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The electron transfer mechanisms of multiheme cytochromes were examined with scanning tunneling microscopy (STM). To simulate bacterial metal reduction mediated by proteins in direct contact with mineral surfaces, monolayers of purified decaheme cytochromes from the metal-reducing bacterium Shewanella oneidensis were prepared on Au(111) surfaces. Recombinant tetracysteine sequences were added to two outermembrane decaheme cytochromes (OmcA and MtrC) from S. oneidensis MR-1 to ensure chemical immobilization on Au(111). STM images of the cytochrome monolayers showed good coverage and their shapes/sizes matched that predicted by their respective molecular masses. Current-voltage (I-V) tunneling spectroscopy revealed that OmcA and MtrC exhibit characteristic tunneling spectra. Theoretical modeling of the single-molecule tunneling spectra revealed a distinct tunneling mechanism for each cytochrome: OmcA mediates tunneling current coherently whereas MtrC temporarily traps electrons via orbital-mediated tunneling. These mechanisms suggest a superexchange electron transfer mechanism for OmcA and a redox-specific (i.e. heme-mediated) electron transfer mechanism for MtrC at mineral surfaces during bacterial metal reduction. Additionally, a novel electrochemical STM configuration was designed to measure tunneling current from multiheme cytochromes to hematite (001) surfaces in various electrolyte solutions. Current-distance (I-s) profiles on hematite (001) reveal predictable electric double layer structure that changes with ionic strength. The addition of the small tetraheme cytochrome c (STC) from S. oneidensis on insulated Au tips resulted in modified tunneling profiles that suggest STC significantly modulates the double layer. This observation is relevant to understanding metal reduction in cases where terminal metal-reducing enzymes are unable to come in direct contact with reducible mineral surfaces. Electronic coupling to the mineral surface might therefore be mediated by a localized ion swarm specific to the mineral surface. / Ph. D.

This dissertation is a study of the relationships between nitrogen (N) availability and spiraling (the paired processes of nutrient cycling and advective transport) in stream ecosystems. Anthropogenic activities have greatly increased rates of N loading to aquatic ecosystems. However, streams may be important sites for retention, removal, and transformation of N. In order to identify controls on NO3-N spiraling in anthropogenically impacted streams, I examined relationships among NO3-N spiraling and a suite of chemical, physical, and biological variables in streams spanning a gradient of N concentration. Across all streams, gross primary production (GPP) accounted for most NO3-N demand. Uptake of NO3-N was also related to GPP but was limited by N availability when N concentrations were low. A combination of GPP and NO3-N explained 80% of the variance in uptake. In chapter 3, I conducted a series of short-term nutrient releases in which streamwater NO3-N concentration was incrementally elevated to identify conditions leading to saturation of uptake capacity. Four of six study streams showed signs of N limitation whereas there was no significant change in uptake with increasing NO3-N amendment in two streams, suggesting N saturation. Proximity to saturation was generally correlated to N concentration but was also predicted by the ratio of N:P. My results suggest complex relationships between N spiraling and availability that depend on resident biota and other limiting factors. In chapter 4, I examined nutrient spiraling methodology by comparing differences between ambient and amendment-derived NO3-N spiraling metrics. I quantified spiraling metrics during a short-term NO3-N amendment and under ambient conditions using a stable isotope (15NO3-N) tracer. Uptake lengths measured during amendments were consistently longer than ambient uptake lengths. Amendment-derived NO3-N uptake velocity and uptake were underestimated relative to ambient conditions. Using a technique to estimate ambient uptake length extrapolated from the relationship between uptake length and nutrient amendment concentration for a series of amendments at different concentrations, I found that extrapolated uptake lengths were generally better predictors of ambient uptake lengths than amendment-derived uptake lengths but the technique was less effective in high N streams that showed signs of weak N limitation. / Ph. D.

