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USGS2015

Application of science-based restoration planning to a desert river system

Persistence of many desert river species is threatened by a suite of impacts linked to water infrastructure projects that provide human water security where water is scarce. Many desert rivers have undergone regime shifts from spatially and temporally dynamic ecosystems to more stable systems dominated by homogenous physical habitat. Restoration of desert river systems could aid in biodiversity conservation, but poses formidable challenges due to multiple threats and the infeasibility of recovery to pre-development conditions. The challenges faced in restoring desert rivers can be addressed by incorporating scientific recommendations into restoration planning efforts at multiple stages, as demonstrated here through an example restoration project. In particular, use of a watershed-scale planning process can identify data gaps and irreversible constraints, which aid in developing achievable restoration goals and objectives. Site-prioritization focuses limited the resources for restoration on areas with the greatest potential to improve populations of target organisms. Investment in research to understand causes of degradation, coupled with adoption of a guiding vision is critical for identifying feasible restoration actions that can enhance river processes. Setting monitoring as a project goal, developing hypotheses for expected outcomes, and implementing restoration as an experimental design will facilitate adaptive management and learning from project implementation. Involvement of scientists and managers during all planning stages is critical for developing process-based restoration actions and an implementation plan to maximize learning. The planning process developed here provides a roadmap for use of scientific recommendations in future efforts to recover dynamic processes in imperiled riverine ecosystems.

San Rafael River watershed↗

USGS2019

Evidence for interactions among environmental stressors in the Laurentian Great Lakes

Co-occurrence of environmental stressors is ubiquitous in ecosystems, but cumulative effects are difficult to predict for effective indicator development. Individual stressors can amplify (synergies) or lessen (antagonisms) each other's impacts or have fully independent effects (additive). Here we use the Laurentian Great Lakes, where a multitude of stressors have been studied for decades, as a case study for considering insights from both a systematic literature review and an expert elicitation (or structured expert judgment) to identify stressor interactions. In our literature search for pairs of stressors and interaction-related keywords, relatively few studies (9%, or 6/65) supported additive interactions with independent stressor effects. Instead, both antagonisms (42%, or 27/65) and synergies (49%, or 32/65) were common. We found substantial evidence for interactions of invasive dreissenid mussels with nutrient loading and between pairs of invasive species (predominantly dreissenids × round goby), yet both sets of records included mixtures of synergies and antagonisms. Complete quantification of individual and joint effects of stressors was rare, but effect sizes for dreissenid mussels × nutrient loading supported an antagonism. Our expert elicitation included discussion in focus groups and a follow-up survey. This process highlighted the potential for synergies of nutrient loading with dreissenid mussels and climate change as seen from the literature review. The elicitation also identified additional potential interactions less explored in the literature, particularly synergies of nutrient loading with hypoxia and wetland loss. To stimulate future research, we built a conceptual model describing interactions among dreissenid mussels, climate change, and nutrient loading. Our case study illustrates the value of considering results from both elicitations and systematic reviews to overcome data limitations. The simultaneous occurrence of synergies and antagonisms in a single ecosystem underscores the challenge of predicting the cumulative effects of stressors to guide indicator development and other management and restoration decisions.

Ecological Indicators↗

USGS2019

Using environmental DNA to extend the window of early detection for dreissenid mussels

Tools that bolster early detection of invasive species are needed to prevent their spread. In this study, we assessed if environmental DNA (eDNA) can extend the seasonal window for dreissenid mussel early detection beyond that of plankton tows, which are limited to warmer seasons when mussel larvae are present. We focused eDNA sampling efforts at multiple sites in Tiber Reservoir (Montana) where dreissenid mussel abundance is hypothesized to be low. Samples were collected in June and October 2017, when water temperatures were cooler than thermal optima for dreissenid reproduction, and in July 2017 when water temperatures were warmer and conducive for reproduction. We detected dreissenid mussel DNA in June, July and October even though no dreissenid mussels were observed using non-molecular tools in 2017. A subset of positive and negative eDNA samples were analyzed by an independent lab and results were corroborated. We then estimated the effort needed for 95% probability detection of dreissenid DNA at each site within Tiber Reservoir and found that as many as 27, 14, and 34 samples needed to be collected in June, July and October, respectively. To further validate the utility of eDNA, we also present ancillary eDNA results from other waters in the Flathead Reservation (Montana) where dreissenid mussels have never been detected and from waters with established zebra mussel populations in the upper Mississippi River, which were sampled in the spring when water temperatures were cooler than thermal optima for dreissenid reproduction. All Flathead Reservation samples were negative for dreissenid mussel DNA, while all upper Mississippi River samples were positive. This study adds to a growing body of research that demonstrates eDNA is a highly sensitive tool for dreissenid mussel surveillance in newly invaded waters, including colder seasons when non-molecular tools are likely to be less effective or more challenging to employ.

