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The Importance of Uncertainty and Sensitivity Analysis in Process-based Models of Carbon and Nitrogen Cycling in Terrestrial Ecosystems with Particular Emphasis on Forest Ecosystems — Selected Papers from a Workshop Organized by the International Society for Ecological Modelling (ISEM) at the Third Biennal Meeting of the International Environmental Modelling and Software Society (IEMSS) in Burlington, Vermont, USA, August 9-13, 2006

Many process-based models of carbon (C) and nitrogen (N) cycles have been developed for terrestrial ecosystems, including forest ecosystems. They address many basic issues of ecosystems structure and functioning, such as the role of internal feedback in ecosystem dynamics. The critical factor in these phenomena is scale, as these processes operate at scales from the minute (e.g. particulate pollution impacts on trees and other organisms) to the global (e.g. climate change). Research efforts remain important to improve the capability of such models to better represent the dynamics of terrestrial ecosystems, including the C, nutrient, (e.g. N) and water cycles. Existing models are sufficiently well advanced to help decision makers develop sustainable management policies and planning of terrestrial ecosystems, as they make realistic predictions when used appropriately. However, decision makers must be aware of their limitations by having the opportunity to evaluate the uncertainty associated with process-based models ( Smith and Heath, 2001 and Allen et al., 2004 ). The variation in scale of issues currently being addressed by modelling efforts makes the evaluation of uncertainty a daunting task.

Ecological Modelling

Heat as a tool for studying the movement of ground water near streams

Stream temperature has long been recognized as an important water quality parameter. Temperature plays a key role in the health of a stream’s aquatic life, both in the water column and in the benthic habitat of streambed sediments. Many fish are sensitive to temperature. For example, anadromous salmon require specific temperature ranges to successfully develop, migrate, and spawn [see Halupka and others, 2000]. Metabolic rates, oxygen requirements and availability, predation patterns, and susceptibility of organisms to contaminants are but a few of the many environmental responses regulated by temperature. Hydrologists traditionally treated streams and ground water as distinct, independent resources to be utilized and managed separately. With increasing demands on water supplies, however, hydrologists realized that streams and ground water are parts of a single, interconnected resource [see Winter and others, 1998]. Attempts to distinguish these resources for analytical or regulatory purposes are fraught with difficulty because each domain can supply (or drain) the other, with attendant possibilities for contamination exchange. Sustained depletion of one resource usually results in depletion of the other, propagating adverse effects within the watershed. An understanding of the interconnections between surface water and ground water is therefore essential. This understanding is still incomplete, but receiving growing attention from the research community. Exchanges between streams and shallow ground-water systems play a key role in controlling temperatures not only in streams, but also in their underlying sediments. As a result, analyses of subsurface temperature patterns provide information about surface-water/ground-water interactions. Chemical tracers are commonly used for tracing flow between streams and ground water. Introduction of chemical tracers in near-stream environments is, however, limited by real and perceived issues regarding introduced contamination and practical constraints. As an alternative, naturally occurring variations in temperature can be used to track (or trace) the heat carried by flowing water. The hydraulic transport of heat enables its use as a tracer. Differences between temperatures in the stream and surrounding sediments are now being analyzed to trace the movement of ground water to and from streams. As shown in the subsequent chapters of this circular, tracing the transport of heat leads to a better understanding of the magnitudes and mechanisms of stream/ground-water exchanges, and helps quantify the resulting effects on stream and streambed temperatures. Chapter 1 describes the general principals and procedures by which the natural transport of heat can be utilized to infer the movement of subsurface water near streams. This information sets the foundation for understanding the advanced applications in chapters 2 through 8. Each of these chapters provides a case study, using heat tracing as a tool, of interactions between surface water and ground water for a different location in the western United States. Technical details of the use of heat as an environmental tracer appear in appendices.

Circular

Scientific and social landscapes: New frameworks and forums for water management and sustainability

The Two Decades of Water Law and Policy Reform conference examines the agenda for reforming and improving water law that has developed during the past two decades in the West, assesses what has (and has not) been accomplished by pursuing these reforms, and explores lessons and implications for future water law and policy. The papers and discussion provide analysis and lessons that can guide the new administration, Congress, federal agencies, state governments, and communities as they seek to find policy solutions to the challenges posed by the tremendous economic and demographic changes occurring in the West, in order to ensure the sustainability of the region’s unique environment. Specific sessions focus on reforms such as improving the scientific and technical basis for water management, water conservation and efficiency, protecting environmental values in meeting water demands, and creating new models of governance for water issues.

