Browsing by Author "Bernhardt, Emily S"

Modern ecotoxicology draws considerable criticism for its lack of ecological relevance despite its history of interdisciplinary research overlap with the fields of conservation biology and ecology. The overarching aim of this dissertation was to unite the goals of these fields in the context of freshwater pollution by coal-fired power plant (CFPP) effluents, which contribute to the largest point source of environmental pollution in the United States and comprise a substantial threat to receiving ecosystems. CFPPs discharge the by-products of coal combustion, collectively referred to as coal combustion residuals (CCRs), into freshwater rivers and lakes through permitted discharges overseen by the National Pollutant Discharge Elimination System. CCRs are characterized by high concentrations of numerous inorganic elements, many of which are toxic to aquatic organisms. For decades, research on this waste stream has focused on selenium (Se) as an especially toxic trace element for oviparous vertebrates, historically causing severe deformities and species extirpations from which affected ecosystems took decades to recover.

The majority of work described here began with a 2015 field survey of three CFPP-associated lakes in North Carolina from which surface waters, sediments, sediment pore waters, biofilm, zooplankton, and resident fish species were collected and analyzed for their trace element profiles by inductively coupled plasma mass spectrometry (ICP-MS). Initial analyses focusing on Se alone revealed significantly higher tissue liver, muscle, and gonad tissue concentrations in fish from lakes receiving CCR inputs than those from reference systems. At two sites, Mayo Lake and Sutton Lake, water samples and fish tissue concentrations additionally exceeded the US Environmental Protection Agency’s recently revised aquatic life criteria. These analyses were subsequently expanded to consider a more comprehensive suite of ten CCR-associated elements. The results of paired univariate and multivariate analyses of abiotic and biotic compartments for each of the three pairs of lakes showed that CCR-receiving lake sediment pore waters are consistently enriched in manganese, arsenic, selenium, strontium, cadmium, and nickel. From this abiotic compartment, preferential uptake by biological compartments differed among species and among lakes such that only Se was consistently enriched in fish across the three systems. Across all lake pairs, the three fish species differed in their aggregate CCR tissue burdens, with bluegill having the highest burden and largemouth bass having the lowest. A lab-based trophic transfer study of field-collected biofilm and zooplankton to the model fish species, fathead minnow (Pimephalas promelas), supported the hypothesis that diet and trophic position are important mediators of fish tissue trace element composition. CCR loading history, lake size, and water residence time influence the magnitude of trace element accumulation in these systems, with important implications for the legacy of this waste stream as CFPPs are retired and their effluent streams to adjacent water bodies are terminated.

An additional lab-based dietary study of organic selenomethionine exposure sought to describe the bioenergetic consequences of low-level Se exposure to adult zebrafish (Danio rerio) and their offspring. Sex-specific metabolic effects were observed in whole organisms and individual tissue types and metabolic partitioning using the Seahorse Extracellular Flux Analyzer indicated that mitochondrial dysfunction could underlie altered metabolic rates, with implications for the ecological fitness of Se-impacted fish communities. This study also explored maternal and paternal exposure routes of Se exposure to F1 generation embryos and found that both routes of exposure resulted in reduced reserve respiratory capacity relative to control fish.

Inorganic trace elements are incorporated into the lattice of metabolically-stable fish otoliths, providing unique records of fishes’ lifetime exposure history. Two distinct otolith applications are explored here. First, time series otolith concentrations of a subset of CCRs were compared to overlapping time series of CFPP loading data to determine whether changes in system inputs were reflected in otolith uptake. Significant time lags, intra-species variation, and differences among species for Se suggested that otolith chemistry could be reflecting Se input legacies and complex biogeochemical cycling through the food webs from which fish are exposed. In contrast, fish otolith 87Sr/86Sr isotopic ratios did distinguish fish from a CCR-receiving lake in agreement with ratios measured in surface and pore water samples. If this initial proof-of-principle result holds for fish collected from larger reservoirs in which water chemistry is less uniform, otoliths could be powerful biological tracers of freshwater CCR impacts.

In tandem with the decreasing reliance on coal in the US, CFPPs are retiring, excavating their coal ash ponds, and otherwise terminating their CCR effluent streams. As these processes unfold, actively-receiving freshwater ecosystems are undergoing a transition to legacy status. An especially important avenue for future research is how CCR stoichiometry will change over time to reflect the relative transformation, sequestration, and transport of individual elements within and through these recovering systems. The ecotoxicological implications of the legacy CCR waste stream will likely evolve as exposure mixtures change.

Rivers interact with their valleys from headwaters to mouth, but nowhere as dynamically as in their floodplains. Rivers deliver water, sediments, and solutes onto the floodplain land surface, and the land in turn supplies solutes, leaves, and woody debris to the channel. These reciprocal exchanges maintain both aquatic and terrestrial biodiversity and productivity. In this dissertation I examine river-floodplain exchanges on the well-studied Nyack Floodplain, a dynamic, gravel-bedded floodplain along the Middle Fork Flathead River in the mountains of northwest Montana. I quantify exchanges at multiple timescales, from moments to centuries, to better understand how connectivity between aquatic and terrestrial habitats shapes their ecology.