Montana↗

USGS2008

Volatile selenium flux from the great Salt Lake, Utah

The removal mechanisms that govern Se concentrations in the Great Salt Lake are unknown despite this terminal lake being an avian habitat of hemispheric importance. However, the volatilization flux of Se from the Great Salt Lake has not been previously measured due to challenges of analysis in this hypersaline environment This paper presents results from recent field studies examining the spatial distribution of dissolved volatile Se (areally and with depth) in the south arm (main body) of the Great Salt Lake. The analyses involved collection of dissolved volatile Se in a cryofocusing trap system via sparging with helium. The cryotrapped volatile Se was digested with nitric acid and analyzed by inductively coupled plasma mass spectrometry (ICP-MS). Results show concentrations of dissolved volatile Se that increase with depth in the shallow brine, suggesting that phytoplankton in the open waters and bioherms in shallow sites (<4 m in depth) may be responsible for volatile Se production. Volatile Se flux to the atmosphere was determined using mass transport models corrected to simulate the highly saline environment of the south arm of the Great Salt Lake. The estimated annual flux of volatile Se was 1455 kg/year within a range from 560 to 3780 kg Se/year for the 95% confidence interval and from 970 to 2180 kg Se/year within the 68% confidence interval. ?? 2009 American Chemical Society.

Environmental Science & Technology↗

USGS2017

Effects of an extreme flood on trace elements in river water—From urban stream to major river basin

Major floods adversely affect water quality through surface runoff, groundwater discharge, and damage to municipal water infrastructure. Despite their importance, it can be difficult to assess the effects of floods on streamwater chemistry because of challenges collecting samples and the absence of baseline data. This study documents water quality during the September 2013 extreme flood in the South Platte River, Colorado, USA. Weekly time-series water samples were collected from 3 urban source waters (municipal tap water, streamwater, and wastewater treatment facility effluent) under normal-flow and flood conditions. In addition, water samples were collected during the flood at 5 locations along the South Platte River and from 7 tributaries along the Colorado Front Range. Samples were analyzed for 54 major and trace elements. Specific chemical tracers, representing different natural and anthropogenic sources and geochemical behaviors, were used to compare streamwater composition before and during the flood. The results differentiate hydrological processes that affected water quality: (1) in the upper watershed, runoff diluted most dissolved constituents, (2) in the urban corridor and lower watershed, runoff mobilized soluble constituents accumulated on the landscape and contributed to stream loading, and (3) flood-induced groundwater discharge mobilized soluble constituents stored in the vadose zone.

Colorado↗

USGS2016

Proceedings of the 12th Biennial Conference of research on the Colorado Plateau

Introduction The Colorado Plateau is a physiographic region that encompasses 330,000 square kilometers in parts of four states in the southwestern United States (Colorado, Utah, New Mexico, and Arizona). Known for its high deserts, the Colorado Plateau also includes isolated mountains, high plateaus, and rugged canyons. Not only is the region topographically diverse, but geologically, biologically, and culturally diverse as well. The landscape is managed by Federal entities including the Bureau of Land Management, the National Park Service, and the U.S. Forest Service; Tribal nations including the Navajo Nation, Kaibab Paiute, Mountain Ute, Southern Ute, Hopi, Zuni, Hualapai, Havasupai, and White Mountain Apache Tribes; State land and wildlife management agencies; and privately owned holdings, creating complex interactions and management challenges. Population growth, increased tourism to Federal and State lands, and energy development have increased water demands and altered land-use patterns, and these changes have emerged as management challenges facing the people working and living in the region. Climate change, particularly the ongoing drought, has exacerbated the effects of population growth, land-use change, and other stressors such as invasive species. As managers seek solutions to the challenges facing the region’s natural and cultural resources, the Biennial Conference of Science and Management of the Colorado Plateau has become an important venue for exchanging information about emerging management concerns and recent scientific research. Each biennial conference has sought to promote discussion, information sharing, and productive communication among the managers, scientists, students, administrators, tribal representatives, and others who attend the conference with the goal of enhancing the use of the best available science to manage the region’s incomparable natural and cultural resources. The publication and dissemination of a conference proceedings series expands the reach of the conference beyond those people in attendance and creates a record on the research presented. The idea of producing a conference proceedings, and its subsequent publication, first occurred in 1993 following the first biennial conference in 1991. A published volume of contributed papers has followed each subsequent biennial conference, including this volume. The venue for publishing proceedings has changed over the years and has included the National Park Service, the Government Printing Office, the U.S. Geological Survey, and University of Arizona Press. Recently, van Riper and others (2015) published a compilation of the abstracts from the 11 previous conference proceedings. Collectively, the proceedings highlight approximately 25 years of natural- and cultural-resources research, promoting the integration of research with resource management across the Colorado Plateau. This volume is freely downloadable by the public, thereby further expanding the influence of this conference beyond the Colorado Plateau. The 12th Biennial Conference held in Flagstaff, Arizona, from September 16 to 19, 2013, covered a range of topics in the physical, biological, and socio-cultural sciences. The conference was organized and hosted by Northern Arizona University’s ( NAU) Merriam-Powell Center for Environmental Research, the Colorado Plateau Cooperative Ecosystem Studies Unit, and the U.S. Geological Survey Southwest Biological Science Center. Financial and in-kind support was provided by a wide range of organizations including the U.S. Forest Service, National Park Service, Bureau of Land Management, Grand Canyon Trust, Colorado Plateau Research Station, and various NAU entities. NAU sponsors include the Landscape Conservation Initiative, School of Forestry, School of Earth Science and Environmental Sustainability, Office of the Provost, and Office of the Vice President of Research. Contributors to these proceedings include researchers and managers from Federal, State, and Tribal governments, universities, private entities, and non-profit organizations. In this regard, this conference has wide-ranging support and participation among private and public entities involved in the science and management of natural resources on the Colorado Plateau.