Conference Paper

The use of scenario analysis to assess water ecosystem services in response to future land use change in the Willamette River Basin, Oregon

Human pressures on the natural resources of the United States have resulted in many unintended changes in our ecosystems, e.g., loss of biodiversity, habitat degradation, increases in the number of endangered species, and increases in contamination and water pollution. Environmental managers are concerned about broad-scale changes in land use and landscape pattern and their cumulative impact on hydrologic and ecological processes that affect stream conditions. The type of land use and land cover has direct consequences for most ecosystem services, including water quantity and water quality, erosion control, and biodiversity. As human pressure continues to increase, ecosystem services worldwide are projected to suffer continued loss and degradation, thus reducing the capacity of ecosystems to provide essential goods and services that contribute to human well-being (MEA 2005). The ability to assess, report, and forecast the life support functions of ecosystems is absolutely critical to our capacity to make informed decisions which will maintain the sustainable nature of our environmental services and secure these resources into the future. This study presents an integrated approach to identify areas with potential water quality problems as a result of land cover change projected by stakeholders within a moderately large river basin in the Pacific Northwest (USA). A process-based hydrologic watershed model was used to examine the contribution of land use/land cover to sediment yield, and nitrate and phosphorous loadings, and identify subwatersheds within the Willamette River basin that would be most affected in the year 2050 relative to three possible future scenarios which include inherent differences related to conservation, existing planning trends, and open development. Thus, the objective of this study was to evaluate the effects of alternative future scenarios that describe varying degrees of urban development and human use on hydrological response related to water quality. Results of this study suggest that the amount of forest along streams and agriculture consistently explained a high percentage of variation in nutrients. The AGWA-SWAT model was used to simulate change in sediment yield, nitrate and phosphorus transported with surface runoff for the three future scenarios. With regard to nitrate, the greatest increase was associated with subwatersheds with agricultural land use and urban areas. Although the model predicted some improvement in basin headwaters for all scenarios, nitrate loadings are expected to decrease under the conservation scenario. The largest decrease was observed in the Coast Range. With regard to phosphorous loadings, the lowest reduction was observed in subwatersheds draining predominantly forest areas. The greatest increase was observed under the open development scenario in subwatersheds with agricultural land use. Urbanization and agriculture are presumed to be the major environmental stressors affecting watershed condition of the Willamette River Basin.

Oregon

A spatiotemporal optimization engine for prescribed burning in the Southeast US

Many ecosystems in the Southeast US are dependent upon frequent low-intensity surface fires to sustain native biodiversity, ecosystem services, and endangered species populations. Today, landscape-scale prescribed fire is required to manage these systems for conservation objectives and to mitigate wildland fire risk. Successful application of prescribed fire in this region requires careful planning and assessment of the risks and tradeoffs involved when deciding whether or not to conduct a burn. Many of these risks are closely tied to ambient environmental conditions and are reflected in sets of ‘prescription’ parameters that define safe and effective operating conditions to meet objectives or regulatory requirements. To facilitate effective decision making and acknowledge growing uncertainties related to climate change effects on wildland fire operations, we developed a spatiotemporal optimization engine to identify near-term optimal burning opportunities for prescribed fire implementation. By mining historical 3-day numerical weather forecasts and observation-based weather data for 2015–2021, we have developed a Bayesian hierarchical model for forecast verification that provides calibrated daily weather forecasts and joint uncertainty estimates on meteorological variables of interest, with the latter serving as a measure of risk associated with prescribed fire activities. Burn allocation decisions are then optimized by considering this risk jointly with the utility of burning a particular habitat parcel. The initial iteration of the optimization engine is demonstrated through a case study of short-term meteorological conditions for the Eglin Air Force Base, located in Florida, USA. Results indicate agreement between the optimization engine and the observed past decision-making, with the largest divergences likely arising primarily from differences between utility functions presumed important and used to develop the optimization engine versus the true utility functions driving management behavior in practice.

