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USGS2019

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↗

USGS2021

Opportunities and challenges of macrogenetic studies

The rapidly emerging field of macrogenetics focuses on analysing publicly accessible genetic datasets from thousands of species to explore large-scale patterns and predictors of intraspecific genetic variation. Facilitated by advances in evolutionary biology, technology, data infrastructure, statistics and open science, macrogenetics addresses core evolutionary hypotheses (such as disentangling environmental and life-history effects on genetic variation) with a global focus. Yet, there are important, often overlooked, limitations to this approach and best practices need to be considered and adopted if macrogenetics is to continue its exciting trajectory and reach its full potential in fields such as biodiversity monitoring and conservation. Here, we review the history of this rapidly growing field, highlight knowledge gaps and future directions, and provide guidelines for further research.

Nature Reviews Genetics↗

USGS2013

Water resources and shale gas/oil production in the Appalachian Basin: critical issues and evolving developments

Unconventional natural gas and oil resources in the United States are important components of a national energy program. While the Nation seeks greater energy independence and greener sources of energy, Federal agencies with environmental responsibilities, state and local regulators and water-resource agencies, and citizens throughout areas of unconventional shale gas development have concerns about the environmental effects of high volume hydraulic fracturing (HVHF), including those in the Appalachian Basin in the northeastern United States (fig. 1). Environmental concerns posing critical challenges include the availability and use of surface water and groundwater for hydraulic fracturing; the migration of stray gas and potential effects on overlying aquifers; the potential for flowback, formation fluids, and other wastes to contaminate surface water and groundwater; and the effects from drill pads, roads, and pipeline infrastructure on land disturbance in small watersheds and headwater streams (U.S. Government Printing Office, 2012). Federal, state, regional and local agencies, along with the gas industry, are striving to use the best science and technology to develop these unconventional resources in an environmentally safe manner. Some of these concerns were addressed in U.S. Geological Survey (USGS) Fact Sheet 2009–3032 (Soeder and Kappel, 2009) about potential critical effects on water resources associated with the development of gas extraction from the Marcellus Shale of the Hamilton Group (Ver Straeten and others, 1994). Since that time, (1) the extraction process has evolved, (2) environmental awareness related to high-volume hydraulic fracturing process has increased, (3) state regulations concerning gas well drilling have been modified, and (4) the practices used by industry to obtain, transport, recover, treat, recycle, and ultimately dispose of the spent fluids and solid waste materials have evolved. This report updates and expands on Fact Sheet 2009–3032 and presents new information regarding selected aspects of unconventional shale gas development in the Appalachian Basin (primarily Virginia, West Virginia, Maryland, Pennsylvania, Ohio, and New York). This document was prepared by the USGS, in cooperation with the U.S. Department of Energy, and reviews the evolving technical advances and scientific studies made in the Appalachian Basin between 2009 and the present (2013), addressing past and current issues for oil and gas development in the region.

Maryl;New York;Ohio;Pennsylvania;Virginia;West Vir↗

USGS2015

A call for conservation scientists to evaluate opportunities and risks from operation of vertical axis wind turbines

A new conservation paradigm ( Kareiva and Marvier, 2012 ) emphasizes the need for scientists to embrace a holistic approach taking into account the social and natural dimensions of conservation in human-dominated landscapes. While there is heavy debate over the new approach ( Tallis and Lubchenco, 2014 ), most conservation scientists seem to agree on to the need to cooperate with corporations when such interaction can benefit people and the environment ( Miller et al., 2014 ; Tallis and Lubchenco, 2014 ). Cooperation can be most productive when established in the early phases of development, but this requires a high capacity for forward looking pre-emptive action (i.e., anticipating potential forthcoming issues before they arise; Sutherland and Woodroof, 2009 ). This framework is particularly salient for rapidly developing and expanding technologies such as those for harvesting renewable energy sources. Here the stakes are very high, as they concern mitigating negative consequences to global climate while generating energy without impacting wildlife. In this vein, past experience is instructional. The environmental impacts of biofuels and wind, among others, have been identified and evaluated rather late ( Sutherland and Woodroof, 2009 ), so that implementation of best management practices on existing facilities is now often prohibitively expensive.