Wetlands self-organize through reciprocal controls between vegetation and hydrology, but external disturbance may disrupt these feedbacks with consequent changes to ecosystem state. Imminent and widespread emerald ash borer (EAB) infestation throughout North America has raised concern over possible ecosystem state shifts in forested wetlands (i.e., to wetter, more herbaceous systems) and loss of forest function, calling for informed landscape-scale management strategies. In this dissertation, I use black ash wetlands as a model system to understand complex ecohydrological dynamics, and I use these dynamics to explain the self-organization of observed patterns in vegetation, hydrology, and microtopographic structure. The combined inferences from the three research chapters strongly implicate black ash trees as autogenic ecosystem engineers, who, through the process of improving their local growing conditions, cause a cascade of environmental changes that result in a unique ecosystem structure. This unique ecosystem structure is under existential threat from the invasive EAB. Through experiment, I show that loss of black ash trees to EAB induces persistent shifts in hydrology that result from reduced evapotranspiration and subsequent changes to water table regime (Chapter 2). These results suggest the potential for catastrophic shifts of black ash wetlands from forested to non-forested, marsh-like states under a do-nothing EAB management scenario. However, research presented here suggests that preemptive management of black ash wetlands can potentially mitigate loss of desirable forested conditions. Forest management to replace black ash with other wetland canopy species may be a slow and steady path towards forest maintenance, and harvesting may facilitate establishment of alternative species. In the case of preemptive harvesting of black ash, I posit that maintenance of microtopographic structure, either through leaving downed woody debris or through physical creation, is paramount to forest recovery. Microtopography in these ecosystems provides crucial relief from anaerobic stress generated by higher water tables, allowing woody species to persist on elevated microsites (e.g., 30 cm above base soil elevation). Moreover, I show that microtopography in black ash wetlands has clear structure and pattern and that its presence arises from self-organizing processes, driven by feedbacks among hydrology, biota, and soils (Chapter 3). I further show that this structured and non-random microtopography has profound influence on biogeochemical processes in black ash wetlands, controlling plant richness and biomass, and soil chemistry gradients (Chapter 4). Based on this work, I propose that structured wetland microtopography is a diagnostic feature of strongly coupled plant-water interactions, and these interactions may be important for ecosystem resilience to disturbance. / Doctor of Philosophy / Plants need water, but not too much nor too little. In wetland ecosystems, plants influence water levels through both water use and their effect on soil surfaces. When wetland plants use water, they take it from the soil, which leads to lowering of water levels and drier soil conditions. In many wetlands, the amount of water that plants take from the soil is a fine-tuned process. Therefore, when disturbances happen to wetland ecosystems, like large-scale tree mortality, major changes can occur to the amount of water in the soil and soils typically become wetter. This change to a wetter ecosystem can persist for long periods, and can affect the types of plants that can live in the wetland. However, plants also affect wetland water levels by engineering the soil around them, essentially lifting themselves to drier conditions. Through this engineering, plants create a mosaic of different habitat types that are important for many organisms and ecological processes. Exactly how plants engineer their environment is still not well understood, but we know that ecosystem engineering by plants is critical to the structure and function of wetlands around the world. Understanding how plants create and maintain their own environmental structures provides a deeper insight into the development of vegetated landscapes and their response to change. This dissertation aims to improve our understanding of ecosystem engineering by plants in forested wetlands so that we may more effectively manage these important natural resources and in turn more accurately predict their response to global change.

Mangroves provide many ecosystem services in coastal environments around the world. These include water quality improvement, creating habitats for terrestrial and aquatic species, and stabilizing shorelines. In central Florida, the red mangrove Rhizophora mangle is a common species in coastal wetlands, and recently the number of individuals successfully recruiting to intertidal oyster reefs has greatly increased, possibly because biogeochemical hot spots are present on oyster reefs due to nutrient-rich biodeposits from the live oysters. To understand how well R. mangle responds in terms of survival and growth to the suite of variables associated within these two unique habitats, I tracked 300 seedlings (n = 30 per site on 5 oyster reefs and 5 shoreline sites) that were approximately 1-year old at the start of my project. Monitoring occurred over 12 months (start: August 2022). Monthly data collection included above-ground measurements for each mangrove (survival, height, stem circumference, light availability, leaf count, herbivory, leaf area, and chlorophyll levels) of the seedlings, while below-ground measurements quantified biogeochemical properties of the soil adjacent to mangroves at each site. Survivorship declined over time for both habitats, but survivorship was greater on oyster reefs (cox regression model, p= 0.002). Results suggest greater stem circumference and ammonium concentrations at oyster reef sites. With the data gathered from this study, I determined that oyster reefs have conditions that provide better chances for long-term survival and growth for R. mangle in Mosquito Lagoon. This possibility should be considered on all subtropical estuarine systems where mangroves and intertidal oyster reefs intersect.