Florida

Comparing environmental flow implementation options with structured decision making: Case study from the Willamette River, Oregon

Many frameworks have been used to identify environmental flows for sustaining river ecosystems or specific taxa in the face of widespread flow alteration for human use. However, these methods mostly focus on identifying suitable flows and largely ignore the important links between management actions, resulting flows, flow variability, and ecosystem or social responses. Structured decision making (SDM) could assist the comparison and implementation of environmental flows by providing a framework to compare effects of flow management actions on objectives via environmental flow science. We describe the SDM process and illustrate its application using a case study focused on comparing environmental flow scenarios for the mainstem Willamette River, Oregon, USA. In a short timeframe, SDM was successfully applied to identify management objectives, develop empirical and expert opinion based models predicting ecological responses, and compare scenarios while accounting for uncertainty and partial controllability. We found that no flow scenario was clearly preferred based on available knowledge, largely because river flows could only be partially controlled through available dam operations. Participants agreed that the SDM process was useful and that an additional iteration focused on refining predictive models and incorporating additional objectives could help better inform dam release decisions for the entire basin. In our view, SDM can provide managers with more realistic comparisons of environmental flows by accounting for partial controllability and uncertainty, which may result in greater implementation of available flow management actions.

Oregon

Water availability and quality from the stratified drift in Anguilla Brook basin, Stonington and North Stonington, Connecticut

The valley of Anguilla Brook is underlain by saturated stratified-drift deposits that, where thick and transmissive, have the potential to yield large quantities of ground water. These deposits are collectively termed the Anguilla Brook aquifer. Long-term yields of four subareas within this aquifer are estimated to range from less than 0.3 to 1.0 million gallons per day. The total yield of all four subareas is estimated to be 2.6 million gallons per day. These yield estimates are based on using the 90-percent duration flow of Anguilla Brook as an index of the water potentially available and on maximum sustainable pumping rates calculated by a mathematical model that used the Theis nonequilibrium equation and image well theory. Development of one or more subareas assumes that most ground water would be derived from induced recharge. This would reduce the flow of Anguilla Brook, and the effect will be most significant during periods when streamflow is low. Limited sampling and analysis indicate that the quality of both surface and ground water in the Anguilla Brook basin is excellent. The concentrations of all constituents analyzed, with the exception of dissolved manganese and iron, were below the drinking-water limits established by the State of Connecticut, or recommended by the U.S. Environmental Protection Agency.

Connecticut

Strategic Science for Coral Ecosystems 2007-2011

Shallow and deep coral ecosystems are being imperiled by a combination of stressors. Climate change, unsustainable fishing practices, and disease are transforming coral communities at regional to global scales. At local levels, excessive amounts of sediments, nutrients, and contaminants are also impacting the many benefits that healthy coral ecosystems provide. This Plan, Strategic Science for Coral Ecosystems, describes the information needs of resource managers and summarizes current research being conducted by U.S. Geological Survey (USGS) scientists and partners. It outlines important research actions that need to be undertaken over the next five years to achieve more accurate forecasting of future conditions and develop more effective decision-support tools to adaptively manage coral ecosystems. The overarching outcome of this Plan, if fully implemented, would be in transferring relevant knowledge to decision-makers, enabling them to better protect and sustain coral ecosystem services. These services include sources of food, essential habitat for fisheries and protected species, protection of coastlines from wave damage and erosion, recreation, and cultural values for indigenous communities. The USGS has a long history of research and monitoring experience in studying ancient and living coral communities and serving many stakeholders. The research actions in this Plan build on the USGS legacy of conducting integrated multidisciplinary science to address complex environmental issues. This Plan is responsive to Federal legislation and authorities and a variety of external and internal drivers that include the President's Ocean Action Plan, the recommendations of the Coral Reef Task Force, the information needs of Bureaus in the Department of Interior, the USGS Bureau Science Strategy (USGS 2007) and the formal plans of several USGS Programs. To achieve this Plan's desired outcomes will require increased funding and more effective coordination and collaboration among USGS managers and scientists within a national and international framework of partnerships in coral ecosystem science.

Circular

Managed aquifer recharge in snow-fed river basins: What, why and how?