Frontiers in Ecology and Evolution↗

USGS2018

A conceptual framework for effectively anticipating water-quality changes resulting from changes in agricultural activities

Agricultural activities can affect water quality and the health of aquatic ecosystems; many water-quality issues originate with the movement of water, agricultural chemicals, and eroded soil from agricultural areas to streams and groundwater. Most agricultural activities are designed to sustain or increase crop production, while some are designed to protect soil and water resources. Numerous soil- and water-protection practices are designed to reduce the volume and velocity of runoff and increase infiltration. This report presents a conceptual framework that combines generalized concepts on the movement of water, the environmental behavior of chemicals and eroded soil, and the designed functions of various agricultural activities, as they relate to hydrology, to create attainable expectations for the protection of—with the goal of improving—water quality through changes in an agricultural activity. The framework presented uses two types of decision trees to guide decision making toward attainable expectations regarding the effectiveness of changing agricultural activities to protect and improve water quality in streams. One decision tree organizes decision making by considering the hydrologic setting and chemical behaviors, largely at the field scale. This decision tree can help determine which agricultural activities could effectively protect and improve water quality in a stream from the movement of chemicals, or sediment, from a field. The second decision tree is a chemical fate accounting tree. This decision tree helps set attainable expectations for the permanent removal of sediment, elements, and organic chemicals—such as herbicides and insecticides—through trapping or conservation tillage practices. Collectively, this conceptual framework consolidates diverse hydrologic settings, chemicals, and agricultural activities into a single, broad context that can be used to set attainable expectations for agricultural activities. This framework also enables better decision making for future agricultural activities as a means to reduce current, and prevent new, water-quality issues.

Scientific Investigations Report↗

USGS2026

Accumulation of per- and polyfluoroalkyl substances (PFAS) and their association with immune parameters in nestling ospreys (Pandion haliaetus) from Chesapeake and Delaware Bays, USA

Per- and polyfluoroalkyl substances (PFAS) are a class of widespread, environmentally persistent compounds that pose a potential threat to wildlife and human health. Despite recent efforts to reduce the use of long-chain PFAS in industrial practices and commercial/consumer products, the persistence and solubility of PFAS have led to their detection in wildlife on a global scale. Osprey ( Pandion haliaetus ) have long been used as a sentinel species with an extensive history of serving as an effective bioindicator of contamination. Here we report on a large-scale evaluation of PFAS and potential health effects in osprey from the Chesapeake and Delaware Bays, USA. In 2011 and 2015, we collected plasma samples from osprey nestlings throughout the Chesapeake and Delaware Bay watersheds. We quantified 40 PFAS congeners in osprey plasma via liquid chromatography-mass spectrometry and analyzed plasma for indicators of immune and thyroid function, and plasma biochemistry. In all birds, perfluorooctanesulfonic acid (PFOS) was the most commonly detected PFAS, followed by perfluoroundecanoic acid, (PFUnA) and perfluorodecanoic acid (PFDA). In nestling plasma from Chesapeake Bay, PFOS tended to be a higher average contributor to PFAS profiles compared to samples from Delaware Bay. In contrast, long-chain perfluoroalkyl carboxylic acids (PFCAs) such as PFUnA and PFDA comprised larger percentages of total PFAS in osprey plasma from Delaware Bay relative to Chesapeake Bay. While some PFAS concentrations were associated with plasma health indicators, the proportion of variation explained was low. Overall, our study provides a more thorough understanding of PFAS presence in the Chesapeake and Delaware Bays and is one of the first to examine whether PFAS exposure is associated with adverse health effects in wildlife.

