U.S. Army Engineer Research and Development Center

Summary Species detection using environmental DNA ( eDNA ) has tremendous potential for contributing to the understanding of the ecology and conservation of aquatic species. Detecting species using eDNA methods, rather than directly sampling the organisms, can reduce impacts on sensitive species and increase the power of field surveys for rare and elusive species. The sensitivity of eDNA methods, however, requires a heightened awareness and attention to quality assurance and quality control protocols. Additionally, the interpretation of eDNA data demands careful consideration of multiple factors. As eDNA methods have grown in application, diverse approaches have been implemented to address these issues. With interest in eDNA continuing to expand, supportive guidelines for undertaking eDNA studies are greatly needed. Environmental DNA researchers from around the world have collaborated to produce this set of guidelines and considerations for implementing eDNA methods to detect aquatic macroorganisms. Critical considerations for study design include preventing contamination in the field and the laboratory, choosing appropriate sample analysis methods, validating assays, testing for sample inhibition and following minimum reporting guidelines. Critical considerations for inference include temporal and spatial processes, limits of correlation of eDNA with abundance, uncertainty of positive and negative results, and potential sources of allochthonous DNA . We present a synthesis of knowledge at this stage for application of this new and powerful detection method.

The Stardust spacecraft collected thousands of particles from comet 81P/Wild 2 and returned them to Earth for laboratory study. The preliminary examination of these samples shows that the nonvolatile portion of the comet is an unequilibrated assortment of materials that have both presolar and solar system origin. The comet contains an abundance of silicate grains that are much larger than predictions of interstellar grain models, and many of these are high-temperature minerals that appear to have formed in the inner regions of the solar nebula. Their presence in a comet proves that the formation of the solar system included mixing on the grandest scales.

Decision making in environmental projects can be complex and seemingly intractable, principally because of the inherent trade-offs between sociopolitical, environmental, ecological, and economic factors. The selection of appropriate remedial and abatement strategies for contaminated sites, land use planning, and regulatory processes often involves multiple additional criteria such as the distribution of costs and benefits, environmental impacts for different populations, safety, ecological risk, or human values. Some of these criteria cannot be easily condensed into a monetary value, partly because environmental concerns often involve ethical and moral principles that may not be related to any economic use or value. Furthermore, even if it were possible to aggregate multiple criteria rankings into a common unit, this approach would not always be desirable because the ability to track conflicting stakeholder preferences may be lost in the process. Consequently, selecting from among many different alternatives often involves making trade-offs that fail to satisfy 1 or more stakeholder groups. Nevertheless, considerable research in the area of multicriteria decision analysis (MCDA) has made available practical methods for applying scientific decision theoretical approaches to complex multicriteria problems. This paper presents a review of the available literature and provides recommendations for applying MCDA techniques in environmental projects. A generalized framework for decision analysis is proposed to highlight the fundamental ingredients for more structured and tractable environmental decision making.

Hurricanes Katrina and Rita showed the vulnerability of coastal communities and how human activities that caused deterioration of the Mississippi Deltaic Plain (MDP) exacerbated this vulnerability. The MDP formed by dynamic interactions between river and coast at various temporal and spatial scales, and human activity has reduced these interactions at all scales. Restoration efforts aim to re-establish this dynamic interaction, with emphasis on reconnecting the river to the deltaic plain. Science must guide MDP restoration, which will provide insights into delta restoration elsewhere and generally into coasts facing climate change in times of resource scarcity.

Phytoplankton blooms over Arctic Ocean continental shelves are thought to be restricted to waters free of sea ice. Here, we document a massive phytoplankton bloom beneath fully consolidated pack ice far from the ice edge in the Chukchi Sea, where light transmission has increased in recent decades because of thinning ice cover and proliferation of melt ponds. The bloom was characterized by high diatom biomass and rates of growth and primary production. Evidence suggests that under-ice phytoplankton blooms may be more widespread over nutrient-rich Arctic continental shelves and that satellite-based estimates of annual primary production in these waters may be underestimated by up to 10-fold.

