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Chapter 10: Occurrence of non-native invasive plants: The role of anthropogenic features

The invasion of non-native plants in the Wyoming Basins Ecoregional Assessment (WBEA) area is a major economic and ecological stress, with invasions thought to be hastened by energy developments. Given the potential impacts of nonnative invasive plants and the rapid changes in land use in the WBEA, broad-scale assessments and predictive models of nonnative invasive plant distribution are needed. Using this information, the current extent of populations for targeting treatment and monitoring can be identified, the habitat affinities for forecasting where weeds may establish next determined, and the responses to individual human disturbances (such as energy developments) predicted. To address these needs, we conducted vegetation surveys across the WBEA area at 317 individual survey blocks (five plots per survey block) during the summers of 2005 and 2006. Survey blocks were stratified by both human disturbance and habitat productivity; in each of five plots per survey block the occurrence of 23 common nonnative invasive plants was recorded during early and late season surveys. Here, we report on the four most common invasive plants, crested wheatgrass ( Agropyron cristatum ), cheatgrass ( Bromus tectorum ), halogeton ( Halogeton glomeratus ), and Russian thistle ( Salsola spp. ). Occurrence models were generated for each species using random-effects logistic regression to account for nesting of plots within sample sites. Predictors of occupancy included local habitat, abiotic condition, and distance to anthropogenic features. Although occurrences of all four invasive plants were affected by habitat, abiotic, and anthropogenic factors, cheatgrass and Russian thistle were most strongly associated with anthropogenic disturbance, primarily major roads and energy well sites. We assessed relationships between environmental and anthropogenic predictors and species occurrences to identify the major factors affecting current species distribution, examined shape of the response in occurrence in relation to proximity to individual anthropogenic disturbances, and provided spatial predictions of the locations where invasive plants are most likely to occur.

Wyoming

Variation and plasticity and their interaction with urbanization in Guadalupe Bass populations on and off the Edwards Plateau

The Colorado River Basin in Texas has experienced major alterations to its hydrologic regime due to changing land and water use patterns. These anthropogenic influences on hydrologic variability have had major implications for riparian and aquatic ecosystems and the species dependent upon them. However, impacts are often assessed at a limited temporal and spatial scale, tending to focus on relatively short and discrete periods or portions of a river basin. It is not clear how basin-wide alterations occurring over decades affect species. Guadalupe Bass Micropterus treculii are endemic to central Texas and are typically associated with shallow runs and riffles in small streams. However, Guadalupe Bass are found throughout the Colorado River Basin, including the mainstem portion of the lower river downstream of the city of Austin where they support a popular fishery. Because Guadalupe Bass exist across a wide range of stream orders within the basin, it is unclear whether populations respond similarly to anthropogenic disturbances or to conservation and restoration activities. Therefore, our objectives were to: Assess the effects of urbanization and hydrology on the population structure and dynamics of Guadalupe Bass. Evaluate the effects of environmental gradients on ecomorphological variation in Guadalupe Bass populations across multiple spatial scales. Describe the life history, habitat use, and behavior of the Guadalupe Bass population in the lower Colorado River and compare it to populations in more “typical” habitats. Results contribute to an understanding of the response of Guadalupe Bass to anthropogenic disturbances, including increased urbanization in central Texas and further assist in the conservation of the species. The ability of the population to not only persist, but flourish downstream of a heavily populated urban area presented a unique opportunity to investigate a native species response to anthropogenic disturbance. This research revealed differences in Guadalupe Bass habitat associations and movements, contrasts in age and growth, and morphological variation across a gradient of disturbance throughout the Colorado River Basin. Results of this work provide information on the potential effects of human population growth and increased water withdrawals on Guadalupe Bass populations. Additionally, this work adds to an understanding of the unique Guadalupe Bass population found in the lower Colorado River and how it differs from upstream tributary populations. Gathering additional population-level information facilitates conservation actions critical to preserving preferred habitat and promoting growth rates for Guadalupe Bass in streams of different sizes and flow conditions while highlighting interpopulation differences that may warrant consideration for stocking programs and other management strategies. Key findings of this study were: The similarity in response of growth rates to streamflow throughout the Colorado Basin suggests phenotypic plasticity in this trait rather than population-specific adaptations. Reductions in streamflows in the Colorado River Basin, whether due to increased frequency of drought or increased anthropogenic water withdrawal, will likely result in lower Guadalupe Bass growth rates with the potential to impact the structure of populations. Growth and recruitment showed a positive correlation with increased baseflows and mean monthly flows; however, continued assessment is necessary to determine a true relationship. We documented morphological divergence among Guadalupe Bass populations in response to spatial and temporal environmental variation. These ecomorphological differences among populations provide insight into the ability of Guadalupe Bass to respond to the differing in-stream habitat and flow conditions between small ‘typical’ tributary systems and the mainstem Colorado River. Morphological variation may be a population-level adaptation that potentially needs to be taken into consideration when choosing broodstock to maximize stocking success within a system. Understanding the morphological differences between Guadalupe Bass populations in response to local conditions could improve the success of restoration and supplemental stocking programs, especially in the ever-changing landscape of central Texas. We established a baseline for understanding the morphological response of Guadalupe Bass to increased population growth and the threats posed by increased water withdrawals and impervious surface. The mainstem population of Guadalupe Bass was generally more mobile, and more responsive to changes in streamflow, than tributary populations. The observed differences could influence the response of Guadalupe Bass populations to conservation and management actions, such as habitat restoration efforts. Continued monitoring of recruitment and angler exploitation may be beneficial to identify any changes that could negatively impact the population. Conservation initiatives solely focused on physical instream or riparian habitat are unlikely to be as beneficial to Guadalupe Bass as those focused on restoring or maintaining adequate streamflow