Chesapeake and Delaware Bays↗

USGS2025

Deformity, erosion, lesion, tumor, and parasite (DELT) anomalies in fish communities of the Chesapeake Bay watershed, USA: A regional assessment and potential landscape drivers

Fish diseases in freshwater ecosystems pose significant ecological and socioeconomic challenges, yet monitoring them in wild populations is complex due to interactions between pathogens, hosts, and environmental conditions. We examine the prevalence and watershed-scale landscape drivers of external deformity, erosion, lesion, tumor, and parasite (DELT) anomalies in 57 riverine fish species using a large dataset (577,266 individuals collected 2008–2019) from the Chesapeake Bay watershed that originated from state and federal agencies. Overall, DELT prevalence was low (1.4%), but was higher in larger, longer-lived species, including Channel Catfish ( Ictalurus punctatus ) (18.9%), Rock Bass ( Ambloplites rupestris ) (7.6%), Smallmouth Bass ( Micropterus dolomieu ) (7.3%), Brown Bullhead ( Ameiurus nebulosus ) (5.6%), and Yellow Bullhead ( Ameiurus natalis ) (5.1%), signifying their potential as regional environmental health indicators. Spatial analysis indicated warmer temperatures increased the estimated probability of DELT occurrence, whereas higher precipitation often mitigated the probability of DELT occurrence. Conservation strategies (e.g., best management practices) had mixed effectiveness in reducing DELT occurrence probability across agricultural and urban landscapes. Across the landscape, various drivers, including harvested forest, impervious land, and pesticide use, influenced DELT occurrence probability differently across species. However, uncertainty remains partly due to low prevalence and variability in sampling methods across agencies. Despite low overall prevalence, DELT occurrence is a rapid fish health indicator. Future research could emphasize species-specific responses and longitudinal studies that incorporate life stages and health indicators. Understanding these intricate, multi-scale interactions is vital for effective monitoring, conservation, and adaptive management of freshwater ecosystems.

Chesapeake Bay watershed↗

USGS2007

Negotiation techniques to resolve western water disputes

There is a growing literature on the resolution of natural resources conflicts. Much of it is practical, focusing on guidelines for hands-on negotiation. This literature can be a guide in water conflicts. This is especially true for negotiations over new environmental values such as instream flow. The concepts of competitive, cooperative, and integrative styles of conflict resolution are applied to three cases of water resource bargaining. Lessons for the effective use of these ideas include: break a large number of parties into small working groups, approach value differences in small steps, be cautious in the presence of an attentive public, keeps decisions at the local level, and understand the opponent's interests.

Journal of the American Water Resources Associatio↗

USGS2015

Suburban watershed nitrogen retention: Estimating the effectiveness of stormwater management structures

Excess nitrogen (N) is a primary driver of freshwater and coastal eutrophication globally, and urban stormwater is a rapidly growing source of N pollution. Stormwater best management practices (BMPs) are used widely to remove excess N from runoff in urban and suburban areas, and are expected to perform under a wide variety of environmental conditions. Yet the capacity of BMPs to retain excess N varies; and both the variation and the drivers thereof are largely unknown, hindering the ability of water resource managers to meet water quality targets in a cost-effective way. Here, we use structured expert judgment (SEJ), a performance-weighted method of expert elicitation, to quantify the uncertainty in BMP performance under a range of site-specific environmental conditions and to estimate the extent to which key environmental factors influence variation in BMP performance. We hypothesized that rain event frequency and magnitude, BMP type and size, and physiographic province would significantly influence the experts’ estimates of N retention by BMPs common to suburban Piedmont and Coastal Plain watersheds of the Chesapeake Bay region. Expert knowledge indicated wide uncertainty in BMP performance, with N removal efficiencies ranging from <0% (BMP acting as a source of N during a rain event) to >40%. Experts believed that the amount of rain was the primary identifiable source of variability in BMP efficiency, which is relevant given climate projections of more frequent heavy rain events in the mid-Atlantic. To assess the extent to which those projected changes might alter N export from suburban BMPs and watersheds, we combined downscaled estimates of rainfall with distributions of N loads for different-sized rain events derived from our elicitation. The model predicted higher and more variable N loads under a projected future climate regime, suggesting that current BMP regulations for reducing nutrients may be inadequate in the future.