Advanced oxidation processes via semiconductor photocatalysis for water treatment have been the subject of extensive research over the past three decades, producing many scientific reports focused on elucidating mechanisms and enhancing kinetics for the treatment of contaminants in water. Many of these reports imply that the ultimate goal of the research is to apply photocatalysis in municipal water treatment operations. However, this ignores immense technology transfer problems, perpetuating a widening gap between academic advocation and industrial application. In this Feature, we undertake a critical examination of the trajectory of photocatalytic water treatment research, assessing the viability of proposed applications and identifying those with the most promising future. Several strategies are proposed for scientists and engineers who aim to support research efforts to bring industrially relevant photocatalytic water treatment processes to fruition. Although the reassessed potential may not live up to initial academic hype, an unfavorable assessment in some areas does not preclude the transfer of photocatalysis for water treatment to other niche applications as the technology retains substantive and unique benefits.

There is great interest in the restoration and conservation of coastal habitats for protection from flooding and erosion. This is evidenced by the growing number of analyses and reviews of the effectiveness of habitats as natural defences and increasing funding world-wide for nature-based defences-i.e. restoration projects aimed at coastal protection; yet, there is no synthetic information on what kinds of projects are effective and cost effective for this purpose. This paper addresses two issues critical for designing restoration projects for coastal protection: (i) a synthesis of the costs and benefits of projects designed for coastal protection (nature-based defences) and (ii) analyses of the effectiveness of coastal habitats (natural defences) in reducing wave heights and the biophysical parameters that influence this effectiveness. We (i) analyse data from sixty-nine field measurements in coastal habitats globally and examine measures of effectiveness of mangroves, salt-marshes, coral reefs and seagrass/kelp beds for wave height reduction; (ii) synthesise the costs and coastal protection benefits of fifty-two nature-based defence projects and; (iii) estimate the benefits of each restoration project by combining information on restoration costs with data from nearby field measurements. The analyses of field measurements show that coastal habitats have significant potential for reducing wave heights that varies by habitat and site. In general, coral reefs and salt-marshes have the highest overall potential. Habitat effectiveness is influenced by: a) the ratios of wave height-to-water depth and habitat width-to-wavelength in coral reefs; and b) the ratio of vegetation height-to-water depth in salt-marshes. The comparison of costs of nature-based defence projects and engineering structures show that salt-marshes and mangroves can be two to five times cheaper than a submerged breakwater for wave heights up to half a metre and, within their limits, become more cost effective at greater depths. Nature-based defence projects also report benefits ranging from reductions in storm damage to reductions in coastal structure costs.

Polychlorinated biphenyls (PCBs) as environmental contaminants often cannot be adequately described by reference to Aroclors or to total PCBs. Although there are 209 possible PCB configurations (congeners), perhaps half that number account for nearly all of the environmental contamination attributable to PCBs. Still fewer congeners are both prevalent and either demonstrably or potentially toxic. If potential toxicity, environmental prevalence, and relative abundance in animal tissues are used as criteria, the number of environmentally threatening PCB congeners reduces to about thirty-six. Twenty-five of these account for 50 to 75% of total PCBs in tissue samples of fish, invertebrates, birds, and mammals. A few PCB congeners that are sterically similar to 2,3,7,8-tetrachlorodibenzo-p-dioxin (2,3,7,8-TCDD) are directly toxic. Other PCB congeners, as well as those that are directly toxic, may also be involved in toxicity indirectly by stimulating the production of (inducing) bioactivating enzyme systems. The most consequential of these have the ability to induce aryl hydrocarbon metabolizing mixed-function oxidases (MFOs). A result can be an increased capacity for bioactivation of otherwise nontoxic foreign compounds such as certain polynuclear aromatic hydrocarbons (PAH) to cytotoxic or genotoxic metabolites. The effectiveness of specific PCB congeners as inducers of different types of cytochrome P-450-dependent MFO systems is determined by their stereochemistry. Although MFO induction is not a proximate cause, it is a strong correlate of certain kinds of toxicities. Structural patterns can thus be used to discriminate among PCB congeners on the basis of toxic potential, if not entirely on toxicity per se. Congeners that demonstrate 3-methylcholanthrene-type (3-MC-type) and mixed-type MFO induction have the greatest toxic potential. These congeners most closely resemble 2,3,7,8-TCDD in their structures and in their toxic effects. The larger group of phenobarbital-type (PB-type) inducers have considerably less potential for contributing to toxic effects. Weak inducers and noninducing congeners have the least potential for toxicity. Using the rationale described in this paper, we assigned the most evironmentally threatening PCB congeners to four groups. Congeners assigned to Group 1 are considered most likely to contribute to adverse biological effects attributable to PCBs in an environmental sample. Group 1A contains the three most potent (pure 3-MC-type inducer) congeners, IUPAC numbers 77, 126, and 169. Six congeners, numbers 105, 118, 128, 138, 156, and 170, are assigned to Group 1B. These congeners are mixed-type inducers that have been reported frequently in environmental samples.(ABSTRACT TRUNCATED AT 400 WORDS)

