Stable isotope analyses are powerful tools for reconstructing ancient ecologies and ecosystems, as they are independent of morphology and directly reflect dietary ecology. The application of stable isotope analyses, however, is not without limitations, as determination of food web dynamics using these methods often relies on poorly tested assumptions. The guiding thread of this thesis is the testing of foundational cornerstones on which these methods rely, in order to validate the suitability of applying these techniques to different mammalian clades, and to more reliably and confidently interpret the isotopic signals preserved in extinct organisms. The first chapter of this thesis tests the validity of an important assumption behind the interpretation of stable carbon isotope analyses for understanding diet in terrestrial mammalian herbivores: if, as assumed for almost two decades, mammalian bioapatite δ¹³C is enriched by 14‰ relative to dietary δ¹³C. By analyzing new isotopic data from a never before assessed herbivorous group spanning a broad range of body masses—sloths (Xenarthra, Mammalia)— and other mammals with experimentally controlled or observationally known diets, I discovered considerable variation in diet–bioapatite δ¹³C enrichment among mammals. Statistical tests (ordinary least squares, quantile, robust regressions, Akaike information criterion model tests) documented independence from phylogeny, and a previously unrecognized strong and significant correlation of δ¹³C enrichment with body mass for all mammalian herbivores. A single-factor body mass model outperformed all other single-factor or more complex combinatorial models evaluated, including for physiological variables (metabolic rate and body temperature proxies), and indicated that body mass alone predicts δ¹³C enrichment. These analyses, spanning more than 5 orders of magnitude of body sizes, yield a size-dependent prediction of isotopic enrichment across Mammalia and for distinct digestive physiologies, permitting reconstruction of foregut versus hindgut fermentation physiologies for fossils and refined mean annual paleoprecipitation estimates based on δ¹³C of mammalian bioapatite. Second, I sought to evaluate the existing paradigm governing identification of closed canopy rainforests in the fossil record using mammalian δ¹³C data: the presence of mammals with dietary δ¹³C <-31‰, which has only been observed in closed canopy rainforests in Equatorial Africa, the only other tropical ecosystem sampled extensively. This chapter provides a characterization of δ¹³Cbioapatite, δ¹³Chair and δ¹⁵Nhair of a modern mammalian community in western Amazonia, in Peru, to test if the isotopic structure of mammals in this Neotropical ecosystem is similar to those in African tropical rainforests. The results indicate that despite their marked geographical and taxonomic differences, median δ¹³Cdiet values from closed canopy rainforests in Amazonia (-27.4‰) and equatorial Africa (-26.9‰) are not significantly different. Amazonian mammals, however, seem to exploit a narrower spectrum of dietary resources than equatorial African mammals, as depicted by the absence of highly negative δ¹³Cdiet values previously proposed as indicative of rainforests (<-31‰). I hypothesize that differential effects of late Pleistocene extinction may be responsible for the ecological disparities among the two rainforests, by significantly reducing evolutionary time and dietary breadth reflected in the modern Amazonian mammalian community. Finally, the third chapter of this dissertation evaluates assumptions behind δ¹⁵N amino acid compound specific analyses in order to test the controversial hypothesis of carnivory and consumption of proteins of animal origin in fossil sloths. This analytical technique relies on three main assumptions. First, that the offset between the δ¹⁵N of glutamic acid (δ¹⁵NGlx) and phenylalanine (d15NPhe) in the organism under study will increase with increasing trophic level. Second, that the offset between δ¹⁵NGlx and δ¹⁵NPhe at the base of the food chain is relatively constant and has a value of -8.4‰ for C3 ecosystems. Third, that the trophic discrimination factor in all ecosystems (the difference in δ¹⁵NGlx relative to δ¹⁵NPhe with increasing trophic level) is 7.6‰. The results of my experiments conducted on extant xenarthrans (sloths and anteaters) with controlled diets document that only the first assumption holds true. Rather than relying on an equation with constants introducing uncertainties and that are not applicable to organisms feeding on a combination of items of different origin (e.g., C3 + C4 plants), δ¹⁵NGlx and δ¹⁵NPhe values by themselves can accurately reconstruct the trophic position of organisms. Indeed, the results on δ¹⁵NGlx and δ¹⁵NPhe herein obtained for five xenarthran species in controlled feeding experiments, combined with mammalian data available from the literature, show strong and significant correlations between these two AAs and with trophic positions. Both the TP equation and the regression analyses of δ¹⁵NGlx and δ¹⁵NPhe suggest that the Pleistocene fossil ground sloths 𝘔𝘺𝘭𝘰𝘥𝘰𝘯 𝘥𝘢𝘳𝘸𝘪𝘯𝘪𝘪 and 𝘕𝘰𝘵𝘩𝘳𝘰𝘵𝘩𝘦𝘳𝘪𝘰𝘱𝘴 𝘴𝘩𝘢𝘴𝘵𝘦𝘯𝘴𝘪𝘴 were not pure herbivores as commonly presumed, but rather that they were both mixed feeders/omnivores, incorporating items of animal origin in their diets.