Maryland↗

USGS2010

Potential mitigation approach to minimize salinity intrusion in the Lower Savannah River Estuary due to reduced controlled releases from Lake Thurmond

The Savannah River originates at the confluence of the Seneca and Tugaloo Rivers, near Hartwell, Ga. and forms the State boundary between South Carolina and Georgia. The J. Strom Thurmond Dam and Lake, located 187 miles upstream from the coast, is responsible for most of the flow regulation that affects the Savannah River from Augusta to the coast. The Savannah Harbor experiences semi-diurnal tides of two high and two low tides in a 24.8-hour period with pronounced differences in tidal range between neap and spring tides occurring on a 14-day and 28-day lunar cycle. The Savannah National Wildlife Refuge is located in the Savannah River Estuary. The tidal freshwater marsh is an essential part of the 28,000-acre refuge and is home to a diverse variety of wildlife and plant communities. The Southeastern U.S. experienced severe drought conditions in 2008 and if the conditions had persisted in Georgia and South Carolina, Thurmond Lake could have reached an emergency operation level where outflow from the lake is equal to the inflow to the lake. To decrease the effect of the reduced releases on downstream resources, a stepped approach was proposed to reduce the flow in increments of 500 cubic feet per second (ft 3 /s) intervals. Reduced flows from 3,600 ft 3 /s to 3,100 ft 3 /s and 2,600 ft 3 /s were simulated with two previously developed models of the Lower Savannah River Estuary to evaluate the potential effects on salinity intrusion. The end of the previous drought (2002) was selected as the baseline condition for the simulations with the model. Salinity intrusion coincided with the 28-day cycle semidiurnal tidal cycles. The results show a difference between the model simulations of how the salinity will respond to the decreased flows. The Model-to-Marsh Decision Support System (M2MDSS) salinity response shows a large increase in the magnitude (> 6.0 practical salinity units, psu) and duration (3-4 days) of the salinity intrusion with extended periods (21 days) of tidal freshwater remaining in the system. The Environmental Fluid Dynamic Code (EFDC) model predicts increases in the magnitude of the salinity intrusion but only to 2 and 3 psu and the intrusion duration greater than a week. A potential mitigation to the increased salinity intrusion predicted by the M2MDSS would be to time pulses of increase flows to reduce the magnitude of the intrusion. Seven-day streamflow pulses of 4,500 ft 3 /s were inserted into the constant 3,100 ft 3 /s streamflow condition. The streamflow pulses did substantially decrease the magnitude and duration of the salinity intrusion. The result of the streamflow pulse scenario demonstrates how alternative release patterns from Lake Thurmond could be utilized to mitigate potential salinity changes in the Lower Savannah River Estuary.

Georgia, South Carolina↗

USGS2020

Smallmouth buffalo (Ictiobus bubalus) growth across a 1200km human use and ecological disturbance gradient in the Upper Mississippi River System