Arizona, Colorado, New Mexico, Utah↗

USGS2006

Performance assessments of nuclear waste repositories: A dialogue on their value and limitations

Performance Assessment (PA) is the use of mathematical models to simulate the long-term behavior of engineered and geologic barriers in a nuclear waste repository; methods of uncertainty analysis are used to assess effects of parametric and conceptual uncertainties associated with the model system upon the uncertainty in outcomes of the simulation. PA is required by the U.S. Environmental Protection Agency as part of its certification process for geologic repositories for nuclear waste. This paper is a dialogue to explore the value and limitations of PA. Two “skeptics” acknowledge the utility of PA in organizing the scientific investigations that are necessary for confident siting and licensing of a repository; however, they maintain that the PA process, at least as it is currently implemented, is an essentially unscientific process with shortcomings that may provide results of limited use in evaluating actual effects on public health and safety. Conceptual uncertainties in a PA analysis can be so great that results can be confidently applied only over short time ranges, the antithesis of the purpose behind long-term, geologic disposal. Two “proponents” of PA agree that performance assessment is unscientific, but only in the sense that PA is an engineering analysis that uses existing scientific knowledge to support public policy decisions, rather than an investigation intended to increase fundamental knowledge of nature; PA has different goals and constraints than a typical scientific study. The “proponents” describe an ideal, sixstep process for conducting generalized PA, here called probabilistic systems analysis (PSA); they note that virtually all scientific content of a PA is introduced during the model-building steps of a PSA, they contend that a PA based on simple but scientifically acceptable mathematical models can provide useful and objective input to regulatory decision makers. The value of the results of any PA must lie between these two views and will depend on the level of knowledge of the site, the degree to which models capture actual physical and chemical processes, the time over which extrapolations are made, and the proper evaluation of health risks attending implementation of the repository. The challenge is in evaluating whether the quality of the PA matches the needs of decision makers charged with protecting the health and safety of the public.

Risk Analysis↗

USGS2018

Prioritization framework for ranking riverine ecosystem stressors using example sites from the Tualatin River Basin, Oregon

As human populations increase, so does their influence over the environment. Altered terrain, degraded water quality, and threatened or endangered species are all-too-common consequences of a growing anthropogenic influence on the landscape. To help manage these effects, researchers have developed new ways to characterize current environmental conditions and help resource managers seek solutions to bring affected areas back to their best attainable health. Before an ecosystem can be improved, however, its current level of ecological stress must be determined. Characterizing environmental conditions at many sites across a landscape helps managers understand the range of current conditions and prioritize where they might focus restoration and protection efforts. This report details the development of a prioritization framework to score riverine ecosystem stressors in a watershed based on example sites from the Tualatin River Basin in northwestern Oregon. The framework incorporated the most influential site-specific stressors throughout the basin built on a long history of data collection. These stressors were characterized with 13 metrics that were organized into 4 groups: hydrologic, water quality, physical habitat, and biological. Each stressor metric used readily accessible data and was translated to a score between 0 and 10. The higher the score, the healthier the site. This initial application of the framework used field observations and measurements to rank site conditions at two Tualatin River sites and four Tualatin River tributary sites. Given the versatility of this framework, it easily could be expanded to include more sites or new metrics, if necessary. Because stressors varied by season, all metrics for the tributary sites were scored separately during the wet season (November through April) and dry season (May through October). Water-quality data were available over a prolonged period; therefore, water-quality metrics were assessed by season and by decade (1990–99 compared to 2000–12) to evaluate long-term stressor trends. Results for the Tualatin River Basin prioritization framework indicated that the urban tributaries demonstrated the greatest stress throughout the year, especially during the dry summer months. Spatially, the upper Tualatin River was healthier than the lower reaches of the river. Water-quality has improved in the last 10 years, mostly due to improvements in the dry period contaminant scores, but challenges remain with high water temperatures and low dissolved-oxygen conditions. The biggest challenge with this type of research derived from inconsistencies within the available data. Both spatial and temporal data gaps must be addressed to improve the prioritization. Incorporating both discrete and continuous datasets into the prioritization framework remains a challenge because the datasets have slightly different information and criteria and are not always comparable. Regardless, this report provides guidelines for developing a prioritization framework that ranks the ecological health of sites in a watershed and provides guidance on management actions for improving conditions by targeting factors that greatly affect the health of river ecosystems.

