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The national mammal of the United States, the American Bison (Bison bison) was once nearly extinct. Populations have recovered to the degree that thousands roam the Great Plains today. Due to their large numbers and body size, this species has an oversized impact on the ecological communities where it lives and is considered a keystone herbivore in modern North American grasslands. This study explores the detailed, seasonally resolved, paleoecology of seven bison from the Greater Yellowstone Ecosystem during the Late Holocene through stable isotope analyses and species niche modeling. Isotopic analyses of δ13C, δ15N, and δ18O reveal that bison within high elevations regularly foraged on C3 vegetation while traveling among the valleys and ridges of ecoregions similar to those of modern-day. Species distribution models provide a bimodal niche, with best-suited temperatures of 4-8°C and 16-26°C, and topographic ranges of 250-800m and 2,000-4000m.

Coastal ecosystems comprise a relatively small area of the ocean, yet they play a disproportionate role in greenhouse gas (carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O)) and nutrient cycling. Vegetated coastal ecosystems (e.g., mangroves, salt marshes, and seagrasses) are key drivers of coastal greenhouse gas and nutrient cycling because of their environmental characteristics (e.g., shallow depths, organic matter rich sediments, etc.). My dissertation addresses the role of vegetated coastal ecosystems in greenhouse gas budgets and biogeochemical cycling. In Chapter 1, I conducted a meta-analysis to quantify the global emissions of CH4 from mangrove, salt marsh, and seagrass ecosystems. Here I show that mangrove ecosystems contribute the most CH4 out of these vegetated areas to the global marine CH4 budget. Further, while a well-known negative relationship between salinity and CH4 fluxes exists for salt marshes globally, this relationship does not hold for mangrove or seagrass meadows, suggesting that other environmental drivers are more important for predicting CH4 fluxes in these ecosystems. In Chapter 2, I present in situ fluxes of CH4 and N2O across the sediment-water interface as well as air-sea fluxes in seagrass meadows and adjacent non-vegetated sediments in two temperate coastal lagoons. Here I demonstrate that seagrass meadows can be sources or sinks of CH4 and that N2O uptake can enhance carbon sequestration in seagrass meadows by ~10%. In Chapter 3, I quantify fluxes of dissolved inorganic carbon, nitrogen, and phosphorous across the sediment-water interface in seagrass meadows and adjacent non-vegetated sediments in the same two coastal lagoons. I found that both seagrass and non-vegetated sediments exhibited dissolved inorganic carbon emission and denitrification, and that dissolved inorganic phosphorous fluxes varied by site and not with vegetation presence. This dissertation highlights the dynamic role coastal ecosystems play in biogeochemical cycling and the importance of vegetated coastal ecosystems in coastal greenhouse gas budgets. / 2024-10-03T00:00:00Z

Thesis (M. Sc. (Geology)) -- University of Limpopo, 2020 / The Glentig, Alma and Swaershoek Formations were deposited after the emplacement of the Bushveld igneous complex (BIC). The sediments accumulated in what is termed as the proto-basin of the Waterberg Group. The Glentig Formation is an unconformity bounded formation that is overlain by the Swaershoek and Alma Formations of the Waterberg Group. This study revisited the stratigraphy and put perception on the petrography, lithofacies, provenance, paleoweathering, tectonic setting and source rock characteristics of the lower parts of Waterberg Group (Swaershoek and Alma Formations) and Glentig Formation. The methodologies employed in achieving the aforementioned goals include stratigraphical analysis, petrographical and modal composition analyses, lithofacies analysis and geochemical analysis. In the study area (northeast of Modimolle town), the Glentig Formation lies or bounded between the Swaershoek Formation and Schrikkloof Formation of the Rooiberg Group. The Glentig, Swaershoek and Alma Formations attained a maximum thickness of about 400 m, 300 m and 190 m, respectively. Based on the stratigraphical analysis, the Swaershoek, Alma and Glentig Formations can be correlated. The basis for the correlation rests solemnly on the similarities in the lithological characteristics that can be found in the three