Smallmouth buffalo (Ictiobus bubalus) is a common and widely distributed large-bodied species of the family Catostomidae. It inhabits large rivers and reservoirs of the eastern continental United States (east of the continental Divide) and is most abundant and common in the large rivers of the Midwest and Central Plains, though it does occur as far north and east as the Hudson Bay drainage and as far south and west as Arizona (Edwards and Twoney 1982). Historically, smallmouth buffalo were an important component of commercial fisheries on both the Mississippi and Illinois Rivers. However, following the introduction of common carp (Cyprinus carpio) in the mid-1800s (Carlander 1954), the construction of a system of navigation dams on Upper Mississippi and Illinois River in the 1930s (USGS 1999), and water quality/pollution issues through the 1980s (Weiner 2010), the role of smallmouth buffalo in the overall UMRS fish community and commercial fishery has generally diminished relative to historical standards. Still, smallmouth buffalo remains an important and valued component of the UMRS commercial fishery. The study area is represented by three study reaches on the Illinois River and three study reaches on the Upper Mississippi River (Figure 1). Collectively, these study reaches represent nearly 1200 river km and exist across strong and pronounced ecological and disturbance gradients. For example, habitat composition, water quality, commercial navigation intensity, aquatic plant prominence, and the number and abundance of nonnative fish species vary strongly across the study domain, with northern Mississippi River reaches exhibiting less navigation traffic, better water quality, markedly greater aquatic plant prominence, more diverse habitat composition, and comparably much smaller numbers of nonnative species than the lower Mississippi River study reach and those on the Illinois River (USGS 1999; Johnson and Hagerty [eds] 2008; Irons et al. 2009). Long term monitoring efforts conducted under the auspices of the Upper Mississippi River Restoration program over the past 27 years have provided tremendous insights into shifts and changes of the overall UMRS fish community (Ickes et al. 2005; Garvey et al. 2010; Schramm and Ickes 2016). However, these monitoring efforts observe only the most basic aspects of the UMRS fish community (i.e., catch, length, weight, distribution, and occurrence). To gain a greater understanding of forces driving community level shifts and changes, more directed study is needed on the functional attributes of fish populations (i.e., growth, mortality, recruitment). Collectively, these functional attributes of populations are termed population dynamics and/or vital rates. It is important to note, the population dynamics of fishes in large rivers is generally poorly understood, especially for non-game species (Ickes 2018). The prevailing view is that abiotic factors largely govern inter-annual population dynamics, typically based upon rather short-term observations and correlations with assorted abiotic river attributes that vary on a seasonal or annual basis (for example, Risotto and Turner 1985). However, the role that longer-term abiotic factors play in regulating population abundance, or that biotic factors internal to the population (e.g., spawner-recruit dynamics, growth dynamics) or external to the population (e.g., predator-prey dynamics, sympatric competitors, disease) remain poorly understood. Achieving a greater understanding of these dynamics is important for stock, game, and invasive species management. In 2017, as part of a larger study designed to gain vital population rate information for smallmouth buffalo in the Upper Mississippi and Illinois Rivers (“Smallmouth Buffalo population demographics of the Upper Mississippi River System”; UMRR LTRM 2018SOW project items 2018MMBF1-2018MMBF6) annual growth patterns in smallmouth buffalo were determined and evaluated. This was accomplished by measuring growth histories recorded in annual growth increments on hard bony parts (here otoliths), a method known generically as biochronology, and somewhat analogous to dendrochronology practiced by foresters. These methods allow one to generate time-series of annual growth histories that depend upon age, year class (i.e., cohort), and annual environmental conditions experienced by the population over time (Weisberg, 1993). Biochronology methods were used to develop a 36-year time series of smallmouth buffalo growth in the Upper Mississippi and Illinois Rivers across a 1200 km ecological and human use disturbance gradient. Annual growth intervals were identified and measured from otoliths to determine fish age and growth history. A mixed model that parses the growth increment into age and year effects was fit to these data. Given the pronounced ecological and disturbance gradients inherent to the UMRS and the study domain, an a priori expectation of differing patterns in growth is accepted as a null hypothesis to test. The goal of this study was to model smallmouth buffalo growth as a function of the age of the fish and the growth year in which the growth was gained. The primary modeling objective was to parse growth observed on each annulus into a portion attributable to the age of the fish and the portion attributable to the year in which the growth was gained. In effect, this modeling approach removes the somewhat trivial age effects on growth so that a non-confounded growth year effect can be gained. Results attributable to growth year provide a time series of growth information that is of the same duration as the oldest fish observed and solely reflects environmental influences on growth. These model responses can then be investigated relative to environmental covariate time-series suspected of influencing growth of smallmouth buffalo in the Upper Mississippi and Illinois Rivers (e.g., temperature, discharge, population density, population mortality, forage availability, sympatric competition, habitat composition, navigation intensity, nonnative fish prominence, etc.). Thus, the primary scientific objective was to investigate if and how smallmouth buffalo growth varies in accordance with innate ecological and disturbance gradients across the study domain.