Cooperator Science Series

Hyperspectral imaging predicts differences in carbon and nitrogen status among representative biocrust functional groups of the Colorado Plateau

Biological soil crusts (biocrusts) are widespread soil photosynthetic communities covering about 12% of Earth's land surface and play crucial roles in terrestrial carbon (C) and nitrogen (N) cycles, yet scalable quantifications of biocrusts and their biogeochemical contributions are notably lacking. While remote sensing has enormous potential to assess, scale, and contextualize biocrusts and their functions, the applicability of hyperspectral data in predicting C- and N-related biocrust traits remains largely unexplored. We address this issue by evaluating the potential of in situ hyperspectral data to predict C and N across a range of biocrust species and different environmental conditions. We found that in situ hyperspectral reflectance measurements can be used to predict biocrust tissue C/N ratios and N concentrations with relatively high accuracy but to a lesser extent for potential biocrust N2 fixation rates. Critical wavelength domains included the visible region of the spectrum from roughly 490–600 nm, which most effectively captured variations in biocrust tissue C, and the shortwave infrared region from 1,150 to 1,350 nm and 1,550–1,650 nm, which most effectively captured biocrust tissue N and N2 fixation potential. Finally, we provide evidence that multi- and hyperspectral missions with targeted band placement, such as the proposed 26-band Landsat Next, could be effective in predicting biocrust traits. This work provides a critical step in understanding how to apply data from new and upcoming satellite missions to the monitoring of biocrusts.

Utah

A comparison of campfire impacts and policies in seven protected areas

Using resource-monitoring data from seven protected areas, the effectiveness of three campfire policies—campfire ban, designated campfires, and unregulated campfires—were assessed based on the number of fire sites and the amount of tree damage. Results indicate that unregulated campfire policies permitted substantial numbers of fire sites and tree damage in campsites, although fire bans did not eliminate or even substantially decrease these problems. A designated campfire policy was effective in decreasing number of fire sites, but little difference was found among policies regarding tree damage. Given the importance of campfires to visitor experiences, campfire prohibitions could be viewed as unnecessarily restrictive based on their limited success in preventing resource damage. Conclusions encourage protected-area managers to consider designated campfire policies and prohibitions on axes, hatchets, and saws to better meet resource protection and visitor experience mandates.

Environmental Management

Prediction uncertainty and data worth assessment for groundwater transport times in an agricultural catchment

Uncertainties about the age of base-flow discharge can have serious implications for the management of degraded environmental systems where subsurface pathways, and the ongoing release of pollutants that accumulated in the subsurface during past decades, dominate the water quality signal. Numerical groundwater models may be used to estimate groundwater return times and base-flow ages and thus predict the time required for stakeholders to see the results of improved agricultural management practices. However, the uncertainty inherent in the relationship between (i) the observations of atmospherically-derived tracers that are required to calibrate such models and (ii) the predictions of system age that the observations inform have not been investigated. For example, few if any studies have assessed the uncertainty of numerically-simulated system ages or evaluated the uncertainty reductions that may result from the expense of collecting additional subsurface tracer data. In this study we combine numerical flow and transport modeling of atmospherically-derived tracers with prediction uncertainty methods to accomplish four objectives. First, we show the relative importance of head, discharge, and tracer information for characterizing response times in a uniquely data rich catchment that includes 266 age-tracer measurements (SF 6 , CFCs, and 3 H) in addition to long term monitoring of water levels and stream discharge. Second, we calculate uncertainty intervals for model-simulated base-flow ages using both linear and non-linear methods, and find that the prediction sensitivity vector used by linear first-order second-moment methods results in much larger uncertainties than non-linear Monte Carlo methods operating on the same parameter uncertainty. Third, by combining prediction uncertainty analysis with multiple models of the system, we show that data-worth calculations and monitoring network design are sensitive to variations in the amount of water leaving the system via stream discharge and irrigation withdrawals. Finally, we demonstrate a novel model-averaged computation of potential data worth that can account for these uncertainties in model structure.