Oregon↗

USGS2023

Understanding drivers of mercury in lake trout (Salvelinus namaycush), a top-predator fish in southwest Alaska's parklands

Mercury (Hg) is a widespread element and persistent pollutant, harmful to fish, wildlife, and humans in its organic, methylated form. The risk of Hg contamination is driven by factors that regulate Hg loading, methylation, bioaccumulation, and biomagnification. In remote locations, with infrequent access and limited data, understanding the relative importance of these factors can pose a challenge. Here, we assessed Hg concentrations in an apex predator fish species, lake trout (Salvelinus namaycush), collected from 14 lakes spanning two National Parks in southwest Alaska, U.S.A. We then examined factors associated with the variation in fish Hg concentrations using a Bayesian hierarchical model. We found that total Hg concentrations in water were consistently low among lakes (0.11–0.50 ng L− 1). Conversely, total Hg concentrations in lake trout spanned a thirty-fold range (101–3046 ng g− 1 dry weight), with median values at 7 lakes exceeding Alaska’s human consumption threshold. Model results showed that fish age and, to a lesser extent, body condition best explained variation in Hg concentration among fish within a lake, with Hg elevated in older, thinner lake trout. Other factors, including plankton methyl Hg content, fish species richness, volcano proximity, and glacier loss, best explained variation in lake trout Hg concentration among lakes. Collectively, these results provide evidence that multiple, hierarchically nested factors control fish Hg levels in these lakes.

Alaska↗

USGS2014

Guidelines for monitoring and adaptively managing restoration of Chinook salmon ( Oncorhynchus tshawytscha ) and steelhead ( O. mykiss ) on the Elwha River