WRKY transcription factors (TFs) are key regulators of many plant processes, including the responses to biotic and abiotic stresses, senescence, seed dormancy and seed germination. For over 15 years, limited evidence has been available suggesting that WRKY TFs may play roles in regulating plant responses to the phytohormone abscisic acid (ABA), notably some WRKY TFs are ABA-inducible repressors of seed germination. However, the roles of WRKY TFs in other aspects of ABA signalling, and the mechanisms involved, have remained unclear. Recent significant progress in ABA research has now placed specific WRKY TFs firmly in ABA-responsive signalling pathways, where they act at multiple levels. In Arabidopsis, WRKY TFs appear to act downstream of at least two ABA receptors: the cytoplasmic PYR/PYL/RCAR-protein phosphatase 2C-ABA complex and the chloroplast envelope-located ABAR-ABA complex. In vivo and in vitro promoter-binding studies show that the target genes for WRKY TFs that are involved in ABA signalling include well-known ABA-responsive genes such as ABF2, ABF4, ABI4, ABI5, MYB2, DREB1a, DREB2a and RAB18. Additional well-characterized stress-inducible genes such as RD29A and COR47 are also found in signalling pathways downstream of WRKY TFs. These new insights also reveal that some WRKY TFs are positive regulators of ABA-mediated stomatal closure and hence drought responses. Conversely, many WRKY TFs are negative regulators of seed germination, and controlling seed germination appears a common function of a subset of WRKY TFs in flowering plants. Taken together, these new data demonstrate that WRKY TFs are key nodes in ABA-responsive signalling networks.

In this Focus article, the authors ask a seemingly simple question: Are harmful algal blooms (HABs) becoming the greatest inland water quality threat to public health and aquatic ecosystems? When HAB events require restrictions on fisheries, recreation, and drinking water uses of inland water bodies significant economic consequences result. Unfortunately, the magnitude, frequency, and duration of HABs in inland waters are poorly understood across spatiotemporal scales and differentially engaged among states, tribes, and territories. Harmful algal bloom impacts are not as predictable as those from conventional chemical contaminants, for which water quality assessment and management programs were primarily developed, because interactions among multiple natural and anthropogenic factors determine the likelihood and severity to which a HAB will occur in a specific water body. These forcing factors can also affect toxin production. Beyond site-specific water quality degradation caused directly by HABs, the presence of HAB toxins can negatively influence routine surface water quality monitoring, assessment, and management practices. Harmful algal blooms present significant challenges for achieving water quality protection and restoration goals when these toxins confound interpretation of monitoring results and environmental quality standards implementation efforts for other chemicals and stressors. Whether HABs presently represent the greatest threat to inland water quality is debatable, though in inland waters of developed countries they typically cause more severe acute impacts to environmental quality than conventional chemical contamination events. The authors identify several timely research needs. Environmental toxicology, environmental chemistry, and risk-assessment expertise must interface with ecologists, engineers, and public health practitioners to engage the complexities of HAB assessment and management, to address the forcing factors for HAB formation, and to reduce the threats posed to inland surface water quality.

The genus Shewanella has been studied since 1931 with regard to a variety of topics of relevance to both applied and environmental microbiology. Recent years have seen the introduction of a large number of new Shewanella-like isolates, necessitating a coordinated review of the genus. In this work, the phylogenetic relationships among known shewanellae were examined using a battery of morphological, physiological, molecular and chemotaxonomic characterizations. This polyphasic taxonomy takes into account all available phenotypic and genotypic data and integrates them into a consensus classification. Based on information generated from this study and obtained from the literature, a scheme for the identification of Shewanella species has been compiled. Key phenotypic characteristics were sulfur reduction and halophilicity. Fatty acid and quinone profiling were used to impart an additional layer of information. Molecular characterizations employing small-subunit 16S rDNA sequences were at the limits of resolution for the differentiation of species in some cases. As a result, DNA-DNA hybridization and sequence analyses of a more rapidly evolving molecule (gyrB gene) were performed. Species-specific PCR probes were designed for the gyrB gene and used for the rapid screening of closely related strains. With this polyphasic approach, in addition to the ten described Shewanella species, two new species, Shewanella oneidensis and 'Shewanella pealeana', were recognized; Shewanella oneidensis sp. nov. is described here for the first time.