Maryland

Physiological development and vulnerability to Ceratomyxa shasta of fall-run Chinook Salmon in the Upper Klamath River Watershed

We evaluated a stock for restoring runs of fall Chinook salmon Oncorhynchus tshawytscha in the Upper Klamath River basin by monitoring its development in Iron Gate Hatchery and in net-pens in the Williamson River and Upper Klamath Lake in Oregon. We transferred age-1 hatchery fall Chinook salmon to net-pens in October 2005 and age-0 fall Chinook salmon in May 2006. Indices of smolt development were assessed in the hatchery and after 3 and 14 d in net-pens. Based on gill Na + , K + -ATPase activity and plasma thyroxine (T4) concentration, age-1 Chinook salmon were not developing smolt characteristics in the hatchery during October. Fish transferred to the river or lake had increased plasma cortisol in response to stress and increased T4 accompanying the change in water, but they did not have altered development. Variables in the age-0 Chinook salmon indicated that the fish in the hatchery were smolting. The fish in the river net-pens lost mass and had gill ATPase activity similar to that of the fish in the hatchery, whereas the fish transferred to the lake gained mass and length, had reduced condition factor, and had higher gill ATPase than the fish in the river. These results, along with environmental variables, suggest that the conditions in the lake were more conducive to smoltification than those in the river and thus accelerated the development of Chinook salmon. No Chinook salmon in the hatchery or either net-pen became infected with the myxosporean parasite Ceratomyxa shasta (the presence of which in the river and lake was confirmed) during either trial or when held for 90 d after a 10-d exposure in net-pens (2006 group). We concluded that that there is little evidence of physiological impairment or significant upriver vulnerability to C. shasta among this stock of fall Chinook salmon that would preclude them from being reintroduced into the Upper Klamath River basin.

North American Journal of Fisheries Management

Using colony monitoring devices to evaluate the impacts of land use and nutritional value of forage on honey bee health

Colony monitoring devices used to track and assess the health status of honey bees are becoming more widely available and used by both beekeepers and researchers. These devices monitor parameters relevant to colony health at frequent intervals, often approximating real time. The fine-scale record of hive condition can be further related to static or dynamic features of the landscape, such as weather, climate, colony density, land use, pesticide use, vegetation class, and forage quality. In this study, we fit commercial honey bee colonies in two apiaries with pollen traps and digital scales to monitor floral resource use, pollen quality, and honey production. One apiary was situated in low-intensity agriculture; the other in high-intensity agriculture. Pollen traps were open for 72 h every two weeks while scales recorded weight every 15 min throughout the growing season. From collected pollen, we determined forage quantity per day, species identity using DNA sequencing, pesticide residues, amino acid content, and total protein content. From scales, we determined the accumulated hive weight change over the growing season, relating to honey production and final colony weight going into winter. Hive scales may also be used to identify the occurrence of environmental pollen and nectar dearth, and track phenological changes in plant communities. We provide comparisons of device-derived data between two apiaries over the growing season and discuss the potential for employing apiary monitoring devices to infer colony health in the context of divergent agricultural land use conditions.

Agriculture

Enhancing the application of Earth observations for improved environmental decision-making using the Early Warning eXplorer (EWX)

The mitigation of losses due to extreme climate events and long-term climate adaptation requires climate informed decision-making. In the past few decades, several remote sensing and modeled-based Earth observations (EOs) have been developed to provide an unprecedented global overview and routine monitoring of climate and its impacts on vegetation and hydrologic conditions, with the goal of supporting informed decision-making. However, their usage in decision-making is particularly limited in climate-risk vulnerable and in situ data-scarce regions such as sub-Saharan Africa, due to lack of access to EOs. Here, we describe the Early Warning eXplorer (EWX), which was developed to address this crucial limitation and facilitate the application of EOs in decision-making, particularly in the food and water-insecure regions of the world. First, the EWX's core framework, which includes (i) the Viewer, (ii) GeoEngine, and (iii) Support Applications, is described. Then, a comprehensive overview of the Viewer, which is a web-based interface used to access EOs, is provided. This includes a description of (i) the maps and associated features to access gridded EO data and anomalies for different temporal averaging periods, (ii) time series graphs and associated features to access EOs aggregated over polygons such as administrative boundaries, and (iii) commonly used EOs served by the EWX that provide assessments of climate and vegetation conditions. Next, examples are provided to demonstrate how EWX can be used to monitor development, progression, spatial extent, and severity of climate-driven extreme events to support timely decisions related to mitigation of food insecurity and flooding impacts. Finally, the value of a regional implementation of EWX at the Regional Centre for Mapping of Resources for Development (RCMRD) in Nairobi, Kenya, is highlighted. Regional implementation of the EWX facilitates access to regionally focused EOs and their availability at polygon boundaries most relevant to the local decision-makers. Similar instances of EWX implemented in other regions, especially those susceptible to food and water security, will likely further enhance the application of EOs for informed decision-making.