As of January, 2014, the removal of the Elwha and Glines Canyon dams on the Elwha River, Washington, represents the largest dam decommissioning to date in the United States. Dam removal is the single largest step in meeting the goals of the Elwha River Ecosystem and Fisheries Restoration Act of 1992 (The Elwha Act) — full restoration of the Elwha River ecosystem and its native anadromous fisheries (Section 3(a)). However, there is uncertainty about project outcomes with regards to salmon populations, as well as what the ‘best’ management strategy is to fully restore each salmon stock. This uncertainty is due to the magnitude of the action, the large volumes of sediment expected to be released during dam removal, and the duration of the sediment impact period following dam removal. Our task is further complicated by the depleted state of the native salmonid populations remaining in the Elwha, including four federally listed species. This situation lends itself to a monitoring and adaptive management approach to resource management, which allows for flexibility in decision-making processes in the face of uncertain outcomes. The Elwha Monitoring and Adaptive Management (EMAM) guidelines presented in this document provide a framework for developing goals that define project success and for monitoring project implementation and responses, focused upon two federally listed salmon species — Puget Sound Chinook salmon (Oncorhynchus tshawytscha) and Puget Sound steelhead (O. mykiss). The framework also should serve as a guide to help managers adaptively manage fish restoration actions during and following dam removal. The document is organized into seven sections, including an introduction (Section 1), a description of the adaptive management approach (Section 2), suggested modifications to the existing restoration strategy developed in previous Elwha River restoration documents (section 3), specific descriptions of an adaptive management framework, including establishment of goals, performance indicators, and potential adaptive management responses to monitoring information (section 4), monitoring tools and methods for use in evaluating performance and project outcomes (section 5), and brief sections on data record keeping and reporting (Section 6) and an estimated budget (section 7). The purpose of the EMAM guidelines is to propose (1) refinement of existing goals established in previous documents (e.g., Ward et al. (2008), U.S. Department of the Interior, Department of Commerce, and Lower Elwha S’Klallam Tribe (1994)); (2) an adaptive management framework, (3) specific trigger values for relevant performance indicators that guide the adaptive management approach, (4) a specific monitoring strategy for evaluating outcomes of restoration activities; (5) a data management strategy, (6) information needed for adjusting goals when observations indicate conditions are different from anticipated. When taken together, our proposed adaptive management guidelines rely upon setting goals and objectives for each species of interest, which are monitored by relevant performance indicators and measurable trigger values that define success within each phase of the project. The guidelines themselves are arranged in a hierarchy for each species of interest. The levels of this hierarchy are goals, objectives, performance indicators, decision rules, triggers, and decisions (i.e., management/policy response). The monitoring and adaptive management approach provided is based on monitoring several categories of performance indicators, each containing associated ‘trigger’ values which, when met, alters restoration activities (e.g., hatchery releases and/or strategies) through four successive restoration phases. Performance indicators proposed in these EMAM guidelines are based upon Viable Salmon Population (VSP) metrics, including abundance, productivity, distribution, and diversity (McElhany et al. 2000). Trigger values for each performance indicator are developed for four different restoration phases: Preservation, Recolonization, Local Adaptation, and Viable Natural Population. These biologically-based phases each have a set of objectives that are based on resource management scenarios, including the dam removal project itself, which change largely based on the level of active management required and the degree, if any, of resource utilization. Thus, details of prescribed management actions for each phase are based upon different needs specific to that phase. The creation of biologically-based phases is one of the major differences between our proposed EMAM guidelines and previously presented plans for Elwha River Restoration Project management. Changed largely in response to the recommendations of the most recent of three Hatchery Scientific Review Group project reviews (HSRG 2012), the goal-oriented phases replaced the previous system of temporal changes centered around the decommissioning of the dams (i.e., before, during, and after dam removal). By focusing on outcomes associated with rebuilding salmon populations instead of an engineering schedule, the guidelines are more amenable to an adaptive management framework and the ability for management actions to influence outcomes, particularly in the periods during and following dam removal. Trigger values for each performance indicator were generally developed using existing data from the Elwha River watershed, the Puget Sound region, or other Pacific Northwest rivers (i.e., elsewhere in Washington State, Oregon, British Columbia) modified to be relevant for Chinook salmon and steelhead recovery in the Elwha River. By meeting all of the trigger value levels for all performance indicators for a set amount of time within a management phase, the guidelines call for moving to the next phase. This next phase has a new set of trigger values for the same performance indicators. For example, upon moving from the Preservation phase to the Recolonization phase, the trigger value for intrinsic potential increases. Intrinsic potential is a pre-defined estimate of the total extent of available habitat within a watershed for adult and juvenile fish, specific to the target species and is therefore a performance indicator of spatial distribution. By the final Viable Natural Population phase, the entire intrinsic potential of the watershed is being occupied by the species of interest. For those cases when a performance indicator is not exceeding the target value for a particular phase after a certain time period, the trigger values provided in this document, as well as a series of exogenous variables, are explored that may help explain why the performance indicator is not being met. These exogenous variables include variables that are not part of the suite of performance indicators, such as hatchery production, harvest, habitat, and ecosystem indicators. In these cases where the program is stuck in a particular recovery phase, the situation could be caused by the selection of inappropriate trigger values or unforeseen environmental conditions. If the former, adaptive management would call for existing monitoring data to be used for modifying trigger values to an appropriate level. If one of the exogenous variables is found to be preventing the program moving to the next phase, then appropriate changes to management would be advised. For each performance indicator and many of the exogenous variables, a set of monitoring tools were proposed. Data standards were also proposed for data generated by each monitoring tool. Data management, record keeping, and reporting of monitoring and adaptive management activities and results are also outlined. Management of data from the focused monitoring program and documenting the outcomes of trigger value evaluations and associated decisions from the adaptive management approach are key components of the EMAM guidelines. Without a clear history of data generated and adaptive management decisions taken by managers, the ability to learn through adaptive management breaks down. In addition to the long time period involved, another complication is the fact that the data will likely be collected by different federal and state agencies, tribal staff, and others. Having a system of reporting developed should help alleviate potential problems. The restoration of the migration route to spawning and rearing habitats upstream of the former Glines Canyon Dam represents a great opportunity for salmon on the Olympic Peninsula. By removing two aging structures, it will be possible for all 5 species of salmon and steelhead to return to wild stretches of the Elwha River and major floodplain habitat characterized by multiple channels, as well as significant portions of numerous tributaries. Measuring the progress of restoration, from the perspective of both salmon populations and the ecosystem upon which they depend, is a great test for a collaborative team of scientists. The normally challenging conditions of working in a steep gradient, high velocity wilderness river are exacerbated by the release of millions of cubic yards of sediment that had accumulated in the reservoirs. After the first two years of the dam decommissioning process, this release has changed the ecology of the river, estuary, and nearshore habitats downstream of the dams. Our goal in developing the guidelines described is to provide a roadmap for tracking what hopefully will become a successful outcome. If successfully implemented, this information should prove useful as others begin planning for the removal, alteration, or reconstruction of dams throughout North America and elsewhere, an inevitable outcome of an aging dam infrastructure.

Washington↗

USGS2007

Cadmium ecophysiology in seven stonefly (Plecoptera) species: Delineating sources and estimating susceptibility

A major challenge in ecotoxicology lies in generating data under experimental conditions that are relevant to understanding contaminant effects in nature. Biodynamic modeling combines species-specific physiological traits to make predictions of metal bioaccumulation that fare well when tested in the field. We generated biodynamic models for seven predatory stonefly (Plecoptera) species representing the families Perlidae (5) and Perlodidae (2). Each taxon was exposed to cadmium independently via diet and via solution. Species varied approximately 2.6 fold in predicted steady-state cadmium concentrations. Diet was the predominant source of accumulated cadmium in five of the seven species and averaged 53.2 ± 9.6% and 90.2 ± 3.7% of net Cd accumulation in perlids and perlodids, respectively. Differences in Cd bioaccumulation between the two families were largely driven by differences in dissolved accumulation rates, which were considerably slower in perlodids than in perlids. We further examined the subcellular compartmentalization of Cd accumulated from independent aqueous and dietary exposures. Predicted steady-state concentrations were modified to only consider Cd accumulated in metal-sensitive subcellular compartments. These values ranged 5.3 fold. We discuss this variability within a phylogenetic context and its implications for bioassessment.