The Mammoth Site in Hot Springs, South Dakota preserves a unique death assemblage of sub-adult and adult male Columbian mammoths (Mammuthus columbi). Extensive work on the site has led to a detailed understanding of the taphonomy of the assemblage; yet the life histories and ecology of these mammoths remain relatively unknown. Tooth enamel from four Mammoth Site mammoth individuals were bulk sampled with one of the individuals (MSL 742) also serially micro-sampled for 𝛿13C, 𝛿18O, and 87Sr/86Sr. Isotopic results indicate that MSL 742 remained within the southern and western Black Hills year-round with no consistent migration patterns. 𝛿13C and 𝛿18O values contain minimal fluctuations, suggesting drinking water and forage was sourced from the local hot springs and surrounding landscape. This study suggests the high level of sloped landscapes in the region may have resulted in a “bull”-only region, explaining the absence of females and juvenile mammoths at the site.

Methylmercury (MeHg) is a global pollutant and potent neurotoxin that bioaccumulates in aquatic and terrestrial foodwebs. As such, predicting the fate of MeHg in the environment is important in addressing ecosystem and human health concerns. Pollution that results from mining activities (i.e. ore roasting and smelting) is one way in which geochemistry of lakes can be altered, in turn altering the cycling of mercury (Hg) overall and the kinetics of MeHg production and bioaccumulation. My thesis is focused on examining the effect of different pollution gradients on the cycling of Hg at two different sites impacted by legacy mining in Canada. In Yellowknife (Northwest Territories, Canada) I assessed the effect of sulfate and arsenic (As) emissions on the production of MeHg in lake sediments, while in Sudbury (Ontario, Canada) I examined the effect of selenium (Se) emissions on the bioaccumulation of Hg and MeHg in freshwater biota. In Yellowknife, an environment polluted with both sulfate and As from mining activities, lakes were sampled using a factorial design which controlled for environmental variables known to affect MeHg production (i.e. sulfate, iron, productivity, pH, and dissolved organic matter). We used stable Hg isotope tracers to quantify Hg methylation and demethylation rate constants in sediments. Results showed that %MeHg in the water is best correlated with sulfate concentrations, while the rate at which Hg is methylated (Km) in sediments is negatively correlated with total As, and positively correlated with dissolved organic carbon, total phosphorus, and %MeHg in the water. Furthermore, a detailed examination of a lake with representative limnological characteristics of the area showed that addition of sulfate and organic carbon does increase the production of MeHg in the sediments, while addition of arsenate (0 to 10 mM) showed significant decrease in MeHg production, regardless of sulfate concentrations. Next, Se emissions in Sudbury (Ontario, Canada) correlated with lower total Hg and MeHg in tissues of zooplankton, amphipods (Hyalella azteca), mayflies (Stenonema femoratum), and young-of-the-year perch (Perca flavescens). However, despite ten years of emission reductions, results show that total Se concentrations in the majority of lakes have increased, most likely due to the long residence time of Se in the watershed and the water column. Consequently, Se continues to exhibit a protective effect on total Hg and MeHg bioaccumulation in biota, even a decade after emissions have greatly decreased. Canada’s numerous mining operations have left a legacy of pollution and it is important to understand the effects of these pollutants on the biogeochemistry of surrounding lakes. The results from my thesis demonstrate how mining emissions can alter the kinetics and bioaccumulation of MeHg in freshwater lakes, highlighting the complexity of Hg cycling in response to mining activities. My thesis is an important step in identifying and modeling the controls of MeHg production and bioaccumulation in environments impacted by emissions from mining operations.