What does climate change mean for snow-fed river basins? Climate change poses unique challenges in snow-fed river basins across the western United States because the majority of water supply originates as snow (Dettinger, Udall, & Georgakakos, 2015). In the Sierra Nevada, recent observations include changes in snow accumulation and snowmelt, and shifts in peak streamflow timing (Barnhart et al., 2016; Hatchett et al., 2017; Kim & Jain, 2010; McCabe, Wolock, & Valentin, 2018; Mote, Li, Lettenmaier, Xiao, & Engel, 2018). Such changes upstream alter surface water deliveries downstream, as well as groundwater recharge utilized as both primary and supplemental water supply (Godsey et al., 2014; Harpold, 2016; Jasechko et al., 2014). basin where snowmelt runoff produces substantial water supply to meet diverse agricultural, environmental and urban water demand (Figure 1). The East and West Forks join at the confluence of the Carson River near the north end of the Carson Valley, a rich agricultural region (40,000 acres) that grows primarily alfalfa hay. The majority of irrigators rely on surface water delivered through a network of earthen ditches constructed in the mid-19th and early 20th centuries. Flow through these earthen networks and the practice of flood irrigation contribute significantly to groundwater recharge. Because no upstream surface water reservoirs exist, snowpack that accumulates through winter and melts slowly through spring has acted as a “natural” reservoir, providing ample supply through the summer irrigati agricultural, environmental and urban water demand (Figure 1). The East and West Forks join at the confluence of the Carson River near the north end of the season. Some irrigators have permitted access to supplemental groundwater that is useful during periods of drought for augmenting shortfalls in surface water delivery. Groundwater is the primary source of municipal and industrial water supply for surrounding communities (e.g., Carson City, Minden, Gardnerville, Dayton). Across the basin, water use is highly regulated through federal, tribal, state and local water-sharing agreements based on prior appropriation doctrine (Wilds, 2014). Carson River surface water allocations follow the Alpine Decree, initiated by the United States Department of Interior in 1925 and signed into law in 1980, following 55 years of litigation, to adjudicate surface water rights to individual parties (NDWP, 1999). The Alpine Decree acknowledges return flows to lower river segments, and thus each river segment is distributed autonomously. This means that the most junior water right on an upper segment can be fulfilled before considering the most senior water right on a lower segment. Ultimately, the ruling is at the discretion of the Federal Water Master to satisfy the needs of each water right Downstream of Carson Valley, surface water flows are stored in Lahontan Reservoir, the nation’s first desert reclamation project (est. 1906), where releases are managed to meet the Newland’s Project irrigation water demand and for environmental use on the Stillwater National Wildlife Refuge. Flows from the Carson River are supplemented through diversions from the Truckee River via the Truckee Canal, resulting in a trans-basin water supply system. How is the Water for the Seasons research program informing snow-fed river basin communities? In the Truckee-Carson River System, researchers and local water managers are working together to assess climate change impacts to water supply and explore how model simulations can produce useful information to support local climate adaptation. Twelve key water managers represent agricultural, environmental, urban and regulatory water-use communities, and bring to the table diverse input and perspectives on how to adapt to climate change. Hydrologists use this input to craft scenarios and simulations that meet the information needs of local water managers. Biannual workshops provide an opportunity for information exchange, where researchers and key water managers generate new knowledge of river system function. That is, researchers share results of models that examine the physical potential, and managers validate the on-the-ground potential, further informing the research process. Coincident to this research program, the region faced a prolonged drought period (2012-2016) with historically low snowpack, followed by a historic wet year (2017) that brought winter and spring flooding as a result of atmospheric river storm events (Sterle et al., 2019). For the Carson River, an important observation made by managers was that peak streamflow that had traditionally coincided with peak irrigation demands, had shifted to earlier in the spring, with summer baseflow also decreasing (Sterle & Singletary, 2017). Managers shared with researchers concerns over potential future impacts that changing snowpack will have on surface water deliveries and reliance on groundwater, as the region’s population and economy continue to grow. During workshops that occurred over this period, local water managers and researchers discussed ways to evaluate water distribution and use that honors the existing legal framework and accounts for changing snowpack regimes (amount, rain versus snow, timing). In response to managers growing interest, researchers introduced the concept of managed aquifer recharge as one potential strategy to adapt and enhance regional water sustainability. What is managed aquifer recharge? Simply stated, managed aquifer recharge is the intentional recharge of structures to spread water over agricultural lands, allowing water to naturally infiltrate into the groundwater system (Bouwer, 1999; Niswonger et al., 2017). The latter may occur during the irrigation season by applying excess water, or during the nonirrigation season when evapotranspiration losses are low. Figure 2 illustrates managed aquifer recharge in a snow-fed river basin, where streamflow generated from snowmelt runoff is diverted to agricultural lands to recharge the aquifer. Such flood irrigation practices, including water delivery through earthen ditch networks, provide incidental but significant aquifer recharge through seepage and deep drainage beneath fields (Niswonger, Allander, & Jeton, 2014). The effects of managed aquifer recharge can vary depending on the location and intensity