Seabed resuspension can impact organic matter fate and water column biogeochemistry in coastal environments. Cycles of erosion and deposition can, for example, affect remineralization rates, seabed-water column fluxes of dissolved oxygen and nutrients, and light attenuation. Yet, models that incorporate both sediment transport and biogeochemical processes are rare, and nearly all neglect the effect of resuspension on oxygen and nutrient dynamics. Development of a novel tool, i.e. a coupled hydrodynamic-sediment transport-biogeochemical model, allowed for an investigation of the role of resuspension on oxygen and nitrogen dynamics within three distinct coastal environments. Called HydroBioSed, the coupled model was built within the Regional Ocean Modeling System and accounted for physical processes including the deposition and erosion of inorganic sediment and particulate organic matter from the seabed, as well as the flux of dissolved inorganic chemical species at the seabed-water column interface. The model also considered biogeochemical reactions including the remineralization of organic matter and oxidation of reduced chemical species, in both the seabed and the water column. HydroBioSed was first implemented as a one-dimensional vertical model for the Rhône River subaqueous delta. Results indicated that cycles of erosion and deposition altered rates of diffusion between the seabed and water column. This process increased fluxes of oxygen into the seabed during erosional periods, and the effect remained significant when results were averaged over time scales longer than individual events. The coupled model was next implemented in three-dimensions for the riverine-influenced northern Gulf of Mexico shelf. In this environment, resuspension-induced effects on bottom water biogeochemistry were dominated by increases in remineralization. Specifically, remineralization of resuspended organic matter increased oxygen consumption and ammonium production, especially in shallow areas where bed stresses were typically high. Finally, HydroBioSed was implemented for the Chesapeake Bay estuary and adapted to account for light attenuation by sediment and resuspended particulate organic matter. Here, resuspension-induced turbidity caused a down-stream shift in primary production. This shift, combined with remineralization of resuspended seabed organic matter, caused oxygen concentrations to decrease and ammonium concentrations to increase throughout the estuary. Overall, use of a novel coupled hydrodynamic-sediment transport-biogeochemical model, showed that cycles of erosion and deposition impact water column biogeochemistry, but the specific effects of resuspension varied across the three distinct environments studied.

Subtropical coastal wetlands are at the forefront of sea-level rise induced vegetation transition. As sea level rises, increased tidal range brings mangrove propagules further inland, promoting the transition of herbaceous wetlands to woody swamps. Freshwater wetland soils are highly reduced and are major sources of non-anthropogenic methane emissions. Sulfate, the third most prevalent ion in seawater, provides an alternative anaerobic respiration pathway to freshwater wetlands, potentially decreasing methane emissions. However, underground biogeochemical conditions are difficult and time-consuming to detect from a land manager's perspective. Chapter 2 assessed the soil biogeochemistry spanning marsh-mangrove ecotones along three rivers on the west coast of Florida to determine if patterns were consistent across the landscape and if visible shifts in vegetation corresponded to belowground processes. Furthermore, how biogeochemical properties respond to salinity was addressed in an intact core set-up from two marsh-mangrove transition in Chapter 3. Results indicated landscape-scale patterns in soil biogeochemistry differed significantly by river and were most strongly correlated with soil organic matter content, regardless of vegetation community or salinity regime. Methane production was observed in moderate- (S = 12) and high- (S = 34) salinity mangrove communities. The vegetation ecotone experienced seasonally variable salinity and did not serve as a true biogeochemical intermediate between the marsh and mangrove communities. Overall, soil origin was determined to be the most important predictor of the biogeochemical response to elevated salinity in chapter 3. Bacterial abundance showed a moderate response to increased salinity 10 days into the manipulations. These studies indicate how biogeochemistry along the marsh-to-mangrove ecotone will not respond in the same ways to sea-level rise at the landscape level.