formations. Six facies were identified based on lithofacies analysis. The lithofacies are grouped into 2 facies association (FA1 and FA2). The two facies associations are FA1: Conglomerate and massive sandstone, and FA2: Cross-bedded sandstone, and planar cross-bedded sandstone. Sedimentological characteristics of the identified facies associations are interpreted as debris flow, and longitudinal and transverse bars (fluvial channel deposits). Petrography and modal composition analyses indicate that the detrital components of the sandstones are dominated by monocrystalline quartz, vi feldspar and lithic fragments. The sandstones of the Swaershoek, Alma and Glentig Formations can be classified as subarkosic arenite and lithic arkosic arenite. Also, provenance analysis indicates that the sandstones are derived from both felsic igneous provenance and intermediate igneous provenance. The modal composition analysis and geochemical tectonic setting discrimination diagrams show that the sediments are from both the passive and active continental margin tectonic settings. Also, the geochemical data of major and trace elements suggested that the studied formations have been derived from the same provenance source area. The indices of weathering indicated that the studied rocks have been subjected to moderate to the high degree of chemical weathering. / Mining Qualification Authority (MQA)

<p>The Athabasca oil sands produce 20% of Canada’s oil, which in turn creates trillions of cubic meters of waste. The Alberta government mandates that oil sands land be reclaimed to its natural state after mining has occurred. Syncrude Canada is currently creating a novel freshwater fen on top of a composite tailings (CT) deposit as a pilot large-scale reclamation project. CT are both microbially and sulfur rich, in addition, the fen could be a potential source of labile organics and sulfate reducing bacteria which could further stimulate sulfur cycling by microorganisms with the potential to stimulate H₂S_(g) generation, a health and safety concern. Therefore, this thesis examines three main research questions regarding this H₂S production within the Sandhill reclamation fen: 1) Is H₂S generation widespread within the porewaters of the CT and sand cap of the developing Sandhill Fen reclamation project? 2)<strong> </strong>Do microbial metabolisms capable of metabolizing Fe and S linked to H₂S generation occur within CT and sand cap of the developing Sandhill Fen? and 3) Will seasonality and ongoing fen construction impact H₂S generation?</p> <p>Field and experimental results herein discuss potential microbial and abiotic metabolisms and pathways that effect sulfur and iron cycling that could affect hydrogen sulfide generation within the composite tailings and developing fen during three seasonal sampling campaigns from June 2010 to July 2011. Results indicate that detectable H₂S_(aq) occurred in the fen porewaters during each sampling campaign, with a trend of increasing H₂S_(aq) concentrations as construction of the fen progressed. Further, enrichment results indicate that microbial sulfur and iron redox reactions are likely affecting the H₂S_(aq) generation. Experimental microcosm results indicate that the CT may contain unstable sulfur species that can contribute to H₂S_(aq) generation and sequestration in the CT as pyrite. Additionally, the evolution of the Sandhill Fen changed the microbial communities that were present <em>in situ</em> as well as shifted dominance of species type in environmental microbial enrichments. The putative function of these bacteria show a shift from autotrophy to increased heterotrophic metabolisms as the fen is being constructed, suggesting the addition of labile organic substrates from the peat and woody debris are both changing the dominant metabolisms and well as increasing microbial diversity to the underlying CT and sand cap of Sandhill Fen. Results of this thesis established widespread microbial Fe and S metabolisms within CT for the first time and indicated that fen reclamation will alter microbial activity with implications for S cycling within CT. Although this thesis covers a short sampling time frame, it is clear that H₂S_(aq) generation is an important factor to consider during large scale CT reclamation. While microorganisms are present and could be impacting Fe and S cycling, the CT materials should be investigated further in regards to their potential for H₂S_(aq) generation. More consideration should be given to inhibiting H₂S_(aq) generation or supporting FeS formation within the reclamation fen.<strong></strong></p> / Master of Science (MSc)