<p>Mercury (Hg) is a globally circulating heavy metal released through both natural and anthropogenic sources. The largest anthropogenic source of mercury to the global atmosphere is artisanal and small-scale gold mining (ASGM). During the ASGM process, miners add elemental mercury to large quantities of sediment or soil in order to create gold-mercury amalgams that separate alluvial gold from the remaining geological host material. Miners then heat the amalgam using a blowtorch or similar device to separate the mercury and gold, exposing themselves to mercury vapor and releasing mercury to the environment. Following amalgam heating, mercury can deposit into aquatic ecosystems. There, anaerobic microorganisms can convert mercury to methylmercury (MeHg), a potent neurotoxin that rapidly accumulates in aquatic food webs. A high concentration of MeHg in fish poses serious human health risks, especially to pregnant women and children. </p><p>In Peru’s Region of Madre de Dios (MDD), mercury use for ASGM is widespread due to increasing global demand for gold. This region in the tropical Amazon is one of the world’s most biodiverse ecosystems and home to more than 150,000 Indigenous and non-Indigenous people, 40% of whom live below the poverty level. Recently, people living in the region have become more aware of negative impacts of Hg pollution through popular press. However, there is lack of controlled scientific studies to examine the environmental impacts of Hg from ASGM and subsequent exposures to surrounding communities. </p><p>This dissertation addresses four questions in order to better understand how mercury from ASGM impacts environmental health in Madre de Dios: (1) How is mercury distributed along the Madre de Dios River in areas of active ASGM activity, and what is the risk for mercury exposure to downstream communities? (2) How does land use change associated with ASGM activity affect soil-mediated mercury transport in the Colorado River, Madre de Dios, Peru? (3) Can sulfurized carbon be manufactured in a feasible way for developing countries and used to capture mercury during ASGM amalgam burning? (4) What is the mercury methylation potential of easy-to-manufacture spent, sulfurized carbon sorbents?</p><p>Despite significant information on the direct health impacts of mercury to ASGM miners, the impact of mercury contamination on downstream communities has not been well characterized, particularly in Madre de Dios. In this area, ASGM has increased significantly since 2000 and has led to substantial political and social controversy. The second chapter of this dissertation examines the spatial distribution and transport of mercury through the Madre de Dios River with distance from ASGM activity. It also characterizes risks for dietary mercury exposure to local residents who depend on fish from the river. River sediment, suspended solids from the water column, and fish samples were collected in 2013 at 62 sites near 17 communities over a 560 km stretch of the Madre de Dios River and its major tributaries. In areas downstream of know ASGM activity, mercury concentrations in sediment, suspended solids and fish within the Madre de Dios River were elevated relative to locations upstream of mining. Fish tissue mercury concentrations were observed at levels representing a public health threat, with greater than one-third of carnivorous fish exceeding the international health standard of 0.5 mg/kg. This research demonstrates that communities located hundreds of kilometers downstream of ASGM activity, including children and indigenous populations who may not be involved in mining, are at risk of dietary mercury exposure that exceed acceptable body burdens. </p><p>This research involved extensive field sampling in an active mining region and indicated suspended particulate transport may be an important source of mercury from mining areas to downstream communities. Chapter three of this research focused on understanding how land use changes can influence soil and sediment transport from mining regions. Within the MDD, a large portion of mining in concentrated within the Colorado River watershed. In the Colorado River watershed, mining and deforestation have increased dramatically since the 1980s, largely concentrated in the Puquiri subwatershed. Field sampling in Feb 2015 identified a strong correlation between Hg and suspended solids concentrations, with especially high suspended solids concentrations downstream of ASGM activity. This supported the hypothesis that Mercury transport in this region is facilitated by soil mobilization and runoff. In order to understand how ASGM activity in the Puquiri affects sediment mobilization from the watershed over time, we employed a watershed-scale soil mobilization model using satellite imagery from 1986 to 2014. The model estimated that soil mobilization in the Colorado River watershed increased by 2.5 times during the time period, and increased by six times in the Puquiri subwatershed, leading to between 10 and 60 kg of mercury mobilized in 2014. If deforestation continues at its current exponential rate through 2030, soil and heavy metal mobilization may increase by five times. This research shows that deforestation associated with ASGM in the Colorado River watershed can exacerbate soil mobilization and mercury contamination. While the impacts of mercury and deforestation are often considered separately, here we studied how deforestation associated with ASGM in the Madre de Dios region can significantly increase soil mobilization and mercury transport to downstream communities.