Frontiers in Climate

Monitoring and modeling wetland chloride concentrations in relationship to oil and gas development

Extraction of oil and gas via unconventional methods is becoming an important aspect of energy production worldwide. Studying the effects of this development in countries where these technologies are being widely used may provide other countries, where development may be proposed, with some insight in terms of concerns associated with development. A fairly recent expansion of unconventional oil and gas development in North America provides such an opportunity. Rapid increases in energy development in North America have caught the attention of managers and scientists as a potential stressor for wildlife and their habitats. Of particular concern in the Northern Great Plains of the U.S. is the potential for chloride-rich produced water associated with unconventional oil and gas development to alter the water chemistry of wetlands. We describe a landscape scale modeling approach designed to examine the relationship between potential chloride contamination in wetlands and patterns of oil and gas development. We used a spatial Bayesian hierarchical modeling approach to assess multiple models explaining chloride concentrations in wetlands. These models included effects related to oil and gas wells (e.g. age of wells, number of wells) and surficial geology (e.g. glacial till, outwash). We found that the model containing the number of wells and the surficial geology surrounding a wetland best explained variation in chloride concentrations. Our spatial predictions showed regions of localized high chloride concentrations. Given the spatiotemporal variability of regional wetland water chemistry, we do not regard our results as predictions of contamination, but rather as a way to identify locations that may require more intensive sampling or further investigation. We suggest that an approach like the one outlined here could easily be extended to more of an adaptive monitoring approach to answer questions about chloride contamination risk that are of interest to managers.

Montana, North Dakota

Quantifying ecosystem states and state transitions of the Upper Mississippi River System using topological data analysis

Aquatic systems worldwide can exist in multiple ecosystem states (i.e., a recurring collection of biological and chemical attributes), and effectively characterizing multidimensionality will aid protection of desirable states and guide rehabilitation. The Upper Mississippi River System is composed of a large floodplain river system spanning 2200 km and multiple federal, state, tribal and local governmental units. Multiple ecosystem states may occur within the system, and characterization of the variables that define these ecosystem states could guide river rehabilitation. We coupled a long-term (30-year) highly dimensional water quality monitoring dataset with multiple topological data analysis (TDA) techniques to classify ecosystem states, identify state variables, and detect state transitions over 30 years in the river to guide conservation. Across the entire system, TDA identified five ecosystem states. State 1 was characterized by exceptionally clear, clean, and cold-water conditions typical of winter (i.e., a clear-water state); State 2 had the greatest range of environmental conditions and contained most the data (i.e., a status-quo state); and States 3, 4, and 5 had extremely high concentrations of suspended solids (i.e., turbid states, with State 5 as the most turbid). The TDA mapped clear patterns of the ecosystem states across several riverine navigation reaches and seasons that furthered ecological understanding. State variables were identified as suspended solids, chlorophyll a , and total phosphorus, which are also state variables of shallow lakes worldwide. The TDA change detection function showed short-term state transitions based on seasonality and episodic events, and provided evidence of gradual, long-term changes due to water quality improvements over three decades. These results can inform decision making and guide actions for regulatory and restoration agencies by assessing the status and trends of this important river and provide quantitative targets for state variables. The TDA change detection function may serve as a new tool for predicting the vulnerability to undesirable state transitions in this system and other ecosystems with sufficient data. Coupling ecosystem state concepts and TDA tools can be transferred to any ecosystem with large data to help classify states and understand their vulnerability to state transitions.

PLOS Computational Biology

Groundwater-quality data for the Madera/Chowchilla–Kings shallow aquifer study unit, 2013–14: Results from the California GAMA Program

Groundwater quality in the 2,390-square-mile Madera/Chowchilla–Kings Shallow Aquifer study unit was investigated by the U.S. Geological Survey from August 2013 to April 2014 as part of the California State Water Resources Control Board Groundwater Ambient Monitoring and Assessment Program’s Priority Basin Project. The study was designed to provide a statistically unbiased, spatially distributed assessment of untreated groundwater quality in the shallow aquifer systems of the Madera, Chowchilla, and Kings subbasins of the San Joaquin Valley groundwater basin. The shallow aquifer system corresponds to the part of the aquifer system generally used by domestic wells and is shallower than the part of the aquifer system generally used by public-supply wells. This report presents the data collected for the study and a brief preliminary description of the results. Groundwater samples were collected from 77 wells and were analyzed for organic constituents, inorganic constituents, selected isotopic and age-dating tracers, and microbial indicators. Most of the wells sampled for this study were private domestic wells. Unlike groundwater from public-supply wells, the groundwater from private domestic wells is not regulated for quality in California and is rarely analyzed for water-quality constituents. To provide context for the sampling results, however, concentrations of constituents measured in the untreated groundwater were compared with regulatory and non-regulatory benchmarks established for drinking-water quality by the U.S. Environmental Protection Agency, the State of California, and the U.S. Geological Survey. Of the 319 organic constituents assessed in this study (90 volatile organic compounds and 229 pesticides and pesticide degradates), 17 volatile organic compounds and 23 pesticides and pesticide degradates were detected in groundwater samples; concentrations of all but 2 were less than the respective benchmarks. The fumigants 1,2-dibromo-3-chloropropane (DBCP) and 1,2-dibromoethane (EDB) were detected at concentrations above their respective regulatory benchmarks in samples from a total of four wells. Most detections of inorganic constituents were at concentrations or activities less than the respective benchmark levels. Five inorganic constituents were detected in groundwater samples from one or more wells at concentrations or activities greater than their respective regulatory, health-based benchmarks: arsenic, uranium, nitrate, adjusted gross alpha particle activity, and gross beta particle activity. Four inorganic constituents were detected in samples from one or more wells at concentrations or activities greater than their respective non-regulatory, health-based benchmarks: manganese, molybdenum, vanadium, and radon-222. Three inorganic constituents were detected in groundwater samples from one or more wells at concentrations greater than their respective non-regulatory, aesthetic-based benchmarks: iron, sulfate, and total dissolved solids. Microbial indicators ( Escherichia coli , total coliform, and enterococci) were analyzed for presence or absence. The presence of Escherichia coli ( E. coli ) was not detected; the presence of total coliform was detected in samples from 10 of the 72 grid wells for which it was analyzed, and the presence of enterococci was detected in samples from 5 of the 73 grid wells analyzed.