of practice. For example, implementing managed aquifer recharge water into the groundwater system (Dillon, 2009). This differs from the incidental recharge that may occur as part of normal irrigation practices. Managed recharge may occur by injection into the aquifer through existingwells, or by using existing conveyance adjacent to/along the river’s floodplain has the potential to enhance late-season instream flows due to increased return flows, resulting in greater downstream deliveries as well as improving ecological conditions (Niswonger et al., 2017). Implementing managed aquifer recharge away from the river’s floodplain has the potential to enhance groundwater supply which is increasingly relied upon during surface water shortage (Green et al., 2011), by storing water in available aquifer space in the deep aquifer. At the basin scale, managed aquifer recharge may lead to regional groundwater sustainability. Is the Carson River Basin a candidate for managed aquifer recharge? The physical limitations to implementing managed aquifer recharge in the Carson River Basin hinges on three key factors. The first factor relates to the physical connectivity between rivers and streams, and the irrigation delivery network of canals and ditches that divert water to agricultural lands (Niswonger et al., 2017). In the Carson River Basin the mechanisms for getting water to fields is already in place. Thus, intentionally routing high flows that occur in wet years through this system during the nonirrigation season would mimic what occurs naturally during the irrigation season. The second factor relates to the occurrence of atmospheric river storm events that deliver large amounts of precipitation to the region, much greater than average (Dettinger et al., 2015). With increased frequency and intensity projected under a warmer climate, such events have the potential to produce excess water over short periods of time that could be stored through mechanisms such as managed aquifer recharge (Niswonger et al., 2017). The third factor relates to the change in snowpack accumulation and shifts in snowmelt timing observed elsewhere in the Sierra Nevada (e.g., Godsey et al., 2014; Mote et al., 2018). Having a mechanism in place to maximize use of earlier snowmelt and shifts in streamflow timing could be advantageous and enhance regional groundwater sustainability. As part of the Water for the Seasons study, a hypothetical scenario was developed to determine the feasibility of managed aquifer recharge in the Carson River Basin, assuming no legal constraints. During “wet” or above-average water years, irrigators in the Upper Carson Valley would divert high flows and spread water over agricultural lands during the nonirrigation season. Assuming flows are abundant and “early,” diversions would begin prior to the growing season, when water would otherwise flow downstream to the Lahontan Reservoir. During “dry” years or drought periods, when surface water availability is less, irrigators in the Upper Carson Valley could augment surface water shortages with groundwater, allowing available surface water flows to flow downstream. Researchers hypothesize the amount of water has the potential to boost baseflow to support environmental instream flows, for example. What concerns have local water managers expressed? The hypothetical managed aquifer recharge scenario was presented to water managers in a workshop setting. Presentations included an overview of the hydrologic and operations modeling tools used to evaluate managed aquifer recharge by simulating the timing and distribution of water in the upper watershed. Specifically, in the Upper Carson Valley, a hydrologic model (GSFLOW) simulates streamflow driven by snowmelt, and surface and groundwater interactions, while a river basin operations model (MODSIM) allocates water according to the prior appropriation doctrine in the basin (see Figure 1) (Morway, Niswonger, & Triana, 2016; Niswonger et al., 2017). Integrating these two modeling tools advances the evaluation of climate impacts on water availability in agricultural communities and the resulting impacts of alternative management strategies (Morway et al., 2016). When asked about the viability of managed aquifer recharge, the perspectives of 11 managers varied (Figure 3). Regardless of rating, all managers questioned, “How would thisreally work?” Several managers questioned whether models could simulate the connectivity between surface and groundwater to accurately quantify changes to instream flow. Others raised concerns that managed aquifer recharge violates the Alpine Decree and Nevada Water Law. Still others requested researchers consider alternatives that could work within the confines of current (2019) water law. Managers posed specific questions that should be considered when evaluating the potential for managed aquifer recharge. For example: What triggers implementation of managed aquifer recharge?How “high” or “low” must annual flows be to initiate managed aquifer recharge? When in the water year is this determined? Where exactly in the Carson Valley is managed aquiferre charge possible? For example, what areas away from the floodplain could ensure long-term storage? Can model simulations quantify potential benefits and consequences system-wide?Would this information support decision-making, such as permitting of additional supplemental groundwater rights? How are researchers going to address managers’ research questions? Managers’ perspectives help to validate the on-the-ground potential of particular strategies and further refine alternative management scenarios. For example, understanding that managers are concerned with oversaturated fields helps researchers to define conditions in the model, such as what defines a wet versus “too” wet type of year and where to focus irrigation for managed aquifer recharge. Incorporating these nuances provides more accurate quantification of the potential benefits and consequences for users across the basin. Modeling is underway to simulate managed aquifer recharge scenarios and explore basin-wide implications. Researchers and local water managers will convene to collaboratively review results and further assess whether this or other strategies could work under the confines of existing water law. Subsequent fact sheets will present these findings.