I first address connectivity in the context of a long-standing question in ecosystem ecology: What determines the rate of ecosystem development during primary succession? Rivers have an immediate effect on floodplains when scouring floods remove vegetation and nutrients such as nitrogen (N) and leave only barren soils, but they might also affect the ensuing primary succession through the gradual delivery of N and other materials to floodplain soils. I quantify N inputs to successional floodplain forest soils of the Nyack Floodplain and find that sediment deposition by river flood water is the dominant source of N to soils, with lesser contributions from dissolved N in the river, biological N fixation, and atmospheric deposition. I also synthesize published rates of soil N accumulation in floodplain and non-floodplain primary-successional systems around the world, and I find that western floodplains often accumulate soil N faster than non-floodplain primary successional systems. My results collectively point to the importance of riverine N inputs in accelerating ecosystem development during floodplain primary succession.

I next investigate the role of river-floodplain exchanges in shaping the spatial distribution of a suite of soil properties. Even after flood waters have receded, dissolved N, carbon (C), and moisture could be delivered from the river to floodplain soils via belowground water flow. Alternatively, C inputs and N withdrawals by floodplain vegetation might be a dominant influence on soil properties. To test these hypotheses, I excavated and sampled soil pits from the soil surface to the water table (50-270 cm) under forests, meadows, and gravel bars of the Nyack Floodplain. Near-surface soils had C and N pools and N flux rates that varied predictably with vegetation cover, but soil properties below ~50 cm reflected influence by neither vegetation cover nor aquifer delivery. Instead, soil properties at these depths appear to relate to soil texture, which in turn is structured by the river's erosional and depositional activities. This finding suggests the revised hypothesis that soil properties in gravel-bedded alluvial floodplains may depend more on the decadal-scale geomorphic influences of floods than on short-term vertical interactions with floodplain vegetation or aquifer water.

Lastly, I explore the potential sources of organic C to the diverse and active community of aquatic organisms in the floodplain aquifer, where the lack of light prohibits in-situ organic C production by photosynthesis. I quantify floodplain carbon pools and the fluxes of organic carbon connecting the aquifer, river, and overlying forest. Spring flood waters infiltrating the soil are responsible for the largest dissolved carbon flux into the aquifer, while very large floods are essential for the other major C input, the burial of woody carbon in the aquifer. These findings emphasize the importance of a dynamic river hydrograph - in particular, annual floods and extreme annual floods - in delivering organic C to the aquifer community.

Overall, this dissertation draws our attention not just to the current exchanges of C, N, water, and sediment but to the episodic nature of those exchanges. To fully understand floodplain ecosystems, we have to consider not just present-day interactions but also the legacies of past floods and their roles in delivering solutes, eroding forests, depositing sediments, and physically shaping the floodplain environment.