Illinois, Iowa, Minnesota, Missouri, Wisconsin↗

USGS2023

Land development and road salt usage drive long-term changes in major-ion chemistry of streamwater in six exurban and suburban watersheds, southeastern Pennsylvania, 1999-2019

In urbanized areas, the “freshwater salinization syndrome” (FSS), which pertains to long-term increases in concentrations of major ions and metals in fresh surface waters, has been attributed to road salt application. In addition to FSS, the water composition changes as an influx of sodium (Na + ) in recharge may displace calcium (Ca 2+ ), magnesium (Mg 2+ ), potassium (K + ), and trace metals by reverse cation exchange. These changing ion fluxes can result in adverse impacts on groundwater and surface waters used for municipal supplies. Few datasets exist to quantify the FSS on a watershed scale or link its manifestation to potential controlling factors such as changes in urban development, land use/land cover (LULC), or wastewater treatment plant (WWTP) discharges in upstream areas. Here, we use two decades (1999–2019) of monthly streamwater quality data combined with daily streamflow for six exurban and suburban watersheds in southeastern Pennsylvania to examine the relations among Ca 2+ , Mg 2+ , K + , Na + , chloride (Cl − ), sulfate (SO 4 2- ), and alkalinity (HCO 3 − ) concentrations and upstream controlling factors. Flow-normalized annual and baseflow (August ̶ November) concentrations for Ca 2+ , Mg 2+ , Na + , and Cl − increased in all six watersheds over the 20-year study, providing evidence of FSS’s impacts on groundwater that sustains streamflow. Additionally, a redundancy analysis using 2019 flow-normalized values identified the following positive associations between solute concentrations and controlling variables: 1) Cl − , Mg 2+ , and Ca 2+ with impervious surface cover (ISC), 2) Na + and SO 4 2- with ISC and total WWTP discharge volume, and 3) HCO 3 − with agriculture and total WWTP discharge volume. From a human health perspective, 2019 flow-normalized Na + concentrations exceeded the U.S. Environmental Protection Agency’s 20 mg L -1 threshold for individuals restricted to a low sodium diet. Furthermore, indices used to evaluate the corrosivity of source waters to drinking water infrastructure and inform municipal water treatment practices, such as the Chloride to Sulfate Mass Ratio and Larson Ratio, increased between two- and seven-fold over the 20-year time. Collectively, the results elucidate the causal factors of the FSS in suburban and exurban watersheds and its potential impacts on human health and drinking water infrastructure.

Pennsylvania↗

USGS2022

Invasive plant hitchhikers: Appalachian Trail thru-hiker knowledge and attitudes of invasive plants and Leave No Trace practices

Hiking and backpacking on American National Scenic Trails has increased in popularity in recent years. To encourage responsible and sustainable outdoor recreation on these much-loved trails, direct and indirect management strategies must be employed by managerial agencies. The Leave No Trace (LNT) education program aims to protect natural resources by promoting minimum-impact behaviours that lessen environmental impacts. The accidental introduction and dispersal of non-native invasive flora by hikers is little studied but can have a detrimental environmental impact on protected areas. The purpose of our study was to understand whether Appalachian Trail thru-hikers are: 1) aware of this problem, 2) adhering to LNT principles to reduce this problem, and 3) willing to learn and adopt minimum-impact behaviours to address this problem. We found that thru-hiker knowledge of invasive plants was limited and that very few thru-hikers adopted low-impact practices to minimise plant introduction and spread. Promisingly, we found that most thru-hikers, once aware of the problems, were willing to learn and apply low-impact practices to minimise plant introduction and spread. We discuss the barriers to their adoption of these behaviours and present a comprehensive list of suggested LNT practices to limit invasive plant introduction and spread. We conclude that, whilst challenging, protected area managers can help deter the spread of invasive plants along trails by improving educational messaging, signage, personal communication, and providing supporting infrastructure that encourages visitors to adopt specific practices to minimise invasive plant introduction and spread within protected areas.

Virginia, West Virginia↗

USGS2016

Do we need demographic data to forecast plant population dynamics?