The impact of agricultural practices on wetland ecosystems in the Prairie Pothole Region (PPR) has long been recognized but little is understood about impacts on the biogeochemistry of the wetlands at depth. Understanding the relationship of multi-elements within the wetland and surrounding landscape can aid in wetland restoration and provide guidance for wetland management. The objectives of this study were to: 1) identify biogeochemical characteristics of PPR wetlands; 2) identifying differences or similarities in biogeochemical characteristics of the landscape; 3) assess the vertical variation in chemical composition at depth in wetland, wetland and fringe, footslope and backslope soils; and 4) interpret the soil chemistry of undisturbed sites (good quality; prairie vegetation) and disturbed sites (poor quality; cultivated) relative to differences in landscape position locations. A field study was conducted on six disturbed (DW) and 6 undisturbed (UW) wetlands with evaluation of fringe (F), footslope (FS), or backslope (BS) positions. Using redundancy analysis (RDA) with selected environmental variables models of element concentrations at depth in each position were generated. The RDA ordination plots of element concentrations to depth of 1m was constrained by variables sand, silt, clay, depth, bulk density, site, organic matter, electrical conductivity, and pH. Pearson correlation coefficients between soil properties and the five most prominent soil elements differed between landscape positions. Anthropogenic activity likely influenced the subsurface hydrology but differed in physical and chemical properties. These differences appear to be related to the vegetation, levels of soil disturbance of surrounding landscapes and unique chemical and physical characteristics of parent material.

Copper (Cu) is required by marine microbes for essential biological processes, including photosynthesis and nitrogen fixation, but can be toxic above a certain threshold. Copper bioavailability in seawater is regulated by complexation with dissolved organic ligands of unknown source and structure. Culturing experiments have demonstrated the production of high-affinity Cu-binding ligands by marine algae in response to metal stress or limitation, suggesting they function either as metal ‘sponges’ to reduce copper toxicity or ‘carriers’ that promote uptake. The goal of my thesis research was to develop methods for the recovery and characterization of Cu ligands from seawater that could then be applied to natural samples to investigate sources and structures of recovered ligands. Using natural seawater spiked with model Cu ligands, I developed an immobilized Cu(II)-ion affinity chromatography (Cu(II)-IMAC) protocol which was shown to be effective in quantifying an operationally defined subset of natural Cu ligands. I then applied Cu(II)-IMAC to seawater collected along transects in the Canadian Arctic and NE Pacific Ocean to assess the abundance of this ligand pool across a diverse set of samples. Ligand distribution profiles and their covariance with other components of seawater (e.g. chlorophyll) were consistent with in situ biological production of some Cu-binding ligands. Model ligands spiked into seawater and recovered by Cu(II)-IMAC were also used to develop protocols for structural characterization of Cu ligands by solid-phase extraction (SPE) and tandem mass spectrometry (MS/MS). This research provides new tools for the isolation and characterization of copper ligands in natural samples, and new insights into the biogeochemical cycling and ecological significance of Cu in the ocean. / Graduate

Emissions of greenhouse gases from the combustion of fossil fuels, in particular carbon dioxide (CO2), are a major contributor to global climate change. In the United States 28% of carbon dioxide emissions from fossil fuel combustion are produced by road vehicles. This dissertation reports the results of three studies that improve on our knowledge of the spatial and temporal distribution of vehicle CO2 emissions in the U.S. over the last 35 years. Using bottom-up data assimilation techniques we produce several new high-resolution inventories of vehicle emissions, and use these new data products to analyze the relationships between emissions, population, employment, traffic congestion, and climate change at multiple spatial and temporal scales across the U.S. We find that population density has a strong, non-linear effect on vehicle emissions, with increasing emissions in low density areas and decreasing emissions in high density areas. We identify large biases in estimates of vehicle CO2 emissions by the most commonly used national and global inventories, and highlight the susceptibility of spatially-downscaled inventories to local biases in urban areas. We also quantify emissions of several air pollutants regulated by the U.S. Environment Protection Agency, including carbon monoxide, nitrogen oxides and particulate matter, at hourly and roadway scales for the metropolitan area surrounding Boston, MA. Emissions of these pollutants show high emissions gradients across identifiable spatial hotspots, considerable diurnal and seasonal variations, and a high sensitivity to the presence or absence of heavy-duty truck traffic. We also find that the impact of traffic congestion on air pollution emissions across the region is minimal as a share of the total emissions. We show that policies that combine a reduction in the number of vehicles on the road with a focus on improving traffic speeds have greater success in reducing emissions of air pollutants and greenhouse gases than policies that focus solely on improving traffic speeds. Finally, we estimate that regional emissions of carbon monoxide will increase by 3% in 2050, but with numerous localized increases of 25-50%, due to an expected rise in mean regional temperatures due to global climate change.

