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  • Variation in Inhibitor Effects on qPCR Assays and implications for eDNA Surveys

    Abstract: Aquatic environmental DNA (eDNA) surveys are sometimes impacted by polymerase chain reaction (PCR) inhibitors. We tested varying concentrations of different inhibitors (humic, phytic, and tannic acids; crude leaf extracts) for impacts on quantitative PCR (qPCR) assays designed for eDNA surveys of bighead and silver carp (Hypophthalmichthys nobilis and Hypophthalmichthys molitrix). We also tested for inhibition by high concentrations of exogenous DNA, hypothesizing that DNA from increasingly closely related species would be increasingly inhibitory. All tested inhibitors impacted qPCR, though only at very high concentrations — likely a function, in part, of having used an inhibitor-resistant qPCR solution. Closer phylogenetic relatedness resulted in inhibition at lower exogenous DNA concentrations, but not at relatively close phylogenetic scales. Inhibition was also influenced by the qPCR reporter dye used. Importantly, different qPCR assays responded differently to the same inhibitor concentrations. Implications of these results are that the inclusion of more than one assay for the same target taxa in an eDNA survey may be an important countermeasure against false negatives and that internal positive controls may not, in the absence of efforts to maximize inhibition compatibility, provide useful information about the inhibition of an eDNA assay.
  • Monitoring the Milwaukee Harbor Breakwater: An Engineering With Nature® (EWN®) Demonstration Project

    Abstract: The US Army Corps of Engineers (USACE) maintains breakwaters in Mil-waukee Harbor. USACE’s Engineering With Nature® (EWN®) breakwater demonstration project created rocky aquatic habitat with cobbles (10–20 cm) covering boulders (6–8 metric tons) along a 152 m section. A prolific population of Hemimysis anomala, an introduced Pontocaspian mysid and important food source for local pelagic fishes, was significantly (p < .05) more abundant on cobbles versus boulders. Food-habits data of ale-wife (Alosa pseudoharengus) and rainbow smelt (Osmerus mordax) pro-vided evidence that H. anomala were a common prey item. Night surveys and gill netting confirmed O. mordax preferred foraging on the cobbles (p < .05) and consumed more H. anomala than at the reference site (p < .05). H. anomala comprised a significant portion of the diets of young-of-the-year (YOY) yellow perch (Perca flavescens), YOY largemouth bass (Micropterus salmoides), and juvenile rock bass (Ambloplites rupestris) caught on the breakwater. The natural features’ construction on the break-water increased the available habitat for this benthopelagic macroinverte-brate and created a novel ecosystem benefiting forage fish and a nursery habitat benefiting nearshore game fish juveniles. These data will encour-age the application of EWN concepts during structural repairs at other built navigation infrastructure.
  • Long-Term Stability and Efficacy of Historic Activated Carbon (AC) Deployments at Diverse Freshwater and Marine Remediation Sites

    Abstract: A number of sites around the United States have used activated carbon (AC) amendments to remedy contaminated sediments. Variation in site-specific characteristics likely influences the long-term fate and efficacy of AC treatment. The long-term effectiveness of an AC amendment to sediment is largely unknown, as the field performance has not been monitored for more than three years. As a consequence, the focus of this research effort was to evaluate AC’s long-term (6–10 yr) performance. These assessments were performed at two pilot-scale demonstration sites, Grasse River, Massena, New York and Canal Creek, Aberdeen Proving Ground (APG), Aberdeen, Maryland, representing two distinct physical environments. Sediment core samples were collected after 6 and 10 years of remedy implementation at APG and Grasse River, respectively. Core samples were collected and sectioned to determine the current vertical distribution and persistence of AC in the field. The concentration profile of polychlorinated biphenyls (PCBs) in sediment pore water with depth was measured using passive sampling. Sediment samples from the untreated and AC-treated zones were also assessed for bioaccumulation in benthic organisms. The data collected enabled comparison of AC distribution, PCB concentrations, and bioaccumulation measured over the short- and long-term (months to years).