</p><p>With a substantial portion of mercury releases coming from a non-industrialized process in developing countries, low-cost and low-tech mercury capture is becoming increasingly necessary. While impregnated activated carbon sorbents are well studied for mercury-capture in developed countries and large industrialized settings, there exist few suitable low-cost alternatives for mercury capture from artisanal and small-scale gold mining (ASGM) in developing countries. Chapter four sought to develop an easy-to-manufacture carbon sorbent using elemental sulfur and activated carbon or hardwood-based biochar for potential use during ASGM gold-amalgam heating. Consumer-grade sulfur powder was melted on granular activated carbon or hardwood biochar in a process feasible for a cook stove setting. Activated carbon and biochar were successfully sulfurized to more than 5% sulfur by weight using powdered, elemental sulfur. The sorbent products were tested for elemental mercury sorption from an air gas stream at room temperature. The sulfurized activated carbon achieved higher elemental mercury adsorption capacity in air stream (500 μg Hg m-3, 2 L min-2) relative to unsulfurized activated carbon and sulfurized biochar. Sorption isotherms were used to examine the sorption mechanism, and indicated that likely a pseudo first order reaction was occurring. This research provides a possible option for mercury control by modifying established mercury capture technologies to be easy to manufacture, locally available, and less hazardous to produce.</p><p>In Chapter 5 of this research, the sulfurized sorbents were examined further to understand methylation potential in sediment slurries. Anaerobic sediment slurries were constructed to examine methylmercury (MeHg) production of spent sorbents. Five sorbent types with approximately 10 mg/kg Hg each were added to slurries at 5 % by mass. Dissolved mercury was used as a control to simulate atmospheric deposition or highly reactive mercury. After a 5 d incubation at room temperature, MeHg production was ten times greater with low-technology sulfurized sorbents as compared to activated carbon or biochar alone. Sulfurized sorbents leached significantly more mercury than their non-sulfurized counterparts during desorption experiments and led to greater dissolved mercury concentrations. This research shows that low-cost mercury-contaminated sorbents can have unintended consequences with increased MeHg production and potential for more harm to local communities than atmospheric release.</p><p>Mercury releases from ASGM are expected to grow, leading to higher concentrations of mercury in the atmosphere that may affect ecosystems throughout the globe. Understanding the importance of mercury from ASGM to toxicity and accumulation requires in depth research on mercury transformations and MeHg production associated with ASGM. This research examines mercury distribution and transport from ASGM active regions. It identifies that deforestation, erosion, and particulate transport play important roles in overall mercury transport, leading to hazardous mercury concentrations downstream of ASGM activity. Effective point-of-use mercury capture technologies would dramatically decrease the mass of mercury released to the environment. The final chapters of this research serve as a proof of concept for using sulfurized activated carbon for mercury capture in developing countries. </p><p>Our research team has built strong relationships with several governmental and non-governmental organizations in Peru who will aid in distributing information. This research will provide invaluable environmental health information to residents, inform political intervention, and reveal a new potential avenue for low-cost mercury control.</p> / Dissertation

Black carbon (BC) is an organic residue formed primarily from biomass burning (e.g., wildfires) and fossil fuel combustion. Until recently, it was understood that BC was highly recalcitrant and stabilized in soils over millennial scales. However, a fraction of the material can be solubilized and transported in fluvial systems as dissolved BC (DBC), which represents on average 10% of the global export of dissolved organic carbon (DOC) from rivers to coastal systems. The composition of DBC controls its reactivity, and it has been linked with a variety of in-stream processes that induce both carbon sequestration and evasion of CO₂ from aquatic systems, which suggest DBC may have a significant contribution within the global carbon cycle. The primary objectives for the thesis were to elucidate environmental factors that control the fate and transport of DBC in fluvial systems. Ultra-high resolution mass spectrometry was used to characterize DBC on a molecular scale whereas benzenepolycarboxylic acids were used to quantify and characterize BC in both dissolved and particulate phases (PBC). Sinks for polycondensed DBC were linked to a series of in-stream biogeochemical processes (e.g., photodegradation, metal interactions); whereas photooxidation of particulate charcoal led to production of DBC, suggesting photodissolution as a previously unrecognized source of DBC to fluvial systems. Coupling of DBC with PBC, however, was hydrologically constrained with sources varying over temporal scales and land use regimes. For DBC in particular, an enrichment of heteroatomic functionality was observed as a function of anthropogenic land use. Furthermore, land use coupled with stream order (a proxy for in-stream processing as defined by the River Continuum Concept) could explain significant spatial variability in organic matter (e.g., DOC) composition within an anthropogenically impacted system. With an increase in wildfire frequency projected with on-going climate change trends, parallel projections for increases in BC production are also expected. Furthermore, conversion of natural landscapes for urban and agricultural practices is also expected to continue in the coming decades. Thus, it is imperative to reach a comprehensive understanding of processes regulating the transport of DBC in fluvial systems with efforts to constrain future BC budgets and climate change models.