Climate change is driving vegetation community shifts in coastal regions of the world, where low topographic relief makes ecosystems particularly vulnerable to sea level rise, salinization, storm surge, and other effects of global climate change. Salinization has clear effects on vegetation, as few plant species can survive in brackish water, and these shifts in vegetation lead to declines in biomass carbon stocks, as well as significant changes in habitat structure and biodiversity. The rate and extent of these impacts on other wetland ecosystem properties and function is far less certain. This dissertation investigates the ecosystem consequences of saltwater intrusion in coastal wetlands, from shifting vegetation at the landscape scale, to soil biogeochemistry and wetland carbon cycling.Coastal plant communities globally are highly vulnerable to future sea-level rise and storm damage, but the extent to which these habitats are affected by the various environmental perturbations associated with chronic salinization remains unclear. In 2016, a series of vegetation plots across the Albemarle-Pamlico Peninsula that had been surveyed 7-13 years earlier were revisited in order to measure changes in tree basal area and community composition over time. I found reduced tree basal area in plots at lower elevations and with higher current soil salt content, while these factors explained only a small fraction of the measured changes in tree community composition. While tree basal area increased in the majority of plots, I measured declines in basal area in multiple sites with high soil salt content or low elevation. This decadal comparison provides convincing evidence that increases in soil salinity and saturation can explain recent changes in tree biomass, and potential shifts in community composition in low-elevation sites along the North Carolina coast. In Chapter 3, I quantified land and land cover change in the Alligator River National Wildlife Refuge (ARNWR), North Carolina’s largest coastal wildlife preserve, from 1985 to 2019 using classification algorithms applied to a long-term record of satellite imagery. Despite ARNWR’s protected status, and in the absence of any active forest management, 32 % (31,600 hectares) of the refuge area has changed land cover classification during the study period. A total of 1151 hectares of land was lost to the sea and ~19,300 hectares of coastal forest habitat were converted to shrubland or marsh habitat. As much as 11 % of all forested cover in the refuge transitioned to ghost forest, a unique land cover class that is characterized by standing dead trees and fallen tree trunks. This is the first attempt to map and quantity coastal ghost forests using remote sensing. These unprecedented rates of deforestation and land cover change due to climate change may become the status quo for coastal regions worldwide, with implications for wetland function, wildlife habitat and global carbon cycling. Salinization of freshwater wetlands is a symptom of climate change induced sea level rise. The ecosystem consequences of increasing salinity are poorly constrained and highly variable within prior observational and experimental studies. Chapter 4 presents the results of the first attempt to conduct a salinization experiment in a coastal forested wetland. Over four years, marine salts were applied to experimental plots several times annually with the goal of raising soil salinity to brackish levels while soil porewater in control plots remained fresh. Each year I measured aboveground and belowground vegetation biomass along with soil carbon stocks and fluxes. Despite adding more than 1.5 kg of salt per m2 to our experimental plots over four years, the ecosystem responses to salt treatments were subtle and varied over the multi-year experiment. In the final year of the experiment, soil respiration was suppressed, and bulk and aromatic soil carbon became less soluble as a result of salt treatments. The more stable carbon pools—soil organic carbon and vegetation associated carbon—remained unaffected by the salt treatment. This experiment demonstrates substantial ecosystem resistance to low dose salinity manipulations. The inconsistent soil carbon responses to experimental salinization I observed in the field led me to question how differences in soil pH and base saturation might alter the impacts of salinity of soil microbial activity. To test this, I performed a salt addition experiment on two series of wetland soils with independently manipulated salt concentrations and solution pH to tease apart the effect of these seawater components on soil carbon cycling (Chapter 5). Microbial respiration and dissolved organic carbon solubility were depressed by marine salts in both soils, while pH manipulation alone had no effect. Salinity treatments had a far greater effect on soil pH than did our intentional pH manipulation and there was a strong interaction between salt treatments and soil type that affected the magnitude of soil carbon responses. Site soils varied significantly in pH and base saturation, suggesting that the interaction between salinity and edaphic factors is mediating soil carbon processes. The degree of salinization and the effective pH shift following seawater exposure may vary widely based on initial soil conditions and may explain much of the variation in reports of salt effects on soil carbon dynamics. I suggest that these edaphic factors may help explain the heretofore inconsistent reports of carbon cycle responses to experimental salinization reported in the literature to date.

While the problem of acid precipitation has been greatly reduced across the developed world, acid-impaired ecosystems still bear important legacies of historic acid deposition, and these ecosystems are only slowly beginning to recover. Early evidence suggests that this recovery may have multiple unexpected, substantial impacts on ecosystem carbon (C) and nitrogen (N) cycling, including large reductions in soil organic C and N pools and greatly increased export of dissolved organic C to aquatic ecosystems. These losses of soil C and N, driven by ecosystem recovery from acid precipitation, have the potential to dwarf any gains in biomass pools due to enhanced forest growth. The mechanisms driving these changes remain poorly understood, however. In this work, I ask the following questions: a) How does ecosystem recovery from acid precipitation alter soil C and N cycling, and b) what are the consequences of these changes for ecosystem N retention?

A watershed acid remediation experiment, performed at Hubbard Brook, White Mountains National Forest, New Hampshire, offers an opportunity to study now processes of ecosystem recovery from acid precipitation that will take decades to centuries to occur naturally. In this experiment, researchers applied calcium (Ca) silicate to a watershed to restore soil Ca fertility and raise soil pH. This treatment caused a rapid, substantial decrease in soil organic C, and greatly increased streamwater export of inorganic nitrogen. My dissertation examines my research questions through the lens of this experiment.

In the first part of my dissertation (Chapter 2), I examined how changes to soil pH and Ca fertility, individually and together, drive changes in the solubility and respiration of soil C, and how vegetation mediates these effects. I examined this topic through a soil mesocosm experiment in which I modified soil pH and soil Ca status individually and in combination. I found that there was a strong interactive effect between increases in soil pH and the presence of vegetation. Increasing soil pH increased soil respiration and soil C solubility, but only in the presence of sugar maple (Acer saccharum) roots. I also found that Ca fertilization stimulated plant growth, but had no effect on soil C dynamics. This suggests that vegetation and soil microbiota may respond to different aspects of ecosystem recovery from acid precipitation, with vegetation sensitive to changes in soil Ca content and microbiota sensitive to changes in soil pH.

In the second part of my dissertation (Chapter 3), I performed a field-based study to examine how the acid remediation treatment altered soil N cycling. I found that the acid remediation treatment increased both gross N mineralization and N uptake in the leaf litter, causing an accelerated N cycle. This accelerated N cycling resulted in larger inorganic N pools throughout the soil profile. These observed changes in N cycling contrast with earlier studies showing no treatment effect on N cycling rates, and this lag may be coupled to changes in plant community structure.