Rapid environmental change has generated growing interest in forecasts of future population trajectories. Traditional population models built with detailed demographic observations from one study site can address the impacts of environmental change at particular locations, but are difficult to scale up to the landscape and regional scales relevant to management decisions. An alternative is to build models using population-level data that are much easier to collect over broad spatial scales than individual-level data. However, it is unknown whether models built using population-level data adequately capture the effects of density-dependence and environmental forcing that are necessary to generate skillful forecasts. Here, we test the consequences of aggregating individual responses when forecasting the population states (percent cover) and trajectories of four perennial grass species in a semi-arid grassland in Montana, USA. We parameterized two population models for each species, one based on individual-level data (survival, growth and recruitment) and one on population-level data (percent cover), and compared their forecasting accuracy and forecast horizons with and without the inclusion of climate covariates. For both models, we used Bayesian ridge regression to weight the influence of climate covariates for optimal prediction. In the absence of climate effects, we found no significant difference between the forecast accuracy of models based on individual-level data and models based on population-level data. Climate effects were weak, but increased forecast accuracy for two species. Increases in accuracy with climate covariates were similar between model types. In our case study, percent cover models generated forecasts as accurate as those from a demographic model. For the goal of forecasting, models based on aggregated individual-level data may offer a practical alternative to data-intensive demographic models. Long time series of percent cover data already exist for many plant species. Modelers should exploit these data to predict the impacts of environmental change.

Methods in Ecology and Evolution↗

USGS2009

Modeling the effects of environmental disturbance on wildlife communities: Avian responses to prescribed fire

Prescribed fire is a management tool used to reduce fuel loads on public lands in forested areas in the western United States. Identifying the impacts of prescribed fire on bird communities in ponderosa pine (Pinus ponderosa) forests is necessary for providing land management agencies with information regarding the effects of fuel reduction on sensitive, threatened, and migratory bird species. Recent developments in occupancy modeling have established a framework for quantifying the impacts of management practices on wildlife community dynamics. We describe a Bayesian hierarchical model of multi-species occupancy accounting for detection probability, and we demonstrate the model's usefulness for identifying effects of habitat disturbances on wildlife communities. Advantages to using the model include the ability to estimate the effects of environmental impacts on rare or elusive species, the intuitive nature of the modeling, the incorporation of detection probability, the estimation of parameter uncertainty, the flexibility of the model to suit a variety of experimental designs, and the composite estimate of the response that applies to the collection of observed species as opposed to merely a small subset of common species. Our modeling of the impacts of prescribed fire on avian communities in a ponderosa pine forest in Washington indicate that prescribed fire treatments result in increased occupancy rates for several bark-insectivore, cavity-nesting species including a management species of interest, Black-backed Woodpeckers (Picoides arcticus). Three aerial insectivore species, and the ground insectivore, American Robin (Turdus migratorius), also responded positively to prescribed fire, whereas three foliage insectivores and two seed specialists, Clark's Nutcracker (Nucifraga columbiana) and the Pine Siskin (Carduelis pinus), declined following treatments. Land management agencies interested in determining the effects of habitat manipulations on wildlife communities can use these methods to provide guidance for future management activities. ?? 2009 by the Ecological Society of America.

Ecological Applications↗

USGS2025

Microbiome data management in action workshop: Atlanta, GA, USA, June 12–13, 2024

Microbiome research is revolutionizing human and environmental health, but the value and reuse of microbiome data are significantly hampered by the limited development and adoption of data standards. While several ongoing efforts are aimed at improving microbiome data management, significant gaps still remain in terms of defining and promoting adoption of consensus standards for these datasets. The Strengthening the Organization and Reporting of Microbiome Studies (STORMS) guidelines for human microbiome research have been endorsed and successfully utilized by many research organizations, publishers, and funding agencies, and have been recognized as a consensus community standard. No equivalent effort has occurred for environmental, synthetic, and non-human host-associated microbiomes. To address this growing need within the microbiome research community, we convened the Microbiome Data Management in Action Workshop (June 12–13, 2024, in Atlanta, GA, USA), to bring together key decision makers in microbiome science including researchers, publishers, funders, and data repositories. The 50 attendees, representing the diverse and interdisciplinary nature of microbiome research, discussed recent progress and challenges, and brainstormed actionable recommendations and paths forward for coordinated environmental microbiome data management and the modifications necessary for the STORMS guidelines to be applied to environmental, non-human host, and synthetic microbiomes. The outcomes of this workshop will form the basis of a formalized data management roadmap to be implemented across the field. These best practices will drive scientific innovation now and in years to come as these data continue to be used not only in targeted reanalyses but in large-scale models and machine learning efforts.