This thesis is comprised of three parts. In the first part, we investigated zyklophin, a novel selective short-acting kappa opioid receptor (KOPR) antagonist, and its effects on scratching behaviors in Swiss-Webster mice. We investigated whether zyklophin was able to induce scratching in a dose-dependent fashion, and whether this scratching behavior could be blocked by pretreatment with nor-binaltorphimine (norBNI). We also used KOPR -/- mice to further clarify the role of the KOPR in this behavior. In the second part, we examined the role of the divergent amino acid at position 6.58 in the mu opioid receptor (MOPR) and the KOPR on the binding of beta-funaltrexamine ß-FNA). ß-FNA is an irreversible antagonist at the MOPR and a reversible agonist at the KOPR. Utilizing the recently published crystal structures of the MOPR and KOPR, we collaborated with Dr. Lei Shi, who employed molecular modeling to choose a residue in transmembrane helix 6 (TM6) to mutate at the same position in MOPR and KOPR. We then characterized the mutants by performing [3H]diprenorphine binding, competition binding by unlabeled &beta;-FNA, irreversible ß-FNA binding and [35S]GTPγS binding. In the third part, we investigated the concept of functional selectivity, or ligand bias, at the KOPR. We studied 23 different KOPR agonists in vitro using [35S]GTPγS binding as a measure of G protein activation and the on-cell Western (OCW) as a measure of ß-arrestin-mediated receptor internalization at the human KOPR (hKOPR), and from the results, chose 13 ligands to study at the mouse KOPR (mKOPR). We then selected biased ligands from the in vitro mKOPR results and studied their effects on scratching behavior, inhibition of pain behaviors and dysphoria as measured by the conditioned place aversion (CPA) test. We predicted that the G biased ligand would produce analgesia and anti-scratching effects at lower doses than would produce aversion in the CPA test, since analgesia has been shown to be G protein mediated and CPA has been shown to be arrestin mediated. Our first set of studies revealed that zyklophin (0.1, 0.3 and 1 mg/kg, s.c., behind the neck), induced vigorous scratching in a dose-dependent manner. 0.3 mg/kg zyklophin induced 150 scratches over a 30 minute period. The scratching was not blocked by pretreatment with 20 mg/kg norBNI (i.p.) 18-20 hours before injection of 0.3 mg/kg zyklophin s.c. in the nape of the neck. The scratching also persisted in KOPR -/- mice, in which the absence of the KOPR was confirmed by [3H]U69,593 binding (2 nM). In our second set of studies, we mutated the lysine at position 303 in the MOPR to glutamic acid (K303E), and the glutamic acid at the equivalent position in the KOPR to lysine (E297K). We transfected these mutant receptors into mouse neuroblastoma (N2A) cells. We found that the mutations had no effect on [3H]diprenorphine binding affinity or competition binding with [3H]diprenorphine and &beta;-FNA indicating a functional intact opioid receptor. The mutations also did not affect [35S]GTPγS binding EC50 or Emax values. The mutation K303E in the MOPR reduced irreversible binding by 2/3 compared to the wildtype MOPR. Finally, we found that there were several ligands that displayed bias at the hKOPR and the mKOPR. At the hKOPR, using dynorphin A as the reference ligand to calculate bias, ICI-199441 was the only G biased ligand, while enadoline, nalbuphine, pentazocine, salvinorin A, tifluadom and butorphanol were arrestin-biased. At the mKOPR, only salvinorin B methoxymethyl ether (MOM-SalB) was G-biased, and salvinorin B ethoxymethyl ether (EOM-SalB), ICI-199441, U50,488H, nalfurafine and 12-epi-salvinorin A (12epiSalA) were ß-arrestin-biased. Enadoline and salvinorin A were slightly arrestin biased with respect to dynorphin A. From the in vitro data at the mKOPR, we selected MOM-SalB as our G biased ligand, U50,488H as our arrestin biased ligand and additionally chose to investigate nalfurafine due to its use in clinical studies. We hypothesized that U50,488H and nalfurafine would produce aversion at lower doses than analgesia or anti-pruritic effects. We found that nalfurafine was the only ligand studied to have a separation between doses that produced analgesia and anti-scratching effects, with A50 values of 5.8 and 8 μg/kg, respectively, and only produced significant dysphoria at a dose of 20 μg/kg. U50,488H and MOM-SalB produced dysphoria at all doses tested (0.25-10 mg/kg and 0.01-0.3 mg/kg, respectively). U50,488H produced a dose-dependent analgesia and anti-scratching with A50 values of 0.58 mg/kg and 2.07 mg/kg, respectively. MOM-SalB was more potent than U50,488H in producing dose-dependent analgesia and anti-scratching, with A50 values of 0.017 mg/kg and 0.070 mg/kg, respectively. Therefore, we concluded that the in vitro bias is not able to accurately predict in vivo behaviors, and nalfurafine is the first selective full agonist at the KOPR to show ligand bias in vivo. / Pharmacology