In the last part of my dissertation (Chapter 4), I examined how these changes in soil N cycling resulted in changes to ecosystem N export, using a combination of re-analysis of long term data sets and intensive stream monitoring. I found that, as a result of the Ca treatment, flushing of inorganic N during storms became a substantially more important mechanism of ecosystem N loss. I found evidence that the flushing of N during stormflow was the result of the mobilization of distal, hydrologically disconnected pools of soil N. This suggests that changes in forest floor N cycling, observed in Chapter 3, were responsible for this response. Finally, I found that in-stream uptake of N was significantly enhanced during baseflow conditions in the Ca-enriched watershed, reducing N export during baseflow.

This dissertation adds new mechanistic insight into the drivers by which ecosystem recovery from acid precipitation will affect C and N cycling. It demonstrates that, while acid precipitation has abated in the developed world, its legacy effects will remain with us for a long while. The changes to ecosystem C and N cycling studied here are concerning from the perspectives of climate change and loading of nutrients to aquatic ecosystems. This suggests the need for further work that couples vegetation dynamics, changes to geochemical properties of soils, and watershed hydrology.

As the human population continues to increase, the effects of land use change on streams and their watersheds will be one of the central problems facing humanity, as we strive to find ways to preserve important ecosystem services, such as drinking water, irrigation, and wastewater processing. This dissertation explores the effects of land use change on watershed nitrate concentrations, and on several biogeochemical ecosystem functions in streams, including nitrate uptake, ecosystem metabolism, and heterotrophic carbon processing.

In a literature synthesis, I was able to conclude that nitrate concentrations in streams in forested watersheds tend to be correlated with soil solution and shallow groundwater nitrate concentrations in those watersheds. Watershed disturbances, such as ice storms or clear-cutting, did not alter this relationship. However both urban and agricultural land use change increased the nitrate concentrations in streams, soil solution, and groundwater, and altered the correlation between them, increasing the slope and intercept of the regression line. I conclude that although the correlation between these concentrations allows for predictions to be made, further research is needed to better understand the importance of dilution, removal, and transformation along the flowpaths from uplands to streams.

From a multi-site comparison of forested, urban, and urban restored streams, I demonstrated that ecosystem functions like nitrate uptake and ecosystem metabolism do not change in a linear unidirectional way with increasing urbanization. I also showed that Natural Channel Design stream restoration as practiced at my study sites had no net effect on ecosystem function, except those effects that came from clearing the riparian vegetation for restoration construction. This study suggested further consideration is needed of the ecosystem effects of stream restoration as it was practiced at these sites. It also suggested that more study was needed of the effects of urbanization on ecosystem metabolism and heterotrophic processes in streams.

In a 16-month study of ecosystem metabolism at four sites along an urbanization gradient, I demonstrated that ecosystem metabolism in urban streams may be controlled by multiple separate effects of urbanization, including eutrophication, light, temperature, hydrology, and geomorphology. One site, with high nutrients, high light, and stable substrate for periphyton growth but flashy hydrology, demonstrated a boom-bust cycle of gross primary production. At another site, high benthic organic matter standing stocks combined with low velocities and high depths to create hypoxic conditions when temperature increased. I propose a new conceptual framework representing different trajectories of these effects based on the balance of increases in scour, thermal energy and light, eutrophication, and carbon loading.

Finally, in a study of 50 watersheds across a landscape urbanization gradient, I show that urbanization is correlated with a decrease in particulate carbon stocks. I suggest that an increase in dissolved organic matter quality may serve to compensate for the loss of particulate carbon as fuel for heterotrophic microbial activity. Although I saw no differences among watershed landuses in microbial activity per gram of sediment, there was a strong increase in the efficiency of microbial activity per unit organic sediment with increasing watershed urbanization. Ultimately, I hope that this research contributes to our understanding of stream ecosystem functions and the way land use change can alter these functions, with the possibility of better environmental management of urban streams in the future.

Whether through sea level rise, farmland abandonment, or wetland restoration, agricultural soils in coastal areas will be inundated at increasing rates, renewing connections to sensitive surface waters and raising critical questions related to environmental tradeoffs. Wetland restoration in particular is often implemented not only to promote wildlife habitat, but also to improve water quality through nutrient removal, especially in agricultural catchments. The microbial process of denitrification is the central mechanism of nitrogen removal in wetlands and flooded soils, and can be seen as a potential environmental benefit of flooding agricultural lands. While denitrification undoubtedly can remove nitrogen from soil and surface water, higher soil moisture or flooding in wetland soils can also increase the production of greenhouse gases, specifically nitrous oxide and methane, representing a potential environmental tradeoff. Understanding the likely benefits of denitrification and the likely greenhouse gas costs of wetland restoration could help inform environmental policies concerning wetland restoration.

Determining whether restored wetlands are larger sources of greenhouse gases compared to contrasting land use types (agriculture and forested wetlands) was the first goal of this dissertation (Chapter 2). We measured gas fluxes from soil and water to the atmosphere, and related environmental variables, in four sites over two years to estimate fluxes of the three major greenhouse gases. We found that carbon dioxide was the major contributor to the radiative balance across all sites, but that in the agricultural site and one of the forested wetland reference sites, nitrous oxide was the second most important contributor. Many studies have shown that methane is more important that nitrous oxide in most freshwater wetlands, as we found in the other forested wetland reference site and in flooded parts of the restored wetland. Overall, we did not find higher greenhouse gas fluxes in the restored wetland compared to agricultural soils or forested wetlands.