Nevada

Scientific developments ISFD3

Highlights, trends, and consensus from the 63 papers submitted to the Scientific Developments theme of the Third International Symposium on Flood Defence (ISFD) are presented. Realizing that absolute protection against flooding can never be guaranteed, trends in flood management have shifted: (1) from flood protection to flood-risk management, (2) from reinforcing structural protection to lowering flood levels, and (3) to sustainable management through integrated problem solving. Improved understanding of watershed responses, climate changes, applications of GIS and remote-sensing technologies, and advanced analytical tools appeared to be the driving forces for renewing flood-risk management strategies. Technical competence in integrating analytical tools to form the basin wide management systems are demonstrated by several large, transnation models. However, analyses from social-economic-environmental points of view are found lag in general. ?? 2006 Taylor & Francis Group.

Conference Paper

Report on the workshop 'Global modelling of biodiversity and ecosystem services'

A three-day workshop on ‘Global Modelling of Biodiversity and Ecosystem Services’, was held in the Hague, Netherlands, from 24th to 26th June 2019. The workshop, attended by 35 modelling and scenario-building experts, was organised on behalf of the former IPBES1 expert group on scenarios and models of the first IPBES work programme by its interim technical support unit, and hosted by the PBL Netherlands Environmental Assessment Agency. The workshop drew on the ‘nature futures’ participatory scenario-building exercise initiated by the IPBES expert group on scenarios and models, and other biodiversity modelling initiatives such as the ISIMIP project2 working on adding biodiversity to the Shared Socioeconomic Pathways (SSPs) scenarios framework, the 'bending the curve' initiative3 led by IIASA4 and WWF5, and GEOBON6 working on modelling Essential Biodiversity Variables. The workshop was a step towards coordinating across biodiversity modelling initiatives, to build on each other’s work, and to seek synergies for the production of innovative scenarios on biodiversity and ecosystem services to inform the post-2020 agenda of the Convention on Biological Diversity, as well as the Sustainable Development Goals. The aims of the workshop were to: 1. Compile material as input for a first draft of the fifth Global Biodiversity Outlook (GBO-5) based on recent scenario work, including the ‘bending the curve’ scenarios and the newly developed PBL scenarios (modified from the Rio+20 scenarios), and existing models (to be completed by August 2019) 2. Develop a protocol for modelling trends and near term projections on indicators relevant to the Nature Futures Framework7 using models that are readily available (to be completed by early 2020) 3. Set the agenda and define the aims for a larger meeting at the end of 2019 to discuss the long term strategy towards the development of appropriate indicators and models to produce Nature Futures scenarios (to continue beyond Jan 2020)

Report

Ten simple rules for creating a scientific web application

The use of scientific web applications (SWApps) across biological and environmental sciences has grown exponentially over the past decade or so. Although quantitative evidence for such increased use in practice is scant, collectively, we have observed that these tools become more commonplace in teaching, outreach, and in science coproduction (e.g., as decision support tools). Despite the increased popularity of SWApps, researchers often receive little or no training in creating such tools. Although rolling out SWApps can be a relatively simple and quick process using modern, popular platforms like R shiny apps or Tableau dashboards, making them useful, usable, and sustainable is not. These 10 simple rules for creating a SWApp provide a foundation upon which researchers with little to no experience in web application design and development can consider, plan, and carry out SWApp projects.

