Making sense of the noise: The effect of hydrology on silver carp eDNA detection in the Chicago area waterway system

Song, Jeffery W.; Small, Mitchell J.; Casman, Elizabeth A.

doi:10.1016/j.scitotenv.2017.06.255

Cited by 44 publications

(39 citation statements)

References 33 publications

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“…Future efforts relating to eDNA detectability in lotic environments should examine physical stream characteristics at and upstream of sampling locations in order to better understand the hydrologic processes governing downstream movement and retention of eDNA molecules. A handful of recent studies have begun investigating some of these relationships, such as the role of streambed substrates on the retention and resuspension of eDNA (Jerde et al., ; Shogren et al., , ) or the importance of flow direction in determining eDNA detection probability (Song, Small, & Casman, ). However, physical stream characteristics potentially influencing downstream transport rates of particulate matter, such as current velocity or depth (Miller & Georgian, ; Reynolds, White, Clarke, & Marker, ), remain understudied for eDNA.…”

Section: Discussionmentioning

confidence: 99%

Environmental DNA detects a rare large river crayfish but with little relation to local abundance

2018

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Environmental DNA (eDNA) is DNA extracted from environmental samples (e.g. water) that can be used to infer presence or abundance of species, sometimes with greater sensitivity than conventional sampling methods. Previous eDNA applications to lotic ecosystems have shown promise in accurately inferring species presence, although studies attempting to estimate species abundance have had mixed results. This may be because eDNA applications in lotic environments are challenged by directional streamflow, which has the potential to transport detectable eDNA downstream from its source. Our study sought to evaluate whether results from eDNA corresponded well with the presence and abundance of the narrowly endemic, large river specialist crayfish Faxonius eupunctus obtained through a rigorous, well‐tested conventional sampling method, or instead, if downstream eDNA transport in this large river system might overwhelm the effect of local species abundance. We used a species‐specific quantitative PCR (qPCR) assay to amplify F. eupunctus eDNA collected in surface water samples from streams within the Eleven Point River drainage, Arkansas and Missouri, U.S.A. We estimated F. eupunctus eDNA detection probabilities and examined relationships between eDNA detection probability and site‐scale variables using a hierarchical occupancy and detection probability modelling framework. Results from eDNA sampling showed ˜90% agreement relative to our conventional sampling method in estimating F. eupunctus presence, although eDNA failed to detect F. eupunctus eDNA at two upstream sites where conventional sampling detected F. eupunctus individuals. We found a poor relationship between F. eupunctus eDNA detection probability and local F. eupunctus abundance, and a strong relationship between eDNA detection probability and upstream river distance, which we used as a proxy for the risk of downstream transport of eDNA from upstream F. eupunctus populations. Our results demonstrate eDNA is a largely reliable tool for estimating the presence of benthic organisms in large, freshwater rivers. However, the likelihood of detecting F. eupunctus eDNA presence in our study increased as we moved down the stream network, even though local species abundances were greatest at more upstream locations. Therefore, the ability of eDNA to accurately reflect species presence or abundance in some lotic environments may be hindered by the downstream transport of detectable eDNA.

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Section: Discussionmentioning

confidence: 99%

Environmental DNA detects a rare large river crayfish but with little relation to local abundance

2018

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“…On the other hand, the eDNA detection rate has a negative relationship with Chl. a in a field survey for silver carp (Song et al, 2017). In our study, the eDNA concentrations have a negative relationship with Chl.…”

Section: Discussionsupporting

confidence: 43%

“…Although these studies are based on laboratory experiments, in rivers, eDNA detection rate has been known to decrease with increasing Chl. a, but increase with increasing water temperature and pH (Song et al, 2017). Chl.…”

Section: Introductionmentioning

confidence: 91%

“…Despite the merits of eDNA methods for turtle surveying, the previous eDNA studies in freshwater systems suggest that a number of environmental factors affect the probability of eDNA detection; for example, the water temperature and water quality, including the pH, suspended solid (SS), total phosphorous (TP), total nitrogen (TN), biological oxygen demand (BOD), and chlorophyll a (Chl. a) (e.g., Barnes et al, 2014;Strickler et al, 2014;Eichmiller et al, 2016b;Song et al, 2017). These factors can lead to false negative detections, which prevents the accurate evaluation of eDNA concentrations and detection of the distribution/quantification of a species.…”