The controls over nitrous oxide are especially complex, because it can be produced by two complementary processes, nitrification and denitrification, which generally occur under different conditions in the environment. In Chapter 3, we determined the soil and environmental factors that best predicted nitrous oxide fluxes for a subset of our data encompassing gas fluxes measured in November 2007. We found that soil temperature and soil carbon dioxide flux, along with ammonium availability and denitrification potential, were good predictors of nitrous oxide (adj R2=0.81). Although the nitrous oxide model did not perform as well when applied to data from another sampling period, we expect to further develop our modeling efforts to include possible non-linear temperature effects and a larger range of environmental conditions.

In Chapter 4, we present results of a stable isotope tracer experiment to determine the relative contribution of nitrification and denitrification to nitrous oxide fluxes in these different land use types, and to determine the response of these processes to changing soil moisture. We added two forms of nitrogen-15 to intact soil cores to distinguish nitrification from denitrification, and subjected the cores to drainage or to a simulated rain event. We found that across the range of soil moisture, the fraction of nitrous oxide produced by denitrification did not change, but within each soil type there was a response to the simulated rain. In mineral soils, the nitrous oxide fraction increased with increasing soil moisture, with the highest mole fraction [N₂O/(N₂+N₂O)] in the agricultural soils, while in the organic soils there was no change or even a decrease. The fraction of nitrous oxide derived from coupled nitrification-denitrification increased with increasing soil moisture, and was much higher than that from denitrification alone in the more organic soils. This suggests that, in these saturated acid-organic soils, nitrification plays an important and underappreciated role in contributing to nitrous oxide fluxes from freshwater wetlands. The results from the laboratory experiment were consistent with patterns we saw in the field and help explain the differential contribution of nitrification and denitrification to nitrous oxide fluxes in different land use types in coastal plain wetlands of North Carolina.

Overall, we found that both nitrification and denitrification contribute to nitrous oxide fluxes in coastal plain wetlands in North Carolina, and that nitrification is an especially important source in acid-organic soils under both field-moist and saturated conditions. Although freshwater wetlands, with an average nitrous oxide mole fraction of 0.08, are generally seen as being insignificant sources of nitrous oxide, our study sites ranged from 0.10 to 0.30, placing them closer to agricultural fields (0.38; Schlesinger 2009). Although the ecosystems in our study produced more nitrous oxide than expected for freshwater wetlands, we found no significant tradeoff between the local water quality benefits conferred by denitrification and the global greenhouse gas costs in the restored wetland. These results suggest that, from a nitrogen perspective, wetland restoration in coastal agricultural lands has a net environmental benefit.

An increasingly large fraction of Earth’s surface has been reshaped and contaminated by humans, leading experts to suggest we’ve entered into a new geologic epoch – the Anthropocene. Nowhere are these changes more obvious than in mining-impacted landscapes. Mining reshapes landscapes, liberates trace elements, and alters the fate, transport, and transformation of trace elements. In this dissertation, I examine the extent to which mining both alters landscape features and mobilizes trace elements, and how these paired changes together determine the bioavailability of toxic trace elements. Specifically, in this dissertation, I focus on the mobilization and transformation of selenium (Se) and mercury (Hg) from mountaintop mining (MTM) in West Virginia; the biogeochemical interactions between Se and Hg in ecosystems and organisms; and the fate of Hg derived from artisanal and small-scale gold mining (ASGM) in Senegal and Peru.

In chapter 2, I examine the fate of Hg and Se from MTM of coal. Coal is naturally enriched in trace elements, including Hg and Se. Alkaline mine drainage from MTM – the dominant form of surface coal mining in Appalachia, USA – releases large quantities of Se into streams draining mined catchments, resulting in elevated bioaccumulation of Se in aquatic and riparian organisms. Yet, the release of Hg into these streams from MTM has not yet been studied. I measured total Hg, methyl Hg (MeHg), and Se in stream water, sediment, biofilm, cranefly larvae, and riparian spiders in alkaline streams (pH range: 6.9-8.4) across a mining gradient (0-98% watershed mined) in central Appalachia. Hg concentrations ranged from below detection limit (BDL)-6.9 ng/L in unfiltered water, BDL-0.05 μg/g in bulk sediment, 0.016-0.098 μg/g in biofilm, 0.038-0.11 μg/g in cranefly larvae, and 0.046-0.25 μg/g in riparian spiders. In contrast to Se, I found that Hg concentrations in all environmental compartments were not related to the proportion of the watershed mined, suggesting that Hg is not being released from, nor bioaccumulating within, MTM-VF watersheds. I also did not find clear evidence for a reduction in Hg methylation or bioaccumulation under elevated Se concentrations: water, sediment, biofilm, and riparian spiders exhibited no relationship between Hg and Se; only cranefly larvae exhibited a negative relationship (p=0.0002, r2=0.42). I suggest that the type of surface mining matrix rock, with resultant alkaline or acid mine drainage, is important for the speciation, mobility, and bioaccumulation of trace elements within watersheds affected by mining activities.