<p>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. </p><p>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.</p><p>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.</p><p>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. </p><p>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.</p> / Dissertation

<p>Afforestation, the conversion of historically treeless areas into forests, is a rapidly spreading land-use change with the potential to sequester carbon. Afforested plantations typically feature fast growing exotic tree species that give landowners rapid returns. The efficient growth of plantations compared to less intensively managed forests also can provide greater timber yields in a smaller area. This increased efficiency in turn could require fewer acres to meet global forest product demands and could also reduce the need to log intact primary forests. Reduced primary forest harvest and high primary productivity make afforestation a highly efficient carbon sequestration tool.</p><p> However, the rapid growth and planting disturbance due to afforestation can have deleterious effects on soils and hydrology that undermine its benefits in some locations. The effects on hydrology include depletion of groundwater and reduced or complete elimination of surface water flow. Additionally, groundwater use can lead to increased concentrations of salts and trace metals in soil that could be deleterious for future plant productivity. Plantations have also been shown to acidify surface soils and stream water and to reduce soil carbon and nitrogen.</p><p> Despite the known effects of afforestation on soils, there has been little research on the mechanisms controlling these effects. For instance, there have been few studies on the effects of afforestation on soil microbes which mediate most biogeochemical processes. There is also little knowledge on what controls the effects of afforestation on soil carbon and nitrogen, vital indexes of soil quality, across regions with high levels of afforestation. The overarching goal of this dissertation is to examine the effects of afforestation on soils, microbes, and biogeochemical processes across local, regional and global scales. Understanding the mechanisms by which afforestation alters soils and biogeochemical cycling and how these mechanisms change across different scales will aid in evaluating the true costs and benefits of afforestation. These results will be useful in determining if the benefits of afforestation will continue to outweigh its costs in the long-term.</p><p> The goal of Chapter 1 is to evaluate how afforestation across the globe affects mineral soil quality, including pH, sodium, exchangeable cations, organic carbon, and nitrogen, and to examine the magnitude of these changes in regions where afforestation rates are high. To control for different initial soil conditions across the globe, I examined paired sites of afforested plantations and controls. Controls included land-use types that are frequently afforested, such as grasslands, shrublands, and pastures. I also examined potential mechanisms to reduce the impacts of afforestation on soils and to maintain long-term productivity. Across diverse plantation types (153 sites) to a depth of 30cm of mineral soil, I observed significant decreases in nutrient cations (Ca, K, Mg), increases in sodium (Na), or both with afforestation. For the global dataset, afforestation reduced soil concentrations of the macronutrient Ca by 29% on average compared with native controls (p<0.05). Afforestation by Pinus alone decreased soil K by 23% (p<0.05). Overall, plantations of all genera also led to an average 71% increase of soil Na (p<0.05). Average pH decreased 0.3 units (p<0.05) with afforestation. Afforestation caused a 6.7% and 15% (p<0.05) decrease in soil C and N content respectively, though the effect was driven principally by Pinus plantations (15% and 20% decrease, p<0.05). Carbon to nitrogen ratios in soils under plantations were 5.7-11.6% higher (p<0.05). The major implication of these results are that in several regions with high rates of afforestation, cumulative losses of C, N, Ca, and Mg are likely in the range of tens of millions of metric tons. The decreases indicate that trees take up considerable amounts of nutrients from soils; harvesting this biomass repeatedly could impair long-term soil fertility and productivity in some locations. Based on this study and a review of other literature, I suggest that proper site preparation and sustainable harvest practices, such as avoiding the removal or burning of harvest residue, could minimize the impact of afforestation on soils. These sustainable practices could in turn slow erosion, organic matter loss, and soil compaction from harvesting equipment, maintaining soil fertility to the greatest extent possible. </p><p> Soil microbes are highly diverse and control most soil biogeochemical reactions. Given the observed changes in Chapter 1, in Chapters 2 and 3 I examined how microbial functional genes and biogeochemical pools responded to the altered chemical inputs accompanying afforestation. I examined paired native grasslands and adjacent Eucalyptus plantations (previously grasslands) in Uruguay, a region