In this dissertation I describe how coupled internal cycling and external forcing from the atmosphere and climate can regulate the dynamics of nitrogen (N) loss from forest watersheds. I address three major gaps in our understanding of the global N cycle: 1) the role of dissolved organic N (DON) in internal N cycling in low-N ecosystems; 2) The influence of atmospheric pollution on DON production and loss from forests; and 3) the inherent climate sensitivity of forest N cycling and loss. In chapter 2, I present the results of a study of DON spiraling that showed enormous capacity for stream microorganisms to immobilize and transform organic nutrients. Although most DON in surface waters is highly refractory products of SOM dissolution, this study revealed very tight internal cycling of DON at the sediment interface and suggested significant production of DON in the hyporheic zone. Most remarkably, this DON was not expressed in stream waters, supporting the idea that watershed DON losses would have been higher in the absence of pronounced benthic demand. The experiments also suggested that coupled dynamics between DOC and DON spiraling may be altered under conditions of elevated N supply. Chapter 3 challenges the idea that soil organic matter (SOM) and its dissolved products are stoichiometrically static as N pools accumulate. Using a broad geographic survey of forest streams, I show that DON losses increase as a consequence of N pollution and that this occurs through a disproportionate enrichment of N on dissolved organic matter rather than alteration of soil and dissolved carbon dynamics. These results have implications for N limitation in forests and aquatic systems. In particular, DOC: DON ratios of DOM draining N-saturated forests were strikingly low suggesting possible increases in DOM bioavailability with increasing N supply. Chapter 4 provides insight into how local forest nutrient cycles may be organized by synchronous global-scale climate-atmosphere dynamics. This study of long term (30 yr) hydro-chemistry from reference forest watersheds provides an integrated example of the overall climate sensitivity of N cycling and underscores the importance of complex synergies between simultaneous vectors of global change. Results from this study argue that the combined influence of N pollution and warming are likely to have pronounced long-term effects on ecosystems globally. / Ph. D.

Headwaters may be small relative to other aquatic ecosystems, but they are neither simple nor static environments. Heterogeneous stream corridors constitute the majority of river network length and regulate cycling of carbon and oxygen as they expand and contract their connections across the landscape. Though headwater streams integrate many biogeochemical signals from the watersheds they drain and provide important ecosystem services, their diverse habitats and dynamic changes in wet length have been under- examined compared to dendritic, perennial streams. This oversight complicates efforts to identify biogeochemical patterns at larger scales. This dissertation sets out to expand our knowledge of stream biogeochemical responses to variable connections both within the channel and the wider stream corridor. First, I investigated how the presence and arrangement of different habitat patches in the stream corridor affected overall emissions of carbon dioxide (CO2) and methane (CH4) from sub-watersheds of a forested mountain stream network. To do this I measured concentration and flux of both gasses along and around 4 streams, including dry reaches and adjacent vernal pools as well as flowing water. I found that emissions were highly variable over space and time; in particular, the presence of a vernal pool enhanced total carbon emissions from the stream corridor. Next, to quantify carbon cycling and export from a non-perennial headwater stream, I monitored concentrations of CO2 and