In chapter 3, I examine evidence for an interaction between Hg and Se. Hg is a pervasive environmental pollutant and contaminant of concern for both people and wildlife that has been a focus of environmental remediation efforts for decades. A growing body of literature has motivated calls for revising Hg consumption advisories to co-consider Se levels in seafood and implies that remediating aquatic ecosystems with ecosystem-scale Se additions could be a robust solution to Hg contamination. Provided that elevated Se concentrations are also known toxicological threats to aquatic animals, I performed a literature search to evaluate the strength of evidence supporting three assertions underpinning the ameliorating benefits of Se: (1) dietary Se reduces MeHg toxicity in consumers; (2) environmental Se reduces Hg bioaccumulation and biomagnification in aquatic food webs; and (3) Se inhibits Hg bioavailability to, and/or MeHg production by, microbial communities. Limited or ambiguous support for each criterion indicates that many scientific uncertainties and gaps remain regarding Se mediation of Hg behavior and toxicity in abiotic and biotic compartments. Significantly more information is needed to provide a strong scientific basis for modifying current fish consumption advisories on the basis of Se:Hg ratios or for applying Se amendments to remediate Hg-contaminated ecosystems.

In chapter 4, I examine evidence for Hg and Se interaction at the base of the food web. Hg, a potent neurotoxin, can biomagnify through food webs once converted into MeHg. Some studies have found that Se exposure may reduce MeHg bioaccumulation and toxicity, though this pattern is not universal. Se itself can also be toxic at elevated levels. We experimentally manipulated the relative concentrations of dietary MeHg and Se (as selenomethionine [SeMet]) for an aquatic grazer (the mayfly, Neocloeon triangulifer) and its food source (diatoms). Under low MeHg treatment (0.2 ng/L), diatoms exhibited a quadratic pattern, with decreasing diatom MeHg concentration up to 2.0 g Se/L and increasing MeHg accumulation at higher SeMet concentrations. Under high MeHg treatment (2 ng/L), SeMet concentrations had no effect on diatom MeHg concentrations. Mayfly MeHg concentrations and biomagnification factors (concentration of MeHg in mayflies: concentration of MeHg in diatoms) declined with SeMet addition only in the high MeHg treatment. Mayfly biomagnification factors decreased from 5.3 to 3.3 in the high MeHg treatment, while the biomagnification factor was constant with an average of 4.9 in the low MeHg treatment. The benefit of reduced MeHg biomagnification was offset by non-lethal effects and high mortality associated with ‘protective’ levels of SeMet exposure. Mayfly larvae escape behavior (i.e., startle response) was greatly reduced at early exposure days. Larvae took nearly twice as long for all to metamorphose to adults at high Se concentrations. The minimum number of days to emergence did not differ by SeMet exposure, with an average of 13 days. We measured an LC50SeMet for mayflies of 3.9 μg Se/L, with complete mortality at concentrations ≥6.0 μg Se/L. High reproductive mortality occurred at elevated SeMet exposures, with only 0-18% emergence at ≥4.12 g Se/L. Collectively our results suggest that while there is some evidence that Se can reduce MeHg accumulation at the base of the food web at specific exposure levels of SeMet and MeHg, Se is also toxic to mayflies and could lead to negative effects that extend across ecosystem boundaries.

In chapter 5, I examine the fate of total and MeHg from ASGM in Senegal. The largest source of global Hg anthropogenic inputs to the environment is derived from ASGM activities in developing countries. While our understanding of global Hg emissions from ASGM is growing, there is limited empirical documentation about the levels of total Hg (THg) and MeHg contamination near ASGM sites. I measured THg and MeHg concentrations in soil (n=119) sediment (n=22), and water (n=25) from four ASGM villages and one non-ASGM reference village in Senegal, West Africa with active ASGM. Nearly all samples had THg and MeHg concentrations that exceeded the reference village concentrations and USEPA regulatory standards. The highest median THg concentrations were found in huts where Hg-gold amalgams were burned (7.5 μg/g), while the highest median MeHg concentrations and percent Hg as MeHg were found in river sediments (4.2 ng/g, 0.41%). Median river water concentrations of THg and MeHg were also elevated compared to values at the reference site (22 ng THg/L, 0.037 ng MeHg/L in ASGM sites). This study provides direct evidence that Hg from ASGM is entering both the terrestrial and aquatic ecosystems where it is converted to the neurotoxic and bioavailable form of MeHg in soils, sediment, and water.