Abstract Laser altimetry (lidar) is a remote-sensing technology that holds tremendous promise for mapping snow depth in snow hydrology and avalanche applications. Recently lidar has seen a dramatic widening of applications in the natural sciences, resulting in technological improvements and an increase in the availability of both airborne and ground-based sensors. Modern sensors allow mapping of vegetation heights and snow or ground surface elevations below forest canopies. Typical vertical accuracies for airborne datasets are decimeter-scale with order 1 m point spacings. Ground-based systems typically provide millimeter-scale range accuracy and sub-meter point spacing over 1 m to several kilometers. Many system parameters, such as scan angle, pulse rate and shot geometry relative to terrain gradients, require specification to achieve specific point coverage densities in forested and/or complex terrain. Additionally, snow has a significant volumetric scattering component, requiring different considerations for error estimation than for other Earth surface materials. We use published estimates of light penetration depth by wavelength to estimate radiative transfer error contributions. This paper presents a review of lidar mapping procedures and error sources, potential errors unique to snow surface remote sensing in the near-infrared and visible wavelengths, and recommendations for projects using lidar for snow-depth mapping.

As part of ice albedo feedback studies during the Surface Heat Budget of the Arctic Ocean (SHEBA) field experiment, we measured spectral and wavelength‐integrated albedo on multiyear sea ice. Measurements were made every 2.5 m along a 200‐m survey line from April through October. Initially, this line was completely snow covered, but as the melt season progressed, it became a mixture of bare ice and melt ponds. Observed changes in albedo were a combination of a gradual evolution due to seasonal transitions and abrupt shifts resulting from synoptic weather events. There were five distinct phases in the evolution of albedo: dry snow, melting snow, pond formation, pond evolution, and fall freeze‐up. In April the surface albedo was high (0.8–0.9) and spatially uniform. By the end of July the average albedo along the line was 0.4, and there was significant spatial variability, with values ranging from 0.1 for deep, dark ponds to 0.65 for bare, white ice. There was good agreement between surface‐based albedos and measurements made from the University of Washington's Convair‐580 research aircraft. A comparison between net solar irradiance computed using observed albedos and a simplified model of seasonal evolution shows good agreement as long as the timing of the transitions is accurately determined.

Recent natural and man‐made catastrophes, such as the Fukushima nuclear power plant, flooding caused by Hurricane Katrina, the Deepwater Horizon oil spill, the Haiti earthquake, and the mortgage derivatives crisis, have renewed interest in the concept of resilience , especially as it relates to complex systems vulnerable to multiple or cascading failures. Although the meaning of resilience is contested in different contexts, in general resilience is understood to mean the capacity to adapt to changing conditions without catastrophic loss of form or function. In the context of engineering systems, this has sometimes been interpreted as the probability that system conditions might exceed an irrevocable tipping point. However, we argue that this approach improperly conflates resilience and risk perspectives by expressing resilience exclusively in risk terms. In contrast, we describe resilience as an emergent property of what an engineering system does , rather than a static property the system has . Therefore, resilience cannot be measured at the systems scale solely from examination of component parts. Instead, resilience is better understood as the outcome of a recursive process that includes: sensing, anticipation, learning, and adaptation. In this approach, resilience analysis can be understood as differentiable from, but complementary to, risk analysis, with important implications for the adaptive management of complex, coupled engineering systems. Management of the 2011 flooding in the Mississippi River Basin is discussed as an example of the successes and challenges of resilience‐based management of complex natural systems that have been extensively altered by engineered structures.

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

It has been observed that the majority of particles in a granular material carries less than the average load and that the number of particles carrying larger than the average load decreases exponentially with increasing contact force. The particles carrying above average load appear to form a strong network of forces while the majority of particles belong to a weak network. The strong network of forces appear to have a spatial characteristic whereby the stronger forces are carried though chainlike particle groups referred to as force chains. There is a strong case for a connection between force chains of the discrete medium and the trajectory of the most compressive principal stress in its continuous idealization. While such properties seem obvious from descriptive analysis of physical and numerical experiments in granular media, progress in quantification of the force chain statistics requires an objective description of what constitutes a force chain. A procedure to quantify the occurrence of force chains is built on a proposed definition having two parts: first, the chain is a quasilinear arrangement of three or more particles, and second, along the chain, stress concentration within each grain is characterized by the vector delineating the most compressive principal stress. The procedure is incorporated into an algorithm that can be applied to large particle assemblies to compile force chain statistics. The procedure is demonstrated on a discrete element simulation of a rigid punch into a half space. It was found that only approximately half of the particles within the group of so-called strong network particles are part of force chains. Throughout deformation, the average length of force chains varied slightly but the number of force chains decreased as the punch advanced. The force chain lengths follow an exponential distribution. The procedure provides a tool for objective analysis of force chains, although future work is required to incorporate branching of force chains into the analysis.

