecosystems.

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Section: Methodsmentioning

confidence: 99%

High stream flows dilute environmental DNA (eDNA) concentrations and reduce detectability

Curtis

Tiemann

Douglass

et al. 2020

Diversity and Distributions

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“…Consequently, the efficiency of these methods is still uncertain over longer time spans, although time represents a crucial factor in sample storage (Murphy et al, 2002;Tatangelo et al, 2014). Curtis et al, 2020 documented that water samples that were chilled and stored in the dark 48 hr before filtration showed no substantial decrease in eDNA detection or concentration of Corbicula fluminea with qPCR compared to samples that were immediately filtered. Using ddPCR, Wegleitner et al (2015) reported no significant differences in DNA concentrations of Neogobius melanostomus when filters were stored in Longmire's buffer over a period of 150 days and at room temperature before DNA extraction, compared to filters that were immediately extracted.…”

Section: Introductionmentioning

confidence: 99%

“…As a result, studies have been conducted, investigating various methodological elements of eDNA measurement procedures, allowing to increase the reliability and robustness of these approaches. Collection methods including filter type, pore size, extraction protocols or sample storage strategies and their impacts on eDNA recovery, and ultimately detection sensitivity, have already been extensively explored (Curtis et al., 2020; Djurhuus et al., 2017; Hinlo et al., 2017; Mauvisseau et al., 2020; Spens et al., 2017; Wegleitner et al., 2015; Yamanaka et al., 2016). Currently, on‐site filtration followed by rapid DNA extraction is generally recommended to reduce DNA degradation and obtain optimal DNA concentrations of specific target organisms or taxonomic groups (Hinlo et al., 2017; Yamanaka et al., 2016).…”

Section: Introductionmentioning

confidence: 99%

“…Consequently, the efficiency of these methods is still uncertain over longer time spans, although time represents a crucial factor in sample storage (Murphy et al., 2002; Tatangelo et al., 2014). Curtis et al., 2020 documented that water samples that were chilled and stored in the dark 48 hr before filtration showed no substantial decrease in eDNA detection or concentration of Corbicula fluminea with qPCR compared to samples that were immediately filtered. Using ddPCR, Wegleitner et al.…”

Section: Introductionmentioning

confidence: 99%

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Effects of preservation strategies on environmental DNA detection and quantification using ddPCR

et al. 2021

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“…Currently, there is not a standardized eDNA sampling protocol for freshwater ecosystems, but the overall sequence of steps includes water collection, preservation, and laboratory analysis ( Ruppert, Kline & Rahman, 2019 ). Further, research suggests that sampling decisions made during water collection ( i.e., volume of water) and handling steps ( i.e., on-site vs. lab filtration) may influence detection ( Sepulveda et al, 2019 ; Curtis, Larson & David, 2021 ). Sales et al (2019) found that samples collected in containers, stored on ice, and then transported back to a lab for filtration yielded higher target species copy numbers than the use of a chemical preservation method.…”

Section: Introductionmentioning

confidence: 99%

Using in-situ environmental DNA sampling to detect the invasive New Zealand Mud Snail (Potamopyrgus antipodarum) in freshwaters

Ponce

Arisméndi

Thomas

2021

PeerJ

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Environmental DNA (eDNA) detection of aquatic invasive species is currently at the forefront of aquatic conservation efforts because the methodology provides a cost effective and sensitive means to detect animals at low densities. Developments in eDNA technologies have improved detection probabilities for rare, indicator, and invasive species over the past decade. However, standard lab analysis can take days or weeks before results are available and is prohibitive when rapid management decisions are required for mitigation. Here, we investigated the performance of a real-time quantitative PCR system for on-site eDNA detection of New Zealand mud snails (Potamopyrgus antipodarum). Six sites in western Washington, USA were sampled using the rapid eDNA technique and traditional methods, with five samples per site. On-site eDNA detection of mud snails resulted in a 10% increase in positive sites (16/30 = 53% positive) relative to visual surveys (13/30 = 43% positive). In addition, positive associations were observed between mud snail eDNA concentration (eDNA copies per reaction) and the number of mud snail individuals at each site (R2 = 0.78). We show that the rapid on-site eDNA technology can be effective for detection and quantification of New Zealand mud snails in freshwaters. This on-site eDNA detection approach could possibly be used to initiate management protocols that allow for more rapid responses during the onset of biological invasions.

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Field storage of water samples affects measured environmental DNA concentration and detection

Cited by 21 publications

References 16 publications

High stream flows dilute environmental DNA (eDNA) concentrations and reduce detectability

High stream flows dilute environmental DNA (eDNA) concentrations and reduce detectability

Effects of preservation strategies on environmental DNA detection and quantification using ddPCR

Using in-situ environmental DNA sampling to detect the invasive New Zealand Mud Snail (Potamopyrgus antipodarum) in freshwaters

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