PLOS Computational Biology

Understanding the Avian-Impact Offset Method—A tutorial

Biodiversity offsetting, or compensatory mitigation, is increasingly being used in temperate grassland and wetland ecosystems to compensate for unavoidable environmental damage from anthropogenic disturbances such as energy development and road construction. Energy-extraction and -generation facilities continue to proliferate across the natural landscapes of the United States, yet mitigation tools to ameliorate the negative behavioral effects on wildlife from these types of facilities are rarely implemented. Scientists from the U.S. Geological Survey conducted a 10-year before-after-control-impact (commonly referred to as BACI) study that evaluated the displacement effects of wind facilities on breeding grassland birds. The study determined behavioral avoidance for 7 of 9 species. This research is notable because of its design, geographical scope, and duration, which allowed for the determination of immediate, short-term effects; delayed or sustained effects; and discrete distances at which effects occurred. In addition, the U.S. Fish and Wildlife Service and Ducks Unlimited conducted a 3-year concurrent-year paired-reference study to determine behavioral avoidance for five species of dabbling ducks. By quantifying displacement rate from these two studies, U.S. Geological Survey and U.S. Fish and Wildlife Service scientists developed the Avian-Impact Offset Method (AIOM) to quantify and compensate for loss in value of breeding habitat. The AIOM converts the biological value (that is, number of bird pairs) lost by way of avoidance and estimates the site-specific number of hectares of grasslands and number of wetlands needed to compensate for displaced pairs of grassland birds and waterfowl. By converting biological value to traditional units of measure in which land is described and purchased or sold, the AIOM lends itself readily to the delivery of offsetting measures such as easement protections and restoration projects. The AIOM tool is applicable to wind, solar, oil, gas, and transportation infrastructure. This tutorial was designed to increase awareness of the AIOM and to promote its proper application. The tutorial is divided into four sections, each of which explains a discrete topic concerning aspects of behavioral displacement. The first section provides geographical and biological context, and the second section describes the field and statistical methods and results. The third section provides step-by-step instructions for applying the AIOM to several scenarios involving grassland birds or waterfowl at wind or oil facilities. The fourth section describes decision-support tools created to implement the AIOM. The appendices provide the actual field protocols constituting the methods for the research, provide detailed results by species and wind facility for that research, and provide detailed instructions for downloading and applying the decision-support tools.

Open-File Report

Reframing fish passage prioritization for human nutrition outcomes

Water control infrastructure forms barriers that fragment river habitats, reducing aquatic biodiversity and the ecosystem services it provides. Irrigation infrastructure, for example, although implemented to support food production, highlights problematic trade-offs against wild food systems like inland fisheries which are a critical food resource for tens of millions of people, particularly in tropical countries. To reduce fragmentation at a broad range of barriers, fish passage technology is sometimes implemented to support migrating fish, aided by frameworks designed to prioritize barriers for remediation. This study critically evaluated 93 fish passage barrier prioritization frameworks globally to explore how they could strategically guide fish passage investments in tropical contexts and identify criteria relevant to delivering on nutrition security outcomes. Results showed prioritization frameworks were ill-equipped to support the broader human development goals that may drive fish passage investments in tropical countries, such as supporting human nutrition under United Nations Sustainable Development Goal (SDG) 2: Zero Hunger. Tropical contexts were underrepresented despite substantial recent fish passage investment, whereas temperate and conservation focused frameworks, particularly from North America, dominated. These findings prompt reflection on the inherent biases in fish passage barrier prioritization frameworks and criteria. Improving understanding of and collaboration with local partners to integrate SDG 2 into future prioritization frameworks could improve fish passage infrastructure and help support better nutrition and food production for communities.

Environmental Management

Effects of permafrost thaw on CO2 and CH4 exchange in a western Alaska peatland chronosequence

Permafrost soils store over half of global soil carbon (C), and northern frozen peatlands store about 10% of global permafrost C. With thaw, inundation of high latitude lowland peatlands typically increases the surface-atmosphere flux of methane (CH 4 ), a potent greenhouse gas. To examine the effects of lowland permafrost thaw over millennial timescales, we measured carbon dioxide (CO 2 ) and CH 4 exchange along sites that constitute a ~1000 yr thaw chronosequence of thermokarst collapse bogs and adjacent fen locations at Innoko Flats Wildlife Refuge in western Alaska. Peak CH 4 exchange in July (123 ± 71 mg CH 4 –C m −2 d −1 ) was observed in features that have been thawed for 30 to 70 (<100) yr, where soils were warmer than at more recently thawed sites (14 to 21 yr; emitting 1.37 ± 0.67 mg CH 4 –C m −2 d −1 in July) and had shallower water tables than at older sites (200 to 1400 yr; emitting 6.55 ± 2.23 mg CH 4 –C m −2 d −1 in July). Carbon lost via CH 4 efflux during the growing season at these intermediate age sites was 8% of uptake by net ecosystem exchange. Our results provide evidence that CH 4 emissions following lowland permafrost thaw are enhanced over decadal time scales, but limited over millennia. Over larger spatial scales, adjacent fen systems may contribute sustained CH 4 emission, CO 2 uptake, and DOC export. We argue that over timescales of decades to centuries, thaw features in high-latitude lowland peatlands, particularly those developed on poorly drained mineral substrates, are a key locus of elevated CH 4 emission to the atmosphere that must be considered for a complete understanding of high latitude CH 4 dynamics.