In chapter 6, I examine pathways of Hg deposition and storage from ASGM in the Peruvian Amazon. Hg emissions from ASGM now exceed coal combustion as the largest global source of Hg to the atmosphere and are being released into some of the most biodiverse ecosystems on Earth. Hg, following microbial conversion to MeHg, is a potent neurotoxin with deleterious impacts on people and wildlife. However, while we know ASGM is an important source of Hg to the atmosphere, we know very little about the fate of this source of Hg. Here, I examine Hg deposition and storage in the Peruvian Amazon by analyzing THg and MeHg in atmospheric, precipitation, leaf, and soil samples from remote and mining-impacted areas. I found that intact forests in the Peruvian Amazon near ASGM receive extremely high inputs of Hg in throughfall (71 µg m-2 yr-1) and litterfall (66 μg m-2 yr-1) and have accumulated significant quantities of soil Hg (9100 μg Hg m-2 within the top five cm). My findings show for the first time that intact forests near ASGM are intercepting high levels of Hg deposition, and that songbirds inhabiting these forests have elevated levels of mercury. Our findings raise important questions about how mercury pollution may constrain modern and future conservation efforts in these ecosystems.

In chapter 7, I examine the combined effects of landscape change and Hg loading from ASGM in the Peruvian Amazon. ASGM is the largest global source of anthropogenic Hg emissions. However, little is known about how effectively Hg released from ASGM is converted into the bioavailable form of MeHg in ASGM-altered landscapes. Through examination of ASGM-impacted river basins in Peru, I show that lake area in heavily mined watersheds has increased by 670% between 1985 and 2018, and that lakes in this area convert Hg into MeHg at net rates 5-7 times greater than rivers. These results suggest that synergistic increases in lake area and Hg loading associated with ASGM are significantly increasing exposure risk for people and wildlife. Similarly dramatic increases in lake area in other ASGM hotspots suggest that ‘hydroscape’ (hydrological landscape) alteration is an important and previously unrecognized component of Hg risk from ASGM.

In chapter 8, I develop several of the emergent themes that connect the distinct elements of this dissertation research. Here I develop a conceptual framework for merging perspectives from geochemistry, landscape ecology, and toxicology to understand the movement, fate and impact of toxic trace elements in the natural world. In the Anthropocene, we typically study the increasing mobilization of toxic trace elements and the changing land cover of our planet as separate issues. Yet the way we alter our landscapes plays a critical role in the likelihood that any particular place will retain, sequester, and alter the transport and bioavailability of trace elements to people and wildlife. The goal of this chapter is to provide examples that demonstrate that the risk of contaminant exposure is not merely a function of loading, but arises through interactions among loading, landscape capture, and biological transformation, all of which are simultaneously altered by human activities. I posit that successful prevention and mitigation of trace element toxicity requires a merging of these diverse perspectives and traditions.

By concentrating materials and increasing the speed with which rainfall is conveyed off of the landscape, nearly all forms of land use change lead to predictable shifts in the hydrologic, thermal, and chemical regimes of receiving waters that can lead to the local extirpation of sensitive aquatic biota. In Central Appalachian river networks, alkaline mine drainage (AlkMD) derived from mountaintop removal mining for coal (MTM) noticeably simplifies macroinvertebrate communities. In this dissertation, I have used this distinct chemical regime shift as a platform to move beyond current understanding of chemical pollution in river networks. In Chapter Two, I applied a new model, the Hierarchical Diversity Decision Framework (HiDDeF) to a macroinvertebrate dataset along a gradient of AlkMD. By using this new modeling tool, I showed that current AlkMD water quality standards allow one-quarter of regional macroinvertebrates to decline to half of their maximum abundances. In Chapter Three, I conducted a field study in the Mud River, WV to understand how AlkMD influences patterns in aquatic insect production. This work revealed roughly 3-fold declines in annual production of sensitive taxa throughout the year in reaches affected by AlkMD. These declines were more severe during summer base flow when pollutant concentrations were higher, thereby preventing sensitive organisms from completing their life cycles. Finally, in Chapter Four I described the idea of chemical fragmentation in river networks by performing a geospatial analysis of chemical pollution in Central Appalachia. In this work I showed that the ~30% of headwaters that remain after MTM intensification over the last four decades support ~10% of macroinvertebrates not found in mined reaches. Collectively my work moves beyond the simple tools used to understand the static, local consequences of chemical pollution in freshwater ecosystems.

To satisfy a growing population, much of Earth’s surface has been designed to suit humanity’s needs. Although these ecosystem designs have improved human welfare, they have also produced significant negative environmental impacts, which applied ecology as a field has attempted to address and solve. Many of the failures in applied ecology to achieve this goal of reducing neg- ative environmental impacts are design failures, not failures in the science. Here, we review (a) how humans have designed much of Earth’s surface, (b) the history of design ideas in ecology and the philosophical and practical critiques of these ideas, (c) design as a conceptual process, (d) how changing approaches and goals in subfields of applied ecology reflect changes and failures in design, and (e) why it is important not only for ecologists to en- courage design fields to incorporate ecology into their practice but also for design to be more thoroughly incorporated into ours.