The effects of a mountain lake on nitrogen dynamics in a sub-alpine watershed were examined via watershed monitoring, mesocosm experiments, microcosm experiments, and enzymatic assays during spring and summer of a single year. Our study addressed the questions: (1) How does hydrologic transport through the lake affect the net fluxes of dissolved nitrogen (N) species? (2) What are the net effects of the littoral zone biota on dissolved N fluxes? (3) What are the seston and benthic uptake rates of nitrate? (4) What is the magnitude of N retention in littoral zone sediments? (5) What role does microbial hydrolysis of amino-groups from organic matter play in the uptake of dissolved nitrogen, relative to rates of nitrate uptake? Our study found a net positive flux of total dissolved N and dissolved organic N (DON), and a net negative flux of nitrate through the lake. During snowmelt, when the majority of nutrients are transported in this watershed, DON was retained in the lake. Several experiments were run to more closely examine the mechanisms behind these observations. Experiments in 2.1 m3 mesocosms in June and July measured rates of DON flux from the littoral zone sediments into the water column that were similar to increments measured in the lake. 15N-nitrate mesocosm and microcosm tracer experiments quantified benthic and pelagic nitrate uptake and retention of that nitrate in the benthic sediments. Areal nitrate uptake was 65-times greater in the sediments than in the water column seston and the turnover rate (half life) of the newly input nitrate pool in the sediments was 33-64 days. Finally, the prevalence of DON relative to dissolved inorganic N (DIN) and high measured rates of enzymatic amino acid hydrolysis suggest the importance of DON as a source of N for this aquatic system.

L'océan côtier subit la convergence de nombreuses perturbations anthropiques, avec le changement climatique en première ligne. Le réchauffement, l'acidification de l'océan, l'eutrophisation et la désoxygénation se combinent en menaçant les écosystèmes côtiers et les activités humaines associées. Malheureusement, la très forte hétérogénéité spatiale et temporelle de l'océan côtier limite la compréhension des processus biogéochimiques impliqués et leurs réponses face aux perturbations anthropiques. Les bases de données actuelles d'observations côtières sont encore insuffisantes et les modèles biogéochimiques océaniques globaux ont longtemps été inadaptés à l'étude de l'océan côtier global. En effet, la résolution spatiale de ces modèles était trop grossière pour résoudre de manière pertinente les processus de petites échelles. L'augmentation de la puissance de calcul des supercalculateurs permet l'utilisation de grilles de modèle plus fines adaptées à l'étude de l'océan côtier. Dans cette thèse, nous proposons d'étudier l'évolution au cours des dernières décennies de la biogéochimie de l'océan côtier à l'échelle globale à l'aide du modèle couplé physique-biogéochimie NEMO-PISCES. Après une évaluation de la représentation globale de la biogéochimie côtière et du cycle du carbone côtier dans notre modèle océanique, nous estimons le rôle actuel de l'océan côtier dans l'absorption océanique de carbone anthropique et nous étudions l'impact de la perturbation anthropique des apports fluviaux sur la biogéochimie côtière. En utilisant 3 grilles de résolutions spatiales différentes (200 km, 50 km et 25 km), il a été estimé que l'utilisation de la grille de 50 km représente le meilleur compromis entre les trois résolutions testées et que le passage à 25 km ne montre pas d'améliorations significatives des champs biogéochimiques côtiers évalués. Après cette première évaluation, le puits de carbone anthropique de l'océan côtier a été estimé pour la première fois à partir d'un modèle 3D global. L'océan côtier absorberait ainsi seulement 4,5 % du carbone anthropique absorbé par l'océan global pour la période 1993-2012 alors qu'il représente 7,5 % de la surface océanique globale. L'absorption côtière est réduite par l'export limité du carbone anthropique vers l'océan ouvert ne permettant pas de réduire la concentration moyenne de carbone anthropique des eaux côtières au niveau de celle de la couche de mélange de l'océan ouvert. Enfin, les effets de la perturbation anthropique des apports fluviaux sur la biogéochimie côtière ont été jugés limités quant intégrés à l'échelle côtière globale. Cependant, ces perturbations sont très contrastées régionalement. La mer du Nord présente des variations biogéochimiques mineures du fait de la tendance locale modérée appliquée aux apports fluviaux en nutriments, comparée à la mer de Chine de l'Est où la forte augmentation des apports fluviaux provoque d'importants phénomènes de désoxygénation et d'acidification. / The coastal ocean suffers from the convergence of multiple anthropogenic stressors with climate change at the forefront. Combined stresses from global warming, ocean acidification, eutrophication and deoxygenation threaten coastal ecosystems and thus their services that humans rely on. Unfortunately, the coastal ocean's large spatiotemporal heterogeneity limits our understanding of the biogeochemical processes involved and their responses to anthropogenic perturbations. The current database of coastal observations remains insufficient, and global biogeochemical ocean models have long been inadequate to the study of the global coastal ocean. Indeed, the spatial resolution of these models has been too coarse to resolve key small-scale coastal processes. However, continual improvements in computational resources now allow global simulations to be made with sufficiently high model resolution that begins to be suitable for coastal ocean studies. In this thesis, we propose to study the evolution of the coastal ocean biogeochemistry at the global scale over recent decades using higher resolution versions of the global physical-biogeochemical model NEMO-PISCES. After evaluating of the global representation of the coastal biogeochemistry in this ocean model, we estimate the current role of the coastal ocean in the ocean uptake of anthropogenic carbon and we study the impact of the anthropogenically driven changes in riverine inputs on the coastal biogeochemistry. From simulations made at 3 different spatial resolutions (200 km, 50 km, 25 km), we esteem that the 50-km model grid offers the best compromise between quality of results and computational cost. The upgrade to 25 km does not appear to provide significant improvement in model skill of simulating coastal biogeochemical fields. After evaluating the model, we provide an estimate of the coastal-ocean sink of anthropogenic carbon, the first study to do so with a global 3-D model. In our simulation, the coastal zone absorbs only 4.5% of the anthropogenic carbon taken up by the global ocean during 1993-2012, less than the 7.5% proportion of coastal-to-global-ocean surface areas. Coastal uptake is weakened due to a bottleneck in offshore transport, which is inadequate to reduce the mean anthropogenic carbon concentration of coastal waters to the average level found in the open-ocean mixed layer. Finally, the anthropogenic perturbation in riverine delivery of nutrients to the ocean has limited impact on the coastal carbon cycle when integrated across all coastal regions, but locally it can induce sharp biogeochemical contrasts. For example, the North Sea shows minor biogeochemical changes following the moderate local trend in nutrient riverine inputs, which is in dramatic contrast to the East China Sea where extensive deoxygenation and acidification are driven by sharp increases in riverine nutrient inputs.