California

Land Disturbance Associated with Oil and Gas Development and Effects of Development-Related Land Disturbance on Dissolved-Solids Loads in Streams in the Upper Colorado River Basin, 1991, 2007, and 2025

Oil and gas resource development in the Upper Colorado River Basin (UCRB) has increased substantially since the year 2000. The UCRB encompasses several significant oil and gas producing areas that have the potential for continued oil and gas resource development. Land disturbance associated with oil and gas resource development is caused by activities related to constructing drill pads to contain drilling and well maintenance equipment and roads to access the drill pad. Land disturbed by oil and gas development has the potential to cause increased erosion, stream degradation, habitat fragmentation and alteration, and increase public use of areas that may be environmentally sensitive. Land disturbance resulting from oil and gas resource development has not been monitored and mapped on a regional scale in the UCRB. However, information on the location and age of oil and gas wells in the UCRB is available. These data combined with geographic data analysis and modeling techniques were used to estimate the total area of disturbed land associated with oil and gas resource development in 1991 and in 2007 in the UCRB. Additional information about anticipated oil and gas development in the UCRB was used to project land disturbance to the year 2025. Results of the analysis indicate that approximately 117,500 acres (183 mi2) of total land disturbance was associated with drill pads and related roads in the UCRB in 1991. The estimated area of disturbed land associated with oil and gas development increased 53 percent to 179,400 acres (280 mi2) in 2007. Projecting oil and gas development through 2025 results in a potential near doubling of the land surface disturbance to approximately 319,300 acres (500 mi2). Estimated land disturbance for 1991 and 2007 were input to a contaminant transport model developed for the UCRB to assess the statistical significance of energy-related land disturbance to contributing dissolved solids to basin streams. The statistical assessment was an observational study based on an existing model and available water-quality monitoring data for the basin. No new data were collected for the analysis. The source coefficient calibrated for the disturbed lands associated with oil and gas development in 2007 was zero, which indicated that estimated land disturbance from oil and gas development is not statistically significant in explaining dissolved solids in UCRB streams. The lack of significance in the contaminant transport modeling framework may be due to the amount of available monitoring data, the spatial distribution of monitoring sites with respect to land disturbance, or the overall quantity of land disturbance associated with oil and gas development basin wide. Finally, dissolved-solids loads derived from natural landscapes may be similar to loads derived from lands disturbed by oil and gas resource development. The model recalibration done for this study confirms calibration results from Kenney and others (2009): the most significant contributor to dissolved solids in the UCRB is irrigated agricultural land, which covers an area substantially larger than the estimated area disturbed by oil and gas development and is subjected to artificially applied water.

Scientific Investigations Report

Relations of fish community composition to environmental variables in streams of central Nebraska, USA

Nine sites on streams in the Platte River Basin in central Nebraska were sampled as part of the US Geological Survey's National Water Quality Assessment Program during 1993-1994. A combination of canonical correspondence analysis and an index of biotic integrity determined from fish community data produced complementary evaluations of water quality conditions. Results of the canonical correspondence analysis were useful in showing which environmental variables were significant in differentiating fish communities at the nine sites. Five environmental variables were statistically significant in the analysis. Median specific conductance of water samples collected at a site accounted for the largest amount of variability in the species data. Although the percentage of the basin as cropland was not the first variable chosen in a forward selection process, it was the most strongly correlated with the first ordination axis. A rangeland- dominated site was distinguished from all others along that axis. Median orthophosphate concentration of samples collected in the year up to the time of fish sampling was most strongly correlated with the second ordination axis. The index of biotic integrity produced results that could be interpreted in terms of the relative water quality between sites. Sites draining nearly 100% cropland had the lowest scores for two individual metrics of the index of biotic integrity that were related to species tolerance. Effective monitoring of water quality could be achieved by coupling methods that address both the ecological components of fish communities and their statistical relationships to environmental factors.