One of the most heavily altered and designed ecosystems in the world is the mountaintop mines of Central Appalachia. Mountaintop mining is the most common form of coal mining in the Central Appalachian ecoregion. Previous estimates suggest that active, reclaimed, or abandoned mountaintop mines cover ∼7% of Central Appalachia. While this is double the areal extent of development in the ecoregion (estimated to occupy <3% of the land area), the impacts are far more extensive than areal estimates alone can convey as the impacts of mines extend 10s to 100s of meters below the current land surface. Here, we provide the first estimates for the total volumetric and topographic disturbance associated with mining in an 11 500 km2 region of southern West Virginia. We find that the cutting of ridges and filling of valleys has lowered the median slope of mined landscapes in the region by nearly 10 degrees while increasing their average elevation by 3 m as a result of expansive valley filling. We estimate that in southern West Virginia, more than 6.4km3 of bedrock has been broken apart and deposited into 1544 headwater valley fills. We used NPDES monitoring datatsets available for 91 of these valley fills to explore whether fill characteristics could explain variation in the pH or selenium concentrations reported for streams draining these fills. We found that the volume of overburden in individual valley fills correlates with stream pH and selenium concentration, and suggest that a three-dimensional assessment of mountaintop mining impacts is necessary to predict both the severity and the longevity of the resulting environmental impacts.

Chemical weathering of bedrock is the ultimate source of solutes for all ecosystems, a geologic sink of C, and controls the rate at which mountains dissolve into the sea. Human activities bring large volumes of bedrock to the surface and enhance global weathering rates. Here, we show watersheds impacted by mountaintop mining for coal have among the highest rates of chemical weathering ever reported. Mined watersheds deliver nearly 9,000 kg ha-1 y-1 of dissolved ions downstream. This translates into a chemical weathering rate ~ 330 mm ky-1, which is 55-times higher than background total (chemical and physical) weathering. These exceptionally high dissolution rates result from the production of sulfuric acid by pyrite oxidation. As this strong acid rapidly weathers surrounding carbonate materials, it not only releases large amounts of dissolved solutes, it also liberates 10-50 g of rock-derived C m-2 yr-1. This shifts mined watersheds from net geologic carbon sinks to net geologic carbon sources, further adding to the carbon costs from burning coal and deforesting these landscapes.

The impact from mining will likely last decades for some aspects of recovery and centuries to millennia for others. To examine the paired forest, hydrologic, and biogeochemical changes from mining we used a combination of remote sensing and watershed monitoring. We show that forest recovery on mines is at least twice as slow as typical forest recovery from clearcutting, and that mined areas have persistent low canopy height gaps. These vegetative changes are coupled with decreases in runoff ratios as mines age and water moves through flatter, vegetated landscapes. However, the vegetation change is uncoupled from biogeochemical processes, with strong alkaline mine drainage signals persisting for decades, even as vegetation recovers.

Microorganisms mediate many biogeochemical processes critical to the functioning of ecosystems, which places them as an intermediate between environmental change and the resulting ecosystem response. Yet, we have an incomplete understanding of these relationships, how to predict them, and when they are influential. Understanding these dynamics will inform ecological principles developed for macroorganisms and aid expectations for microbial responses to new gradients. To address this research goal, I used two studies of environmental gradients and a literature synthesis.

With the gradient studies, I assessed microbial community composition in stream biofilms across a gradient of alkaline mine drainage. I used multivariate approaches to examine changes in the non-eukaryote microbial community composition of taxa (chapter 2) and functional genes (chapter 3). I found that stream biofilms at sites receiving alkaline mine drainage had distinct community composition and also differed in the composition of functional gene groups compared with unmined reference sites. Compositional shifts were not dominated by groups that could benefit from mining associated increases of terminal electron acceptors; two-thirds of responsive taxa and functional gene groups were negatively associated with mining. The majority of subsidies and stressors (nitrate, sulfate, conductivity) had no consistent relationships with taxa or gene abundances. However, methane metabolism genes were less abundant at mined sites and there was a strong, positive correlation between selenate reductase gene abundance and mining-associated selenium. These results highlighted the potential for indirect factors to also play an important role in explaining compositional shifts.

In the fourth chapter, I synthesized studies that use environmental perturbations to explore microbial community structure and microbial process connections. I examined nine journals (2009–13) and found that many qualifying papers (112 of 148) documented structure and process responses, but few (38 of 112 papers) reported statistically testing for a link. Of these tested links, 75% were significant. No particular approach for characterizing structure or processes was more likely to produce significant links. Process responses were detected earlier on average than responses in structure. Together, the findings suggested that few publications report statistically testing structure-process links; but when tested, links often occurred yet shared few commonalities in linked processes or structures and the techniques used for measuring them.

Although the research community has made progress, much work remains to ensure that the vast and growing wealth of microbial informatics data is translated into useful ecological information. In part, this challenge can be approached through using hypotheses to guide analyses, but also by being open to opportunities for hypothesis generation. The results from my dissertation work advise that it is important to carefully interpret shifts in community composition in relation to abiotic characteristics and recommend considering ecological, thermodynamic, and kinetic principles to understand the properties governing community responses to environmental perturbation.