Here, we report a catalytic beacon sensor for uranyl (UO2(2+)) based on an in vitro-selected UO2(2+)-specific DNAzyme. The sensor consists of a DNA enzyme strand with a 3' quencher and a DNA substrate with a ribonucleotide adenosine (rA) in the middle and a fluorophore and a quencher at the 5' and 3' ends, respectively. The presence of UO2(2+) causes catalytic cleavage of the DNA substrate strand at the rA position and release of the fluorophore and thus dramatic increase of fluorescence intensity. The sensor has a detection limit of 11 parts per trillion (45 pM), a dynamic range up to 400 nM, and selectivity of >1-million-fold over other metal ions. The most interfering metal ion, Th(IV), interacts with the fluorescein fluorophore, causing slightly enhanced fluorescence intensity, with an apparent dissociation constant of approximately 230 microM. This sensor rivals the most sensitive analytical instruments for uranium detection, and its application in detecting uranium in contaminated soil samples is also demonstrated. This work shows that simple, cost-effective, and portable metal sensors can be obtained with similar sensitivity and selectivity as much more expensive and sophisticated analytical instruments. Such a sensor will play an important role in environmental remediation of radionuclides such as uranium.

The Greenland Ice Sheet Project 2 (GISP2) depth‐age scale is presented based on a multiparameter continuous count approach, to a depth of 2800 m, using a systematic combination of parameters that have never been used to this extent before. The ice at 2800 m is dated at 110,000 years B.P. with an estimated error ranging from 1 to 10% in the top 2500 m of the core and averaging 20% between 2500 and 2800 m. Parameters used to date the core include visual stratigraphy, oxygen isotopic ratios of the ice, electrical conductivity measurements, laser‐light scattering from dust, volcanic signals, and major ion chemistry. GISP2 ages for major climatic events agree with independent ages based on varve chronologies, calibrated radiocarbon dates, and other techniques within the combined uncertainties. Good agreement also is obtained with Greenland Ice Core Project ice core dates and with the SPECMAP marine timescale after correlation through the δ 18 O of O 2 . Although the core is deformed below 2800 m and the continuity of the record is unclear, we attempted to date this section of the core on the basis of the laser‐light scattering of dust in the ice.

Over the past few decades the Arctic sea ice cover has decreased in areal extent. This has altered the solar radiation forcing on the Arctic atmosphere‐ice‐ocean system by decreasing the surface albedo and allowing more solar heating of the upper ocean. This study addresses how the amount of solar energy absorbed in areas of open water in the Arctic Basin has varied spatially and temporally over the past few decades. A synthetic approach was taken, combining satellite‐derived ice concentrations, incident irradiances determined from reanalysis products, and field observations of ocean albedo over the Arctic Ocean and the adjacent seas. Results indicate an increase in the solar energy deposited in the upper ocean over the past few decades in 89% of the region studied. The largest increases in total yearly solar heat input, as much as 4% per year, occurred in the Chukchi Sea and adjacent areas.

Hydrodynamics and Transport for Water Quality Modeling presents a complete overview of current methods used to describe or predict transport in aquatic systems, with special emphasis on water quality modeling. The book features detailed descriptions of each method, supported by sample applications and case studies drawn from the authors' years of experience in the field. Each chapter examines a variety of modeling approaches, from simple to complex. This unique text/reference offers a wealth of information previously unavailable from a single source.The book begins with an overview of basic principles, and an introduction to the measurement and analysis of flow. The following section focuses on rivers and streams, including model complexity and data requirements, methods for estimating mixing, hydrologic routing methods, and unsteady flow modeling. The third section considers lakes and reservoirs, and discusses stratification and temperature modeling, mixing methods, reservoir routing and water balances, and dynamic modeling using one-, two-, and three-dimensional models. The book concludes with a section on estuaries, containing topics such as origins and classification, tides, mixing methods, tidally averaged estuary models, and dynamic modeling. Over 250 figures support the text.This is a valuable guide for students and practicing modelers who do not have extensive backgrounds in fluid dynamics.