Environmental Management

Processes influencing the transport and fate of contaminated sediments in the coastal ocean– Boston Harbor and Massachusetts Bay

Most of the major urban centers of the United States including Boston, New York, Washington, Chicago, New Orleans, Miami, Los Angeles, San Francisco, and Seattle—are on a coast (fig. 1.1). All of these cities discharge treated sewage effluent into adjacent waters. In 2000, 74 percent of the U.S. population lived within 200 kilometers (km) of the coast. Between 1980 and 2002, the population density in coastal communities increased approximately 4.5 times faster than in noncoastal areas of the U.S. (Perkins, 2004). More people generate larger volumes of wastes, increase the demands on wastewater treatment, expand the area of impervious land surfaces, and use more vehicles that contribute contaminants to street runoff. According to the National Coastal Condition Report II (U.S. Environmental Protection Agency, 2005a), on the basis of coastal habitat, water and sediment quality, benthic index, and fish tissue, the overall national coastal condition is only poor to fair and the overall coastal condition in the highly populated Northeast is poor. Scientific information helps managers to prioritize and regulate coastal-ocean uses that include recreation, commercial fishing, transportation, waste disposal, and critical habitat for marine organisms. These uses are often in conflict with each other and with environmental concerns. Developing a strategy for managing competing uses while maintaining sustainability of coastal resources requires scientific understanding of how the coastal ocean system behaves and how it responds to anthropogenic influences. This report provides a summary of a multidisciplinary research program designed to improve our understanding of the transport and fate of contaminants in Massachusetts coastal waters. Massachusetts Bay and Boston Harbor have been a focus of U.S. Geological Survey (USGS) research because they provide a diverse geographic setting for developing a scientific understanding of the geology, geochemistry, and oceanography of coastal systems in general. Scientific data from this region can also be used to inform decisions about important economic, environmental, and political issues. From the economic viewpoint, the annual value of tourism and shipping in Massachusetts and Cape Cod Bays is about $1.5 billion and $1.9 billion, respectively. Commercial and recreational fishing generates about $240 million per year in the same region (U.S. Environmental Protection Agency, 2005b). The environmental issue is the 300-year history of waste discharge from the Boston metropolitan area into the harbor. This history is punctuated by cycles of environmental degradation, public outcry, and improvements in the sewage treatment system. With each improvement, however, the continuous growth of population in greater Boston (fig. 1.2) and the resulting increase in the volume of waste exceeded the capacity of the treatment system, thereby setting the stage for a new contamination crisis. By the 1980s, the levels of contaminants in sediments of Boston Harbor were among the highest in the nation (National Oceanic and Atmospheric Administration, 1987). Fish were diseased, shellfish beds were closed, and swimming beaches were unsafe after heavy rains; in general, water quality and aesthetics were below acceptable standards. Legal and political issues have always been part of Boston Harbor’s history. The environmental conditions in the 1980s were highlighted in a 1983 legal suit brought by the city of Quincy against the Metropolitan District Commission (MDC, the state agency responsible for sewage treatment) and heads of three state agencies for discharging untreated or poorly treated sewage into the harbor (Dolin, 2004). The suit never went to trial, but through the actions of a Massachusetts Superior Court, the issue of Boston Harbor contamination remained on the political and public agenda. The judge called the harbor “unsafe, unsanitary, indecent, in violation of the law (Clean Water Act), and a danger to the health and welfare of the people” (Forman, 1984). To force the state legislature to implement a plan to improve harbor conditions, the judge threatened to place the MDC in receivership and curtail new sewage hookups for industry. Under intense lobbying by business, the legislature created the Massachusetts Water Resources Authority (MWRA) in December 1984. The independent MWRA was established to manage Boston’s waste treatment system and was given the authority to float bonds to pay for major improvements in the treatment system. In 1985, a Federal court began hearings on a suit brought by the Conservation Law Foundation, the Environmental Protection Agency (USEPA), and towns of Quincy and Winthrop against the MDC and MWRA (as heir to responsibilities of the MDC) for years of violation of the Clean Water Act. The judge ruled against the defendants and required all the parties to submit a construction plan and schedule for a new sewage treatment system. From these submissions, he developed a schedule for treatment system upgrades that would give the “citizens of this commonwealth a public assurance that Boston Harbor will be cleaned up within a defined period of time” (Dolin, 2004). The MWRA’s Boston Harbor cleanup program (Levy and Connor, 1992) has transformed the Boston sewage system. Key improvements were to (1) reduce contaminants at the industrial source; (2) remediate leaks in the sewage-collection system; (3) eliminate sewage sludge discharge to the harbor; (4) upgrade sewage treatment from primary to secondary; (5) construct a new ocean outfall 15.2 km offshore in Massachusetts Bay for discharge of treated effluent (fig. 1.3); and (6) implement improvements in the combined-sewer-overflow system. As part of the harbor cleanup program, the MWRA developed a comprehensive monitoring program (summarized in MWRA, 2004) to assess changes in the harbor and bays that specifically related to the new sewage system. Additional information about conditions and processes in the coastal system on a regional scale and over a long time period was and continues to be important in predicting and interpreting local change. Implementation of the MWRA’s program and the mission of the USGS to understand the geology of the nation’s offshore waters provided an opportunity to conduct a cooperative multidisciplinary research program. This USGS program addresses basic scientific questions as well as concerns raised by management regarding the design, implementation, and assessment of the new sewage treatment system. Already active in Boston Harbor during the late 1970s, the USGS expanded research into Massachusetts Bay with a multidisciplinary program in 1989.