Environmental Science & Technology↗

USGS2013

Probabilistic analysis showing that a combination of bacteroides and methanobrevibacter source tracking markers is effective for identifying waters contaminated by human fecal pollution

Microbial source tracking assays to identify sources of waterborne contamination typically target genetic markers of host-specific microorganisms. However, no bacterial marker has been shown to be 100% host-specific, and cross-reactivity has been noted in studies evaluating known source samples. Using 485 challenge samples from 20 different human and animal fecal sources, this study evaluated microbial source tracking markers including the Bacteroides HF183 16S rRNA, M. smithii nifH, and Enterococcus esp gene targets that have been proposed as potential indicators of human fecal contamination. Bayes' Theorem was used to calculate the conditional probability that these markers or a combination of markers can correctly identify human sources of fecal pollution. All three human-associated markers were detected in 100% of the sewage samples analyzed. Bacteroides HF183 was the most effective marker for determining whether contamination was specifically from a human source, and greater than 98% certainty that contamination was from a human source was shown when both Bacteroides HF183 and M. smithii nifH markers were present. A high degree of certainty was attained even in cases where the prior probability of human fecal contamination was as low as 8.5%. The combination of Bacteroides HF183 and M. smithii nifH source tracking markers can help identify surface waters impacted by human fecal contamination, information useful for prioritizing restoration activities or assessing health risks from exposure to contaminated waters.

Environmental Science & Technology↗

USGS2023

GRiMeDB: The Global River Database Methane Database of concentrations and fluxes

Despite their small spatial extent, fluvial ecosystems play a significant role in processing and transporting carbon in aquatic networks, which results in substantial emission of methane ( CH 4 ) into the atmosphere. For this reason, considerable effort has been put into identifying patterns and drivers of CH 4 concentrations in streams and rivers and estimating fluxes to the atmosphere across broad spatial scales. However, progress toward these ends has been slow because of pronounced spatial and temporal variability of lotic CH 4 concentrations and fluxes and by limited data availability across diverse habitats and physicochemical conditions. To address these challenges, we present a comprehensive database of CH 4 concentrations and fluxes for fluvial ecosystems along with broadly relevant and concurrent physical and chemical data. The Global River Methane Database (GriMeDB; https://doi.org/10.6073/pasta/f48cdb77282598052349e969920356ef , Stanley et al., 2023) includes 24 024 records of CH 4 concentration and 8205 flux measurements from 5029 unique sites derived from publications, reports, data repositories, unpublished data sets, and other outlets that became available between 1973 and 2021. Flux observations are reported as diffusive, ebullitive, and total CH 4 fluxes, and GriMeDB also includes 17 655 and 8409 concurrent measurements of concentrations and 4444 and 1521 fluxes for carbon dioxide ( CO 2 ) and nitrous oxide ( N 2 O ), respectively. Most observations are date-specific (i.e., not site averages), and many are supported by data for 1 or more of 12 physicochemical variables and 6 site variables. Site variables include codes to characterize marginal channel types (e.g., springs, ditches) and/or the presence of human disturbance (e.g., point source inputs, upstream dams). Overall, observations in GRiMeDB encompass the broad range of the climatic, biological, and physical conditions that occur among world river basins, although some geographic gaps remain (arid regions, tropical regions, high-latitude and high-altitude systems). The global median CH 4 concentration (0.20 µmol L −1 ) and diffusive flux (0.44 mmol m -2 d -1 ) in GRiMeDB are lower than estimates from prior site-averaged compilations, although ranges (0 to 456 µmol L −1 and − 136 to 4057 mmol m -2 d -1 ) and standard deviations (10.69 and 86.4) are greater for this larger and more temporally resolved database. Available flux data are dominated by diffusive measurements despite the recognized importance of ebullitive and plant-mediated CH 4 fluxes. Nonetheless, GriMeDB provides a comprehensive and cohesive resource for examining relationships between CH 4 and environmental drivers, estimating the contribution of fluvial ecosystems to CH 4 emissions, and contextualizing site-based investigations.