dissolved organic carbon (DOC) at the stream outlet. I found that CO2 concentration had a negative relationship with stream discharge, and that exports of both CO2 and DOC were driven by storms reconnecting isolated surface water reaches. I also found that carbon biogeochemistry of intermediate flow states were unique from driest and highest-flow conditions. Finally, to explore how isolated pools in the stream channel respond to flow decrease and cessation, I measured dissolved oxygen (DO) as well as CO2 and CH4 from persistent pools of two non- perennial streams throughout an unusually dry summer and fall. I found that hypoxia was common in all isolated pools, but swings in DO were not consistent between pools even of the same stream. In using diel changes in DO to estimate metabolism, I also found that ecosystem respiration varied by stream, but gross primary production was more driven by stream surface water connectivity. Climate change is inducing many new patterns in stream hydrology with critical implications for biogeochemical activity, from reducing durations of connectivity to causing stronger storms. Improving our understanding of how surface water and landscape connectivity both influence the movement of carbon within and through streams is essential to resolving questions about the contributions of freshwaters to the global carbon cycle. / Doctor of Philosophy / Headwater streams may seem inconsequential to larger ecosystem processes due to their small size. However, the majority of a river's network length, or the total length of all the streams and rivers from spring to ocean, is made up of headwater streams. The widespread presence of headwater streams over all types of land, along with the unique layout of different aquatic habitats near streams and the fact that small streams often grow and shrink in length, mean that studying headwaters can tell us many things about how energy moves through ecosystems. This dissertation explores how we can use changing headwater connectivity to understand how carbon moves through ecosystems. Connectivity in aquatic science refers to how water can move through space in ways that rocks and trees and even many animals cannot. This idea is useful because water carries things around as it moves, and its presence or absence enables reactions that are essential for the cycling of energy and nutrients. For instance, when water moves from high ground to low ground, it navigates through soil and holes in the ground; it may get slowed down at flat spots where little pools form. I measured emissions of carbon dioxide and methane from streams as well as soils, holes, and pools near mountain streams to try to understand how the path water takes influences how much carbon dioxide and methane escapes into the air. My measurements were surprisingly different depending on where and when I took them. I found that if a seasonal pond is connected to a stream channel, the stream will emit more greenhouse gasses than if the pond goes dry. Connectivity can also describe if water moves continuously along a stream, or if the stream goes dry in places and is then disconnected from different parts of itself. I asked how a stream becoming disconnected affected carbon dioxide emissions as well as the movement of dissolved organic carbon, a food source for microorganisms. I found that the less water moving through the stream channel, the higher carbon dioxide concentrations were. I also found that storms move both carbon dioxide and dissolved organic carbon out of streams quickly, even if the stream had been disconnected. Finally, I investigated the water that is left when streams disconnect. I measured dissolved oxygen, carbon dioxide, and methane in isolated pools of two disconnected streams. By tracking how microbes and algae consume and produce oxygen when a stream is not flowing, I can understand how these lifeforms adapt. I found that isolated pools frequently have very low levels of dissolved oxygen. This means that microorganisms in the pools have to use special ways of getting energy, which in turn affects how different forms of carbon move through the stream ecosystems. Headwater stream ecosystems are very sensitive to small changes in flow and precipitation; however, climate change means that streams are going dry more often than they used to. My findings contribute to our understanding of how changes in stream connectivity have many biological effects that are important for water quality and ecosystem health.

