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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.
  • Development of Three-Dimensional Wetting and Drying Algorithm for the Geophysical Scale Transport Multi-Block Hydrodynamic Sediment and Water Quality Transport Modeling System (GSMB)

    Introduction: The Environmental Laboratory (EL) and the Coastal and Hydraulics Laboratory (CHL) have jointly completed a number of large-scale hydrodynamic, sediment and water quality transport studies. EL and CHL have successfully executed these studies utilizing the Geophysical Scale Transport Modeling System (GSMB). The model framework of GSMB is composed of multiple process models as shown in Figure 1. Figure 1 shows that the United States Army Corps of Engineers (USACE) accepted wave, hydrodynamic, sediment and water quality transport models are directly and indirectly linked within the GSMB framework. The components of GSMB are the two-dimensional (2D) deep-water wave action model (WAM) (Komen et al. 1994, Jensen et al. 2012), data from meteorological model (MET) (e.g., Saha et al. 2010 http://journals.ametsoc.org/doi/pdf/10.1175/2010BAMS3001.1), shallow water wave models (STWAVE) (Smith et al. 1999), Coastal Modeling System wave (CMS-WAVE) (Lin et al. 2008), the large-scale, unstructured two-dimensional Advanced Circulation (2D ADCIRC) hydrodynamic model (http://www.adcirc.org), and the regional scale models, Curvilinear Hydrodynamics in three dimensions-Multi-Block (CH3D-MB) (Luong and Chapman 2009), which is the multi-block (MB) version of Curvilinear Hydrodynamics in three-dimensions-Waterways Experiments Station (CH3D-WES) (Chapman et al. 1996, Chapman et al. 2009), MB CH3D-SEDZLJ sediment transport model (Hayter et al. 2012), and CE-QUAL Management - ICM water quality model (Bunch et al. 2003, Cerco and Cole 1994). Task 1 of the DOER project, “Modeling Transport in Wetting/Drying and Vegetated Regions,” is to implement and test three-dimensional (3D) wetting and drying (W/D) within GSMB. This technical note describes the methods and results of Task 1. The original W/D routines were restricted to a single vertical layer or depth-averaged simulations. In order to retain the required 3D or multi-layer capability of MB-CH3D, a multi-block version with variable block layers was developed (Chapman and Luong 2009). This approach requires a combination of grid decomposition, MB, and Message Passing Interface (MPI) communication (Snir et al. 1998). The MB single layer W/D has demonstrated itself as an effective tool in hyper-tide environments, such as Cook Inlet, Alaska (Hayter et al. 2012). The code modifications, implementation, and testing of a fully 3D W/D are described in the following sections of this technical note.
  • A Framework and Pilot Tool for the Risk-based Prioritization and Grouping of Nano-enabled Consumer Products

    Abstract: The use of engineered nanomaterials (ENMs) in consumer products has expanded rapidly, revealing both innovative improvements over conventional materials, and the potential for novel risks to human health and the environment. As the number of new nano-enabled products and the volume of toxicity data on ENMs continues to grow, regulatory agencies like the U.S. Consumer Product Safety Commission (CPSC) – a small, independent federal agency responsible for protecting consumers from unreasonable risks associated with product use – will require the ability to screen and group a diverse array of nano-enabled consumer products based on their potential risks to consumers. Such prioritization would allow efficient allocation of limited resources for subsequent testing and evaluation of high-risk products and materials. To enable this grouping and prioritization for further testing, we developed a framework that establishes a prioritization score by evaluating a nano-enabled product's potential hazard and exposure, as well as additional consideration of regulatory importance. We integrate the framework into a pilot version software tool and, using a hypothetical case study, we demonstrate that the tool can effectively rank nano-enabled consumer products and can be adjusted for use by agencies with different priorities. The proposed decision-analytical framework and pilot-version tool presented here could enable a regulatory agency like the CPSC to triage reported safety concerns more effectively and allocate limited resources more efficiently.
  • Methods for Simultaneous Determination of Legacy and Insensitive Munition (IM) Constituents in Aqueous, Soil/Sediment, and Tissue Matrices