Earth System Science Data↗

USGS2015

Encapsulating model complexity and landscape-scale analyses of state-and-transition simulation models: an application of ecoinformatics and juniper encroachment in sagebrush steppe ecosystems

State-and-transition simulation modeling relies on knowledge of vegetation composition and structure (states) that describe community conditions, mechanistic feedbacks such as fire that can affect vegetation establishment, and ecological processes that drive community conditions as well as the transitions between these states. However, as the need for modeling larger and more complex landscapes increase, a more advanced awareness of computing resources becomes essential. The objectives of this study include identifying challenges of executing state-and-transition simulation models, identifying common bottlenecks of computing resources, developing a workflow and software that enable parallel processing of Monte Carlo simulations, and identifying the advantages and disadvantages of different computing resources. To address these objectives, this study used the ApexRMS® SyncroSim software and embarrassingly parallel tasks of Monte Carlo simulations on a single multicore computer and on distributed computing systems. The results demonstrated that state-and-transition simulation models scale best in distributed computing environments, such as high-throughput and high-performance computing, because these environments disseminate the workloads across many compute nodes, thereby supporting analysis of larger landscapes, higher spatial resolution vegetation products, and more complex models. Using a case study and five different computing environments, the top result (high-throughput computing versus serial computations) indicated an approximate 96.6% decrease of computing time. With a single, multicore compute node (bottom result), the computing time indicated an 81.8% decrease relative to using serial computations. These results provide insight into the tradeoffs of using different computing resources when research necessitates advanced integration of ecoinformatics incorporating large and complicated data inputs and models. - See more at: http://aimspress.com/aimses/ch/reader/view_abstract.aspx?file_no=Environ2015030&flag=1#sthash.p1XKDtF8.dpuf

AIMS Environmental Science↗

USGS2016

Seeing the forest through the trees: Considering roost-site selection at multiple spatial scales

Conservation of bat species is one of the most daunting wildlife conservation challenges in North America, requiring detailed knowledge about their ecology to guide conservation efforts. Outside of the hibernating season, bats in temperate forest environments spend their diurnal time in day-roosts. In addition to simple shelter, summer roost availability is as critical as maternity sites and maintaining social group contact. To date, a major focus of bat conservation has concentrated on conserving individual roost sites, with comparatively less focus on the role that broader habitat conditions contribute towards roost-site selection. We evaluated roost-site selection by a northern population of federally-endangered Indiana bats ( Myotis sodalis ) at Fort Drum Military Installation in New York, USA at three different spatial scales: landscape, forest stand, and individual tree level. During 2007–2011, we radiotracked 33 Indiana bats (10 males, 23 females) and located 348 roosting events in 116 unique roost trees. At the landscape scale, bat roost-site selection was positively associated with northern mixed forest, increased slope, and greater distance from human development. At the stand scale, we observed subtle differences in roost site selection based on sex and season, but roost selection was generally positively associated with larger stands with a higher basal area, larger tree diameter, and a greater sugar maple ( Acer saccharum ) component. We observed no distinct trends of roosts being near high-quality foraging areas of water and forest edges. At the tree scale, roosts were typically in American elm ( Ulmus americana ) or sugar maple of large diameter (>30 cm) of moderate decay with loose bark. Collectively, our results highlight the importance of considering day roost needs simultaneously across multiple spatial scales. Size and decay class of individual roosts are key ecological attributes for the Indiana bat, however, larger-scale stand structural components that are products of past and current land use interacting with environmental aspects such as landform also are important factors influencing roost-tree selection patterns.

PLoS ONE↗

USGS2009

Evaluating remediation alternatives for mine drainage, Little Cottonwood Creek, Utah, USA

The vast occurrence of mine drainage worldwide, documented in descriptive studies, presents a staggering challenge for remediation. Any tool that can move beyond descriptive study and helps to evaluate options for remediation in a way that maximizes improvements to the water quality of streams and minimizes cost of remediation could save valuable resources and time. A reactive solute transport model, calibrated from two detailed mass-loading studies in Little Cottonwood Creek (LCC), Utah, provides a tool to evaluate remediation options. Metal loading to LCC is dominated by discharge from two mine drainage tunnels. Discharge from an upstream tunnel has been treated by a fen to reduce metal loading. Discharge from the downstream tunnel (WDT) can be controlled because of a bulkhead that creates a mine pool. Simulations of remedial options for three compliance locations suggest that the water-quality standards for Cu and Zn at upstream and downstream compliance locations are met using various combinations of fen treatment and WDT regulation, but the complete compliance at the middle compliance location requires the highest level of fen treatment and the greatest regulation of WDT discharge. Reactive transport modeling is an useful tool for the evaluation of remedial alternatives in complex natural systems, where multiple hydrologic and geochemical processes determine metal fate.

Utah↗

USGS2007

Scale-dependent approaches to modeling spatial epidemiology of chronic wasting disease.