Environmental Microbiome↗

USGS2017

Pairing field methods to improve inference in wildlife surveys while accommodating detection covariance

It is common to use multiple field sampling methods when implementing wildlife surveys to compare method efficacy or cost efficiency, integrate distinct pieces of information provided by separate methods, or evaluate method-specific biases and misclassification error. Existing models that combine information from multiple field methods or sampling devices permit rigorous comparison of method-specific detection parameters, enable estimation of additional parameters such as false-positive detection probability, and improve occurrence or abundance estimates, but with the assumption that the separate sampling methods produce detections independently of one another. This assumption is tenuous if methods are paired or deployed in close proximity simultaneously, a common practice that reduces the additional effort required to implement multiple methods and reduces the risk that differences between method-specific detection parameters are confounded by other environmental factors. We develop occupancy and spatial capture–recapture models that permit covariance between the detections produced by different methods, use simulation to compare estimator performance of the new models to models assuming independence, and provide an empirical application based on American marten ( Martes americana ) surveys using paired remote cameras, hair catches, and snow tracking. Simulation results indicate existing models that assume that methods independently detect organisms produce biased parameter estimates and substantially understate estimate uncertainty when this assumption is violated, while our reformulated models are robust to either methodological independence or covariance. Empirical results suggested that remote cameras and snow tracking had comparable probability of detecting present martens, but that snow tracking also produced false-positive marten detections that could potentially substantially bias distribution estimates if not corrected for. Remote cameras detected marten individuals more readily than passive hair catches. Inability to photographically distinguish individual sex did not appear to induce negative bias in camera density estimates; instead, hair catches appeared to produce detection competition between individuals that may have been a source of negative bias. Our model reformulations broaden the range of circumstances in which analyses incorporating multiple sources of information can be robustly used, and our empirical results demonstrate that using multiple field-methods can enhance inferences regarding ecological parameters of interest and improve understanding of how reliably survey methods sample these parameters.

Maine↗

USGS2016

Developing population models with data from marked individuals

Population viability analysis (PVA) is a powerful tool for biodiversity assessments, but its use has been limited because of the requirements for fully specified population models such as demographic structure, density-dependence, environmental stochasticity, and specification of uncertainties. Developing a fully specified population model from commonly available data sources – notably, mark–recapture studies – remains complicated due to lack of practical methods for estimating fecundity, true survival (as opposed to apparent survival), natural temporal variability in both survival and fecundity, density-dependence in the demographic parameters, and uncertainty in model parameters. We present a general method that estimates all the key parameters required to specify a stochastic, matrix-based population model, constructed using a long-term mark–recapture dataset. Unlike standard mark–recapture analyses, our approach provides estimates of true survival rates and fecundities, their respective natural temporal variabilities, and density-dependence functions, making it possible to construct a population model for long-term projection of population dynamics. Furthermore, our method includes a formal quantification of parameter uncertainty for global (multivariate) sensitivity analysis. We apply this approach to 9 bird species and demonstrate the feasibility of using data from the Monitoring Avian Productivity and Survivorship (MAPS) program. Bias-correction factors for raw estimates of survival and fecundity derived from mark–recapture data (apparent survival and juvenile:adult ratio, respectively) were non-negligible, and corrected parameters were generally more biologically reasonable than their uncorrected counterparts. Our method allows the development of fully specified stochastic population models using a single, widely available data source, substantially reducing the barriers that have until now limited the widespread application of PVA. This method is expected to greatly enhance our understanding of the processes underlying population dynamics and our ability to analyze viability and project trends for species of conservation concern.

Biological Conservation↗