From the time of their discovery in the early 1980's, hyperthermophilic microorganisms have been at the center of intense research to describe their diversity as well as the extreme geologic environments they inhabit. Although much has been learned about the metabolism of a select few pure culture isolates, very little is known about the great diversity of their metabolic potential, particularly in situ. Recent models for the fate of short-chain organic acids, and presumably aromatics and long-chain fatty acids, indicated that they must diffuse out of hydrothermal environments before being metabolized because no hyperthermophilic microorganisms in pure culture or in actual sediment or rock were known to utilize these substrates. In this study, the metabolism of the key fermentation product, acetate, as well as aromatic compounds was investigated in the hyperthermophilic microorganisms, Ferroglobus placidus and Geoglobus ahangari. In addition, the fate of 14C-radiolabeld organic compounds was evaluated in hydrothermal sediments collected from a shallow marine vent on Vulcano, Italy. F. placidus and G. ahangari grew at 85°C in anaerobic medium with acetate as the sole electron donor and poorly crystalline Fe(III) oxide as the electron acceptor. Additionally, F. placidus was capable of using a variety of aromatic compounds as the sole electron donor for the reduction of Fe(III). In hydrothermal sediments from Vulcano, Italy, the radiolabeled acetate, palmitate, and glucose were completely oxidized to carbon dioxide coupled to sulfate reduction. Radiolabeled L-glutamate and benzoate were primarily oxidized to carbon dioxide, although incompletely. These results are the first indication that complex organic matter can be oxidized to carbon dioxide by hyperthermophilic microorganisms, and thus a complete carbon cycle may be modeled for hydrothermal systems.

No description available.

Northern permafrost regions contain vast stores of organic carbon (OC) and rapidly rising temperatures make these frozen soil OC stores increasingly vulnerable to thaw and mobilization. While considerable attention has been given to carbon export from large Arctic river systems and lowland areas, significant gaps remain in characterizing OC quality and export in headwater catchments and in alpine regions. Northern wetlands and lakes have been highlighted as critical areas for OC storage and processing, and while ubiquitous in alpine regions, there have been few studies to examine their integrated role in DOM dynamics at the watershed scale. This study examines controls on DOM quality and concentration in Wolf Creek Research Basin (WCRB), Yukon, over four years using repeat spatial sampling. Optical indices were used to assess changes in DOM quality from different landscape types including permafrost influenced alpine headwater streams, lake and wetland complexes, and the catchment outlet in a low elevation boreal forest. Results indicate that DOM export in WCRB is transport-limited with greater exports during years with greater snowpack and higher spring discharge. Principal component analysis revealed that the predominant driver of DOM quality was seasonality, but landscape type was also an important control during the open water season. High SUVA254 /HIX in headwater streams indicated primarily humic, terrestrially derived DOM while high BIX and comparatively lower SUVA254 /HIX in a mid-catchment lake indicated autotrophic production of new DOM. DOM quality at the catchment outlet reflected a mixture of upstream sources and increased influence of groundwater. The results of this study highlight the importance of evaluating DOM quality in all seasons and provide insight into the diverse nature of DOM at a watershed scale. These characterizations help to elucidate potential DOM response in a rapidly changing and understudied environment. / Thesis / Master of Science (MSc)

Soil organic matter decomposition is a critical process that affects nutrient cycling, CO2 emissions, and carbon storage in terrestrial environments. Recent evidence suggests reactive manganese (Mn) phases, potent oxidants that depolymerize compounds like lignocellulose in soil organic matter, act as critical drivers of organic matter decomposition in soil and sediment environments. Furthermore, oxic-anoxic interfaces (OAIs) have been shown to be crucial hotspots for the formation of reactive Mn(III) species and associated organic matter degradation. However, the extent to which microbially mediated Mn(III) formation and subsequently Mn(III)-driven organic matter oxidation depends on Mn availability remains largely unknown. Additionally, the relative contributions between abiotic and biotic Mn-mediated organic matter oxidation pathways have been poorly quantified. In this study, we quantified the impact of Mn availability on Mn-mediated particulate organic carbon (POC) oxidation across the redox gradient and the specific contributions of abiotic and biotic reactions. To accomplish this, we established soil redox gradients in diffusion reactors and varied Mn(IV) oxide concentrations in the anoxic zone. The ensuing reductive mobilization of Mn(IV) oxides in the anoxic zone was meant to manipulate Mn(II) supply towards the OAI. The addition or exclusion of microbial inoculum allowed us to examine the abiotic contributions to Mn translocation and POC oxidation. Mn(II) translocation, Mn(III) formation, and C transformations across the redox gradient were quantified over a 12-week incubation period. Wet-chemical extractions combined with Mn XANES indicated that reactive Mn(III) formation at OAIs increased with enhanced Mn availability. Comparison of inoculated and uninoculated treatments revealed microbial Mn oxide reduction to be the critical driver of Mn translocation to oxic-anoxic interfaces. Subsequent enhanced Mn availability at the OAI enhanced POC oxidation and increased CO2 production rates due to enhanced microbial translocation and primarily attributed to microbially mediated Mn(III) formation. Our study emphasizes the importance of Mn(III)-mediated C oxidation across OAIs and its dependence on the provision of Mn(II) through microbial Mn reduction. Combined, our results show Mn–C coupled cycling across redox gradients as a critical biogeochemical process that has profound impacts on ecosystem scale soil C storage and CO2 fluxes.