Section: Introductionmentioning

confidence: 99%

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Environmental DNA (eDNA) is a powerful tool for monitoring the distribution of aquatic macro-organisms. However, environmental factors, including the water temperature and water quality, can affect the inhibition and/or degradation of eDNA, which prevents accurate estimations of eDNA concentrations and the detection of the presence/absence of species in natural habitats. Also, very few eDNA studies have been conducted for reptiles, especially with respect to estimating their biomass and/or abundances. Here we examined the relationship between the visually-observed number of red-eared sliders (Trachemys scriptaelegans) and the eDNA concentrations. Additionally, we evaluated the effect of water quality on the eDNA concentration in 100 ponds. We found that there was a significant positive correlation between the observed number of red-eared sliders and the eDNA concentration in the ponds. On comparing various water quality indicators, including dissolved nitrogen, dissolved phosphorous, organic matter, and chlorophyll a (Chl. a), we found that only Chl. a had a negative correlation with the red-eared slider eDNA concentration, while we did not find any inhibitions in the quantitative PCR. We conclude that concentrations of eDNA can potentially be used for estimating the abundance of the red-eared slider. Additionally, Chl. a might indirectly influence the degradation of eDNA through the microorganisms bonded to the phytoplankton in the ponds, which microbial activity thought to be decreasing eDNA.

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“…Asian carp threaten to harm the Great Lakes' fishing industry, which produces on average $7 billion of economic activity annually (Buck, Upton, Stern, & Nicols, ). Since 2009, the University of Notre Dame (UND), the US Army Corps of Engineers (USACE) and the US Fish and Wildlife Service (USFWS) have been developing and applying an eDNA sampling protocol in rivers and tributaries near the Great Lakes, such as the Chicago Area Waterway System (CAWS), with the expectation that eDNA sampling will be able to detect the presence of BH and SC at the early stages of an invasion, when the population densities are low (for more background on the situation, see Song, Small, & Casman, ; US Fish & Wildlife Service, ). We investigate the changes made by USFWS to the BH and SC eDNA sampling protocols from 2013 to 2018 and evaluate how these changes may have influenced the protocol's overall detection sensitivity.…”

Section: Introductionmentioning

confidence: 99%

A probabilistic model for designing and assessing the performance of eDNA sampling protocols

Song

Schultz

Casman

et al. 2019

Molecular Ecology Resources

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Environmental DNA (eDNA) sampling, the detection of species‐specific genetic material in water samples, is an emerging tool for monitoring aquatic invasive species. Optimizing eDNA sampling protocols can be challenging because there is imperfect understanding of how each step of the protocol influences its sensitivity. This paper develops a probabilistic model that characterizes each step of an eDNA sampling protocol to evaluate the protocol's overall detection sensitivity for one sample. The model is then applied to analyse how changes over time made to the eDNA sampling protocol to detect bighead (BH) and silver carp (SC) eDNA have influenced its sensitivity, and hence interpretation of the results. The model shows that changes to the protocol have caused the sensitivity of the protocol to fluctuate. A more efficient extraction method in 2013, new species‐specific markers with a qPCR assay in 2014, and a more efficient capture method in 2015 have improved the sensitivity, while switching to a larger elution volume in 2013 and a smaller sample volume in 2015 have reduced the sensitivity. Overall, the sensitivity of the current protocol is higher for BH eDNA detection and SC eDNA detection compared to the original protocol used from 2009 to 2012. The paper shows how this model of eDNA sampling can be used to evaluate the effect of proposed changes in an eDNA sampling and analysis protocol on the sensitivity of that protocol to help researchers optimize their design.

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Making sense of the noise: The effect of hydrology on silver carp eDNA detection in the Chicago area waterway system

Cited by 44 publications

References 33 publications

Environmental DNA detects a rare large river crayfish but with little relation to local abundance

Environmental DNA detects a rare large river crayfish but with little relation to local abundance

Untitled

A probabilistic model for designing and assessing the performance of eDNA sampling protocols

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