In freshwater networks, the sources, movement, and cycling of carbon and nutrients are shaped both by in-stream processes and the surrounding landscape. Streams receive and transport materials from upstream and terrestrial sources that support in-stream ecosystem processes and regulate downstream water quality. Understanding how these processes within a stream alter downstream carbon and nutrient fluxes is needed to assess the functional role of lotic ecosystems on the landscape. Further, predictions of how materials cycle and move throughout freshwater networks are derived from measurements at the stream reach scale which deliberately avoid complex geomorphology such as stream confluences. As a result, the impact of stream confluences on in-stream ecosystem processes and the fate of carbon and nutrients in freshwater networks has been overlooked. In this dissertation, I seek to address the following questions: (1) How are coupled carbon and nitrogen cycles altered by land use? (2) To what extent can rates of in-stream organic carbon removal inform our understanding of the role of streams in landscape carbon fluxes? (3) How are carbon metabolism and nutrient uptake altered downstream of a stream confluence? (4) How do confluences alter the transport and fate of carbon and nutrients within a freshwater network? In Chapter 2, I showed that the fate of organic carbon and nitrate are similar in headwater streams across the United States. Organic carbon travels longer distances before being respired in agricultural and urban streams compared to reference streams, suggesting that human modifications to landscapes impact carbon cycling and transport in streams. In Chapter 3, I demonstrated how rates of in-stream organic carbon removal can be used to quantify terrestrial-aquatic linkages and showed that laboratory bioassays systematically underestimate ecosystem organic carbon fluxes compared to whole-stream metabolism measurements. In Chapter 4, I conducted whole-ecosystem manipulation experiments to assess how ecosystem processes are altered by a confluence. I found that carbon metabolism and phosphorus uptake are suppressed downstream of a confluence and that rates of organic carbon uptake are spatially variable throughout a confluence mixing zone. In Chapter 5, I examined potential reach-scale and watershed-scale drivers to explain patterns of organic matter and nutrient chemistry downstream of confluences throughout a stream network. Reaches downstream of confluences were geomorphically and biogeochemically distinct from upstream reaches, and differences in upstream and tributary reach chemistry or drainage area did not explain patterns of biologically reactive parameters at confluences. My dissertation highlights the importance of in-stream ecosystem processes in driving the cycling and downstream fate of carbon and nutrients. I show how rates of whole-stream carbon metabolism can be used to better constrain terrestrial-aquatic organic carbon fluxes. I investigate the potentially disproportionate role of ecosystem interfaces, namely stream confluences, in determining the cycling and fate of carbon and nutrients in freshwater networks. This work challenges assumptions around controls over water quality in freshwater networks and asserts that by ignoring (1) contributions of all in-stream processes to whole-ecosystem function and (2) how confluences alter those processes, we risk misrepresenting the role of running waters in determining the fluxes and fate of carbon and nutrients from the reach- to the network-scale. / Doctor of Philosophy / Streams receive and use materials from upstream and the surrounding landscape to fuel in-stream ecosystem processes (e.g. carbon and nutrient cycling). Understanding how these processes within a stream alter concentrations of carbon and other nutrients is needed to assess how the ecosystem is functioning and what the consequences are on water quality downstream. Further, predictions of how materials cycle and move at the scale of streams networks are derived from measurements at the stream reach scale. As a result, the impact of stream confluences (i.e., where two streams meet and mix) on in-stream carbon and nutrient cycling and the consequences on downstream water quality has been overlooked. In this dissertation, I seek to address the following questions: (1) How are carbon and nitrogen cycles linked in streams and how those links altered by land use? (2) How can rates of in-stream carbon cycling inform our understanding of the role of streams in landscape carbon budgets? (3) How are carbon and nutrient removal altered downstream of a stream confluence? (4) How do confluences alter water chemistry within a freshwater network? In Chapter 2, I showed that organic carbon and nitrate shared similar fates in streams across the United States. Organic carbon traveled longer distances before being respired in agricultural and urban streams compared to natively-vegetated streams, suggesting that human modifications to landscapes impact carbon cycling and transport in streams. In Chapter 3, I demonstrated how rates of in-stream organic carbon removal can be used to understand land-stream connections. In Chapter 4, I conducted whole-ecosystem experiments to assess how carbon and nutrient removal are altered by a confluence. I showed that carbon metabolism and phosphorus removal are suppressed downstream of a confluence and that rates of organic carbon removal are spatially variable throughout where water from the two streams are mixing. In Chapter 5, I examined potential drivers to explain patterns of organic matter and nutrient chemistry downstream of confluences throughout a stream network. Reaches downstream of confluences were physically, chemically, and biologically distinct from upstream reaches and differences in upstream and tributary reach chemistry or drainage area did not explain patterns of water chemistry downstream of confluences. Overall, my dissertation highlights the importance of processes within a stream in driving carbon and nutrient cycling, and how rates of whole-stream carbon cycling can be used to better understand connections between streams and the surrounding landscape. I investigate the role of stream confluences in determining the cycling and downstream fate of carbon and nutrients in freshwater networks. This work shows that ecosystem functioning and downstream water quality in freshwater networks are affected by processes occurring within streams and by the interfaces between streams and other ecosystems (e.g., land-water interfaces, stream confluences).