Massachusetts

Life-history attributes of Arctic-breeding birds drive uneven responses to environmental variability across different phases of the reproductive cycle

Animals exhibit varied life-history traits that reflect adaptive responses to their environments. For Arctic-breeding birds, traits related to diet, egg nutrient allocation, clutch size, and chick growth are predicted to be under increasing selection pressure due to rapid climate change and increasing environmental variability across high-latitude regions. We compared four migratory birds (black brant [ Branta bernicla nigricans ], lesser snow geese [ Chen caerulescens caerulescens ], semipalmated sandpipers [ Calidris pusilla ], and Lapland longspurs [ Calcarius lapponicus ]) with varied life histories at an Arctic site in Alaska, USA, to understand how life-history traits help moderate environmental variability across different phases of the reproductive cycle. We monitored aspects of reproductive performance related to the timing of breeding, reproductive investment, and chick growth from 2011 to 2018. In response to early snowmelt and warm temperatures, semipalmated sandpipers advanced their site arrival and bred in higher numbers, while brant and snow geese increased clutch sizes; all four species advanced their nest initiation dates. During chick rearing, longspur nestlings were relatively resilient to environmental variation, whereas warmer temperatures increased the growth rates of sandpiper chicks but reduced growth rates of snow goose goslings. These responses generally aligned with traits along the capital-income spectrum of nutrient acquisition and altricial–precocial modes of chick growth. Under a warming climate, the ability to mobilize endogenous reserves likely provides geese with relative flexibility to adjust the timing of breeding and the size of clutches. Higher temperatures, however, may negatively affect the quality of herbaceous foods and slow gosling growth. Species may possess traits that are beneficial during one phase of the reproductive cycle and others that may be detrimental at another phase, uneven responses that may be amplified with future climate warming. These results underscore the need to consider multiple phases of the reproductive cycle when assessing the effects of environmental variability on Arctic-breeding birds.

Alaska

Integration of coral reef ecosystem process studies and remote sensing

Worldwide, local-scale anthropogenic stress combined with global climate change is driving shifts in the state of reef benthic communities from coral-rich to micro- or macroalgal-dominated (Knowlton, 1992; Done, 1999). Such phase shifts in reef benthic communities may be either abrupt or gradual, and case studies from diverse ocean basins demonstrate that recovery, while uncertain (Hughes, 1994), typically involves progression through successional stages (Done, 1992). These transitions in benthic community structure involve changes in community metabolism, and accordingly, the holistic evaluation of associated biogeochemical variables is of great intrinsic value (Done, 1992). Effective reef management requires advance prediction of coral reef alteration in the face of anthropogenic stress and change in the global environment (Hatcher, 1997a). In practice, this goal requires techniques that can rapidly discern, at an early stage, sublethal effects that may cause long-term increases in mortality (brown, 1988; Grigg and Dollar, 1990). Such methods would improve our understanding of the differences in the population, community, and ecosystem structure, as well as function, between pristine and degraded reefs. This knowledge base could then support scientifically based management strategies (Done, 1992). Brown (1988) noted the general lack of rigor in the assessment of stress on coral reefs and suggested that more quantitative approaches than currently exist are needed to allow objective understanding of coral reef dynamics. Sensitive techniques for the timely appraisal of pollution effects or generalized endemic stress in coral reefs are sorely lacking (Grigg and Dollar, 1990; Wilkinsin, 1992). Moreover, monitoring methods based on population inventories, sclerochronology, or reproductive biology tend to myopic and may give inconsistent results. Ideally, an improved means of evaluating reef stress would discriminate mortality due to natural causes from morality to anthropogenic causes (Brown, 1988). Models of coral reef ecosystems, parameterized by process measurements and scaled in time-space using remote sensing, have the potential to address pressing research questions that are central to devising valid management strategies (Grigg el al., 1984; Hatcher, 1997b). To attain this goal, ecosystem-level models that integrate studies of physical and chemical forcing with observed biological and geological responses are required. This interdisciplinary approach to understanding reef biogeochemical dynamics can allow investigations that integrate the scales of time and space (Hatcher, 1997a), thereby enabling prediction of coral reef change (Andréfouët and Payri, 2001). In turn, prediction of holistic ecosystem function within various environmental focusing scenarios has substantial promise in mitigating future disturbance. Indeed, management of coral reefs at the ecosystem level has been suggested as the only meaningful approach to preserving coral reefs (Bohnsack and Ault, 1996; Christensen et al., 1996).