This e-book is the product of a second workshop that was funded and promoted by the United States Geological Survey to enhance cooperation between states for the management of chronic wasting disease (CWD). The first workshop addressed issues surrounding the statistical design and collection of surveillance data for CWD. The second workshop, from which this document arose, followed logically from the first workshop and focused on appropriate methods for analysis, interpretation, and use of CWD surveillance and related epidemiology data. Consequently, the emphasis of this e-book is on modeling approaches to describe and gain insight of the spatial epidemiology of CWD. We designed this e-book for wildlife managers and biologists who are responsible for the surveillance of CWD in their state or agency. We chose spatial methods that are popular or common in the spatial epidemiology literature and evaluated them for their relevance to modeling CWD. Our opinion of the usefulness and relevance of each method was based on the type of field data commonly collected as part of CWD surveillance programs and what we know about CWD biology, ecology, and epidemiology. Specifically, we expected the field data to consist primarily of the infection status of a harvested or culled sample along with its date of collection (not date of infection), location, and demographic status. We evaluated methods in light of the fact that CWD does not appear to spread rapidly through wild populations, relative to more highly contagious viruses, and can be spread directly from animal to animal or indirectly through environmental contamination. We discovered that many of the wellpublished methods were developed for fast-spreading human diseases, such as influenza and measles. While these methods are applicable to fast spreading wildlife diseases, such as foot-and-mouth disease or West Nile virus, many are not likely to work well for CWD. Only limited data exist to evaluate geographic and spatial spread because many locations where we find CWD tend to be locations where samples have just been taken or sample sizes have just become large enough to have a high probability of detecting a low prevalence. Consequently, methods that work well to describe or predict the spread of foot-and-mouth disease throughout England, which occurred within a year, do not work well for describing or predicting CWD spread. We did not exclude methods that we regarded as inappropriate; rather, we included methods that are commonly used for disease epidemiology and then discussed their applicability for modeling the spatial epidemiology of CWD. We hope including inappropriate methods with an explanation of why they are ill-suited for CWD will make it easier to drop them from consideration and explain to others why they were not recommended for spatial modeling of CWD. We organized the three chapters by scale and extent for which each method was developed or best suited. The first chapter covers methods appropriate to multi-jurisdictional or multi-state modeling, which we call “regional” scale. The second chapter covers methods appropriate for within state areas such as wildlife management units or metapopulations, which we call “landscape” scale. The third chapter covers methods appropriate for population or individual-based modeling, which we call “fine” scale. We know this rubric is somewhat artificial because many methods work at multiple scales. We hope, however, that this structure addresses some of the challenges faced by managers that work at local, regional, state, and national scales. Further, the resolution of empirical data often changes with spatial scale, which affects the utility of different modeling approaches. For example, individual-based models work best at modeling spread within populations, while risk analysis is most useful for summarizing data over larger scales such as a region. Because some methods are applicable at several scales, however, we included a graphic at the beginning of each method that indicates the range of scales for which it applies. For example, the graphic to the right indicates that the method is most applicable for regional-scale modeling. There is also a question of resolution as well as scale and extent for each method. CWD surveillance data have been collected over large areas, such as a wildlife management unit or state, but the resolution of the data may be fine scale with GPS locations for many samples. For each method, we described the required resolution of the data and describe the type of data required, as well as what questions the method could answer and how useful the method is, given typical CWD data. For each scale, we presented a focal approach that would be useful for understanding the spatial pattern and epidemiology of CWD, as well as being a useful tool for CWD management. The focal approaches include risk analysis and micromaps for the regional scale, cluster analysis for the landscape scale, and individual based modeling for the fine scale of within population. For each of these methods, we used simulated data and walked through the method step by step to fully illustrate the “how to”, with specifics about what is input and output, as well as what questions the method addresses. We also provided a summary table to, at a glance, describe the scale, questions that can be addressed, and general data required for each method described in this e-book. We hope that this review will be helpful to biologists and managers by increasing the utility of their surveillance data, and ultimately be useful for increasing our understanding of CWD and allowing wildlife biologists and managers to move beyond retroactive fire-fighting to proactive preventative action.

Book↗

USGS2020

Climate has contrasting direct and indirect effects on armed conflicts

There is an active debate regarding the influence that climate has on the risk of armed conflict, which stems from challenges in assembling unbiased datasets, competing hypotheses on the mechanisms of climate influence, and the difficulty of disentangling direct and indirect climate effects. We use gridded historical non-state conflict records, satellite data, and land surface models in a structural equation modeling approach to uncover the direct and indirect effects of climate on violent conflicts in Africa and the Middle East (ME). We show that climate–conflict linkages in these regions are more complex than previously suggested, with multiple mechanisms at work. Warm temperatures and low rainfall direct effects on conflict risk were stronger than indirect effects through food and water supplies. Warming increases the risk of violence in Africa but unexpectedly decreases this risk in the ME. Furthermore, at the country level, warming decreases the risk of violence in most West African countries. Overall, we find a non-linear response of conflict to warming across countries that depends on the local temperature conditions. We further show that magnitude and sign of the effects largely depend on the scale of analysis and geographical context. These results imply that extreme caution should be exerted when attempting to explain or project local climate–conflict relationships based on a single, generalized theory.

Environmental Research Letters↗