    Abstract: Currently, no standard method exists for analyzing insensitive munition (IM) compounds in environmental matrices, with or without concurrent legacy munition compounds, resulting in potentially inaccurate determinations. The primary objective of this work was to develop new methods of extraction, pre-concentration, and analytical separation/quantitation of 17 legacy munition compounds along with several additional IM compounds, IM breakdown products, and other munition compounds that are not currently included in U.S. Environmental Protection Agency (EPA) Method 8330B. Analytical methods were developed to enable sensitive, simultaneous detection and quantitation of the 24 IM and legacy compounds, including two orthogonal high-performance liquid chromatography (HPLC) column separations with either ultraviolet (UV) or mass spectrometric (MS) detection. Procedures were developed for simultaneous extraction of all 24 analytes and two surrogates (1,2-dinitrobenzene, 1,2-DNB; o-NBA) from high- and low-level aqueous matrices and solid matrices, using acidification, solid phase extraction (SPE), or solvent extraction (SE), respectively. The majority of compounds were recovered from four tissue types within current limits for solids, with generally low recovery only for Tetryl (from 4 to 62%). A preparatory chromatographic interference removal procedure was adapted for tissue extracts, as various analytical interferences were observed for all studied tissue types.
  • Sustainable Infrastructure in Conflict Zones: Police Facilities’ Impact on Perception of Safety in Afghan Communities

    Abstract: The notion of sustainable infrastructure for the delivery of social services is to fulfill basic human needs; in war-torn societies, human safety is a critical basic need. The relationship between sustainable infrastructure development and human safety remains under-researched in Afghan neighborhoods. Therefore, this study examined the effectiveness of the police facilities constructed for stability enhancement in Afghan communities. To do so, this study used Afghans’ polling datasets on the police presence and the public safety perceptions, including newly collected survey data related to the influence of the police facilities on human safety and other factors contributing to the neighborhoods’ well-being. The datasets are organized with a multilevel structure in which different individuals are sampled within neighborhoods and analyzed using a multilevel model approach to capture the randomness of the responses. The results showed that police facilities are more important to perceptions of safety in less safe areas and that Afghans in villages perceived themselves as safer than in urban areas, relative to their own immediate region. Those perceiving themselves as being safer were older, more highly educated, and widowed respondents. Overall, Afghans perceived the police facilities as institutional symbol for promoting improvements and opportunities for fulfilling basic human safety need.
  • Hydrologic Analysis of Field Delineated Ordinary High Water Marks for Rivers and Streams

    Abstract: Streamflow influences the distribution and organization of high water marks along rivers and streams in a landscape. The federal definition of ordinary high water mark (OHWM) is defined by physical and vegetative field indicators that are used to identify inundation extents of ordinary high water levels without any reference to the relationship between streamflow and regulatory definition. Streamflow is the amount, or volume, of water that moves through a stream per unit time. This study explores regional characteristics and relationships between field-delineated OHWMs and frequency-magnitude streamflow metrics derived from a flood frequency analysis. The elevation of OHWM is related to representative constant-level discharge return periods with national average return periods of 6.9 years using partial duration series and 2.8 years using annual maximum flood frequency approaches. The range in OHWM return periods is 0.5 to 9.08, and 1.05 to 11.01 years for peaks-over-threshold and annual maximum flood frequency methods, respectively. The range of OHWM return periods is consistent with the range found in national studies of return periods related to bankfull streamflow. Hydraulic models produced a statistically significant relationship between OHWM and bank-full, which reinforces the close relationship between the scientific concept and OHWM in most stream systems.
  • Aligning research and monitoring priorities for benthic cyanobacteria and cyanotoxins : a workshop summary