<p>Water-quality in freshwater ecosystems is linked to metal contaminant sequestration and transport by suspended aquatic floc. This doctoral thesis investigates the combined microscale biogeochemical processes as well as macroscale hydrodynamic mechanisms controlling trace metal dynamics of freshwater floc, through comparative assessments of floc versus bottom bed sediment metal(loid) (Ag, As, Co, Cu, Ni and Pb) sequestration/mobilization across aquatic ecosystems ranging in physico-chemistry (e.g. pH, organic carbon, Fe/trace metal concentrations) in the Boreal Forest Region of Ontario and under variable energy-regimes (i.e. calm, windy, prolonged-storm) in a shallow wave-dominated urban beach in Lake Ontario, Canada.</p> <p>The results establish differential biogeochemical controls in suspended floc versus bed sediments influencing the abundance, reactivity and type of Fe minerals affecting trace metal abundance and solid-phase partitioning patterns between these two compartments. Specifically, this work demonstrates a microbial underpinning to floc collection of amorphous Fe oxyhydroxides (FeOOH) controlling floc metal sorption, retention and overall metal concentrations that are significantly greater in suspended floc than bed sediment. In contrast, crystalline Fe oxides (FeOx) dominate sediment metal retention, due to reductive dissolution and/or mineral aging of FeOOH, where sediment solid-solution metal partitioning is more influenced by system physico-chemistry (i.e pH). Further, rapid fluctuations in energy regime influencing re-suspension/settling of floc and sediment (i.e. surficial fine-grained lamina (SFGL) versus underlying consolidated sediments) result in temporal and spatial hydrodynamic-dependent mixing of Fe mineral phases, altering metal abundance and solid-phase metal partitioning in each compartment.</p> <p>Collectively, findings of this innovative integrated thesis work provide new understanding of the physical and biogeochemical controls on Fe cycling/mineral transformations between floc and bed sediments, ultimately affecting trace metal iv behaviour between these compartments and fate in freshwater environments. This insight has important implications for policy development in improving risk management of aquatic systems under varying physico-chemical and hydrodynamic conditions.</p> / Doctor of Philosophy (PhD)

<p> Before their death, plant tissues undergo the essential process of senescence. Senescence is characterized by a coordinated recovery of nutrients and their retranslocation to surviving structures, such as seeds of annual plants. In monocarpic crops (e.g., maize, wheat, and barley), timing and efficiency of senescence can impact yield and grain quality. However, our understanding of senescence regulation and nutrient remobilization is limited, and protein- and metabolite-level analyses of the process are scarce, particularly in crops. To improve understanding of physiology in barley (<i> Hordeum vulgare</i> L.) leaf senescence, a systems-level comparison of near-isogenic germplasm, late-senescing/low-grain protein content variety 'Karl' and an early-senescing/high-grain protein content line ('10_11'), was performed. Protein levels in flag leaves (topmost leaves) of 'Karl' and '10_11' were compared at 14 and 21 days past anthesis (dpa) using both two-dimensional fluorescence difference gel electrophoresis (2-D DIGE) and shotgun proteomic approaches. Conspicuously, proteins with roles in plant pathogen defense were present at higher levels in '10_11' as compared to 'Karl'. These included membrane receptors, glucanases, pathogenesis-related and disease resistance proteins. Proteins involved in protein degradation and organic acid/amino acid metabolism were upregulated in line '10_11' as compared to 'Karl', expectedly in early-senescing leaves involved in nitrogen remobilization. Metabolite levels were compared in the same plant material as protein levels except that analyses were also performed at anthesis (0 dpa), using mass spectrometry-based non-targeted metabolic profiling techniques. Metabolites with higher abundance in early-senescing line '10_11' included gibberellin catabolites, Yang cycle intermediates and intermediates of jasmonic acid biosynthesis. These differences were mostly observed at 0 dpa, indicating an early shift in phytohormone metabolism that may be important for senescence regulation and plant disease resistance between 'Karl' and '10_11' during the senescence phase, as jasmonic acid and ethylene have roles in plant pathogen defense. Overall, proteomic and metabolomic analyses performed here shed new light on the regulation of the senescence process, on the importance of plant defense against pathogens during senescence, and possibly on crosstalk between senescence regulation and pathogen defense. Proteins and metabolites identified in this study may become targets for ongoing efforts at improving crop yield, quality and environmental stress resistance. </p>