I estimated yield, population metrics, production costs, and evaluated consumer acceptability and nutritive content of crayfish (Procambarus clarkii, P. zonangulus) harvested from moist-soil wetlands in the Lower Mississippi Alluvial Valley (MAV) during springs 2009-2011. I also compared nutrient and sediment concentrations and loads exported from moist-soil wetlands and nearest agriculture fields in the MAV during winters 2010-2012. Daily yield of crayfish from moist-soil wetlands was 2.4 kg (wet) ha-1 (SE = 0.50; 95% CI = 1.3-3.4). When graded by size, yield of large crayfish (> 30 g) from wetlands dominated by P. clarkii was four times greater (P < 0.05) than yield of large crayfish from wetlands dominated by P. zonangulus. Crayfish harvesting costs (2013 US dollars [$]) ranged from $405.69 ha-1 to $917.88 ha-1 and breakeven selling prices ranged from $3.74 kg-1 to $8.49 kg-1. Consumer acceptability, proximate composition, and total fatty acid content of P. clarkii did not differ (0.73 > P > 0.11) between crayfish harvested from moist-soil wetlands and rice-crayfish culture fields in Louisiana. Although selling prices likely will not compete with prices for crayfish harvested from Louisiana rice fields ($2.75 kg-1; 2012 US$), harvesting crayfish from moist-soil wetlands may enhance recreational opportunities while increasing awareness of ecosystem benefits of these wetlands. Although concentrations (mg L-1) of soluble reactive phosphorus (SRP) in runoff from moist-soil wetlands and adjoining croplands did not differ (P = 0.95), concentrations of total and particulate phosphorus, nitrate-nitrogen, and total suspended solids were 42, 52, 86, and 89% lower (P < 0.03) in runoff from moist-soil wetlands. However, the load (kg ha-1) of SRP from moist-soil wetlands was six times (P = 0.08) greater than load from croplands. Estimated loading rate of total phosphorus from moistsoil wetlands (2.36 kg ha-1 year-1) was greater than the rate reported by regulatory agencies in Mississippi (1 kg ha-1 year-1), but field replication is needed to verify these results. Nearly 80% of the total loads exported from moist-soil wetlands occurred during < 30% runoff events. Retention of runoff from storm events may reduce phosphorus loss from moist-soil wetlands while not interfering with conservation objectives.

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