    Abstract: In 2018, the US Army Engineer Research and Development Center partnered with the US Army Corps of Engineers–Buffalo District, the US Environmental Protection Agency, Bowling Green State University, and the Cawthron Institute to host a workshop focused on benthic and sediment-associated cyanobacteria and cyanotoxins, particularly in the context of harmful algal blooms (HAB). Technical sessions on the ecology of benthic cyanobacteria in lakes and rivers; monitoring of cyanobacteria and cyanotoxins; detection of benthic and sediment-bound cyanotoxins; and the fate, transport, and health risks of cyanobacteria and their associated toxins were presented. Research summaries included the buoyancy and dispersal of benthic freshwater cyanobacteria mats, the fate and quantification of cyanotoxins in lake sediments, and spatial and temporal variation of toxins in streams. In addition, summaries of remote sensing methods, omic techniques, and field sampling techniques were presented. Critical research gaps identified from this workshop include (1) ecology of benthic cyanobacteria, (2) identity, fate, transport, and risk of cyanotoxins produced by benthic cyanobacteria, (3) standardized sampling and analysis protocols, and (4) increased technical cooperation between government, academia, industry, nonprofit organizations, and other stakeholders. Conclusions from this workshop can inform monitoring and management efforts for benthic cyanobacteria and their associated toxins.
  • Spatial Distribution and Thickness of Fine-Grained Sediment along the United States Portion of the Upper Niagara River, New York

    Abstract: Over 220 linear miles of geophysical data, including sidescan sonar and chirp sub-bottom profiles, were collected in 2016 and 2017 by the US Army Corps of Engineers and the US Fish and Wildlife Service in the upper Niagara River. In addition, 36 sediment grab samples were collected to groundtruth the geophysical data. These data were used to map the spatial distribution of fine-grained sediment, including volume data in certain locations, along the shallow shorelines of the upper Niagara River. Overall, the most extensive deposits were spatially associated with either small tributaries or with man-made structures that modified the natural flow of the system. Extensive beds of submerged aquatic vegetation (SAV) were also mapped. Although always associated with a fine-grained matrix, the SAV beds were patchy in distribution, which might reflect subtle differences in the grain size of the sediment matrix or could simply be a function of variations in species or growth. The maps generated from this effort can be used to guide sampling plans for future studies of contamination in fine-grained sediment regions.
  • Expert Elicitation Workshop for Planning Wetland and Reef Natural and Nature-Based Features (NNBF) Futures

    Abstract: This special report discusses the outcomes of a September 2019 workshop intended to identify barriers to the consideration and implementation of natural and nature-based features (NNBF) in US Army Corps of Engineers (USACE) civil works projects. A total of 23 participants representing seven USACE districts, the US Army Engineer Research and Development Center (ERDC), and the University of California–Santa Cruz met at USACE’s South Atlantic Division Headquarters in Atlanta, Georgia, to discuss how to facilitate the implementation of NNBF into USACE project planning for wetlands and reefs using six categories: (1) site characterization, (2) engineering and design analysis, (3) life-cycle analysis, (4) economic analysis, (5) construction analysis, (6) and operation and maintenance (and monitoring). The workshop identified seven future directions in wetland and reef NNBF research and development: • Synthesize existing literature and analysis of existing projects to better define failure modes. • Determine trigger points that lead to loss of feature function. • Identify performance factors with respect to coastal storm risk management (CSRM) performance as well as ecological performance. • Focus additional research into cobenefits of NNBF. • Quantify the economic life-cycle costs of a project. • Improve technology transfer with regards to NNBF research and topics.
  • Geographic and Genetic Variation in Susceptibility of Butomus umbellatus to Foliar Fungal Pathogens

    Abstract: Large-scale patterns of plant invasions may reflect regional heterogeneity in biotic and abiotic factors and genetic variation within and between invading populations. Having information on how effects of biotic resistance vary spatially can be especially important when implementing biological control because introduced agents may have different Impacts through interactions with host-plant genotype, local environment, or other novel enemies. We conducted a series of field surveys and laboratory studies to determine whether there was evidence of biotic resistance, as foliar fungal pathogens, in two introduced genotypes (triploid G1, diploid G4) of the Eurasian wetland weed, Butomus umbellatus L. in the USA. We tested whether genotypes differed in disease attack and whether spatial patterns in disease incidence were related to geographic location or climate for either genotype. After accounting for location (latitude, climate), G1 plants had lower disease incidence than G4 plants in the field (38% vs. 70%) but similar pathogen richness. In contrast, bioassays revealed G1 plants consistently received a higher damage score and had larger leaf lesions regardless of pathogen. These results demonstrate that two widespread B. umbellatus genotypes exhibit different susceptibility to pathogens and effectiveness of pathogen biological controls may depend on local conditions.