Replicate column experiments were done to quantify the effects of temperature and bacterial motility on advective transport through repacked, but otherwise unaltered, natural aquifer sediment. Greater microsphere removal observed at the higher temperature agreed with the physical-chemical model, but bacteria removal at 18°C was only half that at 4°C. The sticking efficiency for non-motile A0500 (4°C) was over three times that of the motile A0500 (18°C), 0.073 versus 0.022 respectively. Motile A0500 bacteria traveled twice as far as non-motile A0500 bacteria before becoming attached. Once attached, non-motile colloids detached on the time scale of 9 to 17 days. The time scale for detachment of motile A0500 bacteria was shorter, 4 to 5 days. Results indicate that bacterial attachment was reversible and detachment was enhanced by bacterial motility. The kinetic energy of bacterial motility changed the attachment-detachment kinetics in favor of the detached state.

<p> To quote famous physicist and Nobel laureate, Dr. Richard Feynman, &ldquo;&hellip;everything that living things do can be understood in terms of the jigglings and wigglings of atoms.&rdquo; It is these jigglings and wigglings of atoms that form the focus of my dissertation, which studies the structural dynamics of two different allosteric proteins through computational simulations. Protein allostery is a field that has been investigated widely. But the structural details of how signals initiating at one site transmit through the network of residues in different proteins and result in the alteration of their functional states, still remains largely unresolved. Here, we independently study the kinesin motor protein and the neuromuscular acetylcholine receptor (nAChR) &ndash; both of which play crucial roles in cellular signaling. Kinesins are intracellular porters, carrying organelles, molecules and other cargo within the cell, while nAChRs are transmembrane receptors that aid in intercellular communication at nerve-to-muscle synapses. These two protein families are structurally and functionally very different, but both are allosteric in nature, with interesting protein dynamics that efficiently convert chemical energy to mechanical motions in order to perform their cellular functions.</p><p> The total timescale of an entire allosteric transition is currently too long for complete all-atom molecular dynamics simulations. Thus, in this dissertation, for both the projects, we begin at different equilibrium states of the proteins and carry out comparative analyses of conformation and dynamics at those states, which aids in elucidating the structural and functional correlates for these systems.</p><p> For the kinesin-microtubule (KIN-MT) system, we have built atomistic structure models for the key nucleotide-binding states of the kinesin-MT complex from lower resolution cryo-EM maps, by suitably modifying the MD potential with the EM map force. We have also studied ligand-protein (ADP/ATP-kinesin) interactions and predicted the sequence of structural changes in kinesin-MT complex during its conformational transitions between important biochemical states and pinpointed key contributing residues.</p><p> Simultaneously, we have also characterized the transmitter binding sites of neuromuscular acetylcholine receptors and analyzed the energy asymmetries between the fetal and adult endplate receptors. Through large-scale simulations of the fetal and adult binding sites, we have come across compelling evidence of the structural causes that explain these asymmetries and were successful in identifying the minimum construct that is both necessary and sufficient to exchange the function between adult and fetal binding sites in AChRs. Our <i> in silico</i> models and predictions act as important tools to further guide mutational and functional experiments.</p>