Florida

Aquatic insect assemblages associated with subalpine stream segment types in relict glaciated headwaters

1. Aquatic habitats and biotic assemblages in subalpine headwaters are sensitive to climate and human impacts. Understanding biotic responses to such perturbations and the contribution of high-elevation headwaters to riverine biodiversity requires the assessment of assemblage composition among habitat types. We compared aquatic insect assemblages among headwater stream segment types in relict glaciated subalpine basins in Mt. Rainier National Park, Washington, USA. 2. Aquatic insects were collected during summer and autumn in three headwater basins. In each basin, three different stream segment types were sampled: colluvial groundwater sources, alluvial lake inlets, and cascade-bedrock lake outlets. Ward's hierarchical cluster analysis revealed high β diversity in aquatic insect assemblages, and non-metric multidimensional scaling indicated that spatial and temporal patterns in assemblage composition differed among headwater stream segment types. Aquatic insect assemblages showed more fidelity to stream segment types than to individual basins, and the principal environmental variables associated with assemblage structure were temperature and substrate. 3. Indicator species analyses identified specific aquatic insects associated with each stream segment type. Several rare and potentially endemic aquatic insect taxa were present, including the recently described species, Lednia borealis (Baumann and Kondratieff). 4. Our results indicate that aquatic insect assemblages in relict glaciated subalpine headwaters were strongly differentiated among stream segment types. These results illustrate the contribution of headwaters to riverine biodiversity and emphasise the importance of these habitats for monitoring biotic responses to climate change. Monitoring biotic assemblages in high-elevation headwaters is needed to prevent the potential loss of unique and sensitive biota.

Washington

Factors affecting reservoir and stream-water quality in the Cambridge, Massachusetts, drinking-water source area and implications for source-water protection

This report presents the results of a study conducted by the U.S. Geological Survey, in cooperation with the city of Cambridge, Massachusetts, Water Department, to assess reservoir and tributary-stream quality in the Cambridge drinking-water source area, and to use the information gained to help guide the design of a comprehensive water-quality monitoring program for the source area. Assessments of the quality and trophic state of the three primary storage reservoirs, Hobbs Brook Reservoir, Stony Brook Reservoir, and Fresh Pond, were conducted (September 1997-November 1998) to provide baseline information on the state of these resources and to determine the vulnerability of the reservoirs to increased loads of nutrients and other contaminants. The effects of land use, land cover, and other drainage-basin characteristics on sources, transport, and fate of fecal-indicator bacteria, highway deicing chemicals, nutrients, selected metals, and naturally occurring organic compounds in 11 subbasins that contribute water to the reservoirs also was investigated, and the data used to select sampling stations for incorporation into a water-quality monitoring network for the source area. All three reservoirs exhibited thermal and chemical stratification, despite artificial mixing by air hoses in Stony Brook Reservoir and Fresh Pond. The stratification produced anoxic or hypoxic conditions in the deepest parts of the reservoirs and these conditions resulted in the release of ammonia nitrogen orthophosphate phosphorus, and dissolved iron and manganese from the reservoir bed sediments. Concentrations of sodium and chloride in the reservoirs usually were higher than the amounts recommended by the U.S. Environmental Protection agency for drinking-water sources (20 milligrams per liter for sodium and 250 milligrams per liter for chloride). Maximum measured sodium concentrations were highest in Hobbs Brook Reservoir (113 milligrams per liter), intermediate in Stony Brook Reservoir (62 milligrams per liter), and lowest in Fresh Pond (54 milligrams per liter). Bed sediments in Hobbs Brook and Stony Brook Reservoirs were enriched in iron, manganese, and arsenic relative to those in the impounded lower Charles River in Boston, Massachusetts. Trophic state indices, calculated for each reservoir based on nutrient concentrations, water-column transparency, and phytoplankton abundances, indicated that the upper and middle basins of Hobbs Brook Reservoir were moderately to highly productive and likely to produce algal blooms; the lower basin of Hobbs Brook Reservoir and Stony Brook Reservoir were similar and intermediate in productivity, and Fresh Pond was relatively unproductive and unlikely to produce algal blooms. This pattern is likely due to sedimentation of organic and inorganic particles in the three basins of Hobbs Brook Reservoir and in Stony Brook Reservoir. Molar ratios of nitrogen to phosphorus ranged from 55 in Stony Brook Reservoir to 120 in Hobbs Brook Reservoir, indicating that phytoplankton algae in these water bodies may be phosphorus limited and therefore sensitive to small increases in phosphorus loading from the drainage basin. Nitrogen loads were found to be less important than phosphorus to the trophic condition of the reservoirs. Hobbs Brook and Stony Brook, the two principle streams draining the Cambridge drinking-water source area, differed in their relative contributions to many of the estimated constituent loads. The estimated load of fecal coliform bacteria was more than seven times larger for the mainly residential Stony Brook subbasin upstream from Kendal Green, Mass., than it was for the more commercial and industrial Hobbs Brook subbasin, though the drainage areas of the two subbasins differ only by about 20 percent. The State standard for fecal coliform bacteria in streams in the Cambridge drinking-water source area (20 colony forming units per 100 milliliters) was exceeded at all sampling stations. Estimated s

Massachusetts