Environmental Research Letters

Potential responses of the Lower Missouri River Shovelnose Sturgeon (Scaphirhynchus platorynchus) population to a commercial fishing ban

We developed an age‐structured population matrix model to perform population viability analysis for Lower Missouri River (LMR) shovelnose sturgeon ( Scaphirhynchus platorynchus ). We investigated potential effects of the commercial fishing moratorium put in place to help protect the similar‐appearing pallid sturgeon ( S. albus ). The model applies different components of total variance in life history parameters at different levels: sampling variance (parameter uncertainty) between model iterations; temporal variance (temporal environmental fluctuations) between time steps within iterations; and individual variance (individual differences) within each time‐step. The model predicted annual rates of population increase of 1.96% under historic fishing and 2.67% with removal of historic fishing. We identified combinations of fishing and harvest size restrictions that would permit a sustainable harvest of shovelnose sturgeon. Overall, the ban on commercial fishing of shovelnose sturgeon in the LMR due to similarity of appearance to pallid sturgeon should help the LMR shovelnose sturgeon population begin to rebound while decreasing any negative effects it may have had on pallid sturgeon populations.

Lower Missouri River basin

Environmental impacts of utility-scale solar energy

Renewable energy is a promising alternative to fossil fuel-based energy, but its development can require a complex set of environmental tradeoffs. A recent increase in solar energy systems, especially large, centralized installations, underscores the urgency of understanding their environmental interactions. Synthesizing literature across numerous disciplines, we review direct and indirect environmental impacts – both beneficial and adverse – of utility-scale solar energy (USSE) development, including impacts on biodiversity, land-use and land-cover change, soils, water resources, and human health. Additionally, we review feedbacks between USSE infrastructure and land-atmosphere interactions and the potential for USSE systems to mitigate climate change. Several characteristics and development strategies of USSE systems have low environmental impacts relative to other energy systems, including other renewables. We show opportunities to increase USSE environmental co-benefits, the permitting and regulatory constraints and opportunities of USSE, and highlight future research directions to better understand the nexus between USSE and the environment. Increasing the environmental compatibility of USSE systems will maximize the efficacy of this key renewable energy source in mitigating climatic and global environmental change.

Renewable and Sustainable Energy Reviews

Shallow groundwater quality in the Village of Patchogue, Suffolk County, New York

The onsite disposal of wastewater within the Patchogue River Basin-a riverine estuary that discharges into Great South Bay, Suffolk County, Long Island, N.Y. -has adversely affected water quality and aquatic habitats within both the tidal and non-tidal portions of the river. In response to increased development within the approximately 14 square mile basin, the Village of Patchogue has expanded efforts to manage and protect the local groundwater resources, which sustain freshwater base flow and aquatic habitats. Water-quality samples from 10 shallow wells within the Village were collected in March 2009, before the start of seasonal fertilizer application, to document the effects of onsite wastewater disposal on groundwater discharging into the Patchogue River. Each sample was analyzed for physical properties (pH, dissolved oxygen, specific conductance, and temperature), nutrients, organic carbon, major ions, and trace elements. Water samples from eight wells were analyzed for stable isotopes of nitrogen. The nitrate concentration in one well was 40 milligrams per liter (mg/L), which exceeded the U.S. Environmental Protection Agency (USEPA) and New York State Department of Health (NYSDOH) maximum contamination level in drinking water of 10 mg/L. Sodium concentrations at nine wells exceeded the USEPA Drinking Water Advisory Taste Threshold of 60 mg/L. Dissolved iron concentrations at three wells exceeded the NYSDOH and USEPA Secondary Drinking Water Standard of 300 micrograms per liter (?g/L). Nitrogen isotope signatures (d15N) were determined and compared with those reported from previous studies in Nassau and Suffolk Counties to identify possible sources of the nitrate. Local variations in measured ammonia, nitrate, total nitrogen, phosphorus, and organic carbon concentrations and d15N signatures indicate that nitrate enters the surficial aquifer from several sources (fertilizer, septic waste, and animal waste) and reflects biogeochemical processes such as denitrification.

Scientific Investigations Report