that lacked forests before European settlement. Along with measurements of soil carbon, nitrogen, and bacterial diversity, I analyzed functional genes using the GeoChip 2.0 microarray that simultaneously quantified several thousand genes involved in soil carbon and nitrogen cycling. Plantations and grasslands differed significantly in functional gene profiles, bacterial diversity, and biogeochemical pool sizes. Afforestation decreased both bacterial diversity and richness compared to grasslands, though diversity remained relatively high. Most grassland functional gene profiles were similar, but plantation profiles generally differed from grasslands due to differences in functional gene abundance across many microbial groups. Eucalypts decreased ammonification and N-fixation functional genes by 11% and 7.9% (p<0.01) which correlated with decreased microbial biomass N and more NH4+ in plantation soils. Chitinase, an important carbon polymer degrading enzyme, decreased in functional gene abundance 7.8% in plantations compared to grasslands (p=0.017), and C polymer degrading genes decreased by 1.5% overall (p<0.05), which likely contributed to 54% (p<0.05) more C in undecomposed extractable soil pools and 27% less microbial C (p<0.01) in plantation soils. In general, afforestation altered the abundance of many microbial functional genes corresponding with changes in soil biogeochemistry. These changes were driven by shifts in the whole community functional gene profile, not just one or two constituent microbial taxa. Such changes in microbial functional genes correspond with altered C and N storage and have implications for long-term productivity in these soils.</p><p> The area studied in Chapters 2 and 3 lies near the middle of a precipitation gradient that stretches across the Rio de la Plata grasslands. In Chapter 4 I studied if the effects of afforestation on soil C and N from Chapters 2 and 3 varied with different precipitation levels. The effect of afforestation on soil C has been shown to depend on mean annual precipitation (MAP), with drier sites gaining C and wetter sites losing C with afforestation. This precipitation dependence of soil C changes with afforestation may be controlled by changes in soil nitrogen (N) cycling. In particular, loss of N due to leaching after afforestation could lead to soil C losses. However, the link between C and N changes due to afforestation has primarily been suggested by models and to my knowledge has never been explicitly tested across a precipitation gradient. The goal of this study was to test how precipitation affects changes in labile and bulk pools of soil C and N across a precipitation gradient, which will provide novel insight into the linkage between land-use change, different pools of soil C and N, and precipitation. I conducted this study across a gradient of precipitation in the Rio de la Plata grasslands of Argentina and Uruguay which ranged from 600mm to 1500mm of precipitation per year. The sites were all former grasslands that had been planted with Eucalyptus. I found that changes in bulk soil C and N were related to MAP with drier sites gaining and wetter sites losing C and N (R2=0.59, p=0.003), which supports the idea that N losses are strongly linked to C losses with afforestation. C and N in microbial biomass and extractable pools followed similar patterns to bulk soil C and N. Interestingly, losses of C and N decreased as the plantations aged, suggesting that longer rotation times for plantations could reduce potential soil carbon and nitrogen losses. These results indicate that afforestation is still be a valuable tool for carbon sequestration, but calculations of the benefits of afforestation must take into account site factors such as age and precipitation to accurately calculate total sequestration benefit and ensure continued high productivity and carbon sequestration.</p><p> In conclusion, afforestation could be an effective tool for carbon sequestration. However, its benefits need to be carefully weighed against its costs for soil such as reduced microbial diversity, decreased soil microbial functional capacity, losses of soil organic matter, and nutrient depletion. Careful management and consideration of afforestation is needed to ensure the greatest benefits with the least long-term damage to soils.</p> / Dissertation

Characterized by high levels of terrestrial organic carbon inputs, estuaries and coastal marshes are among the most productive ecosystems on earth and significantly impact the global carbon cycle. Unfortunately, rates of natural organic matter (NOM) degradation in these environments are difficult to quantify directly due to the complex interaction between microbial respiration processes and abiotic reactions in these sediments, yet estuaries and marshes are considered both net sources and sinks of carbon. Typically carbon remineralization rates are determined by measuring total (TOU) and diffusive (DOU) oxygen uptake fluxes assuming oxygen is the ultimate oxidant. This assumption, however, requires any reduced metabolites produced during microbial respiration to be reoxidized by oxygen. In this study, voltammetric sensors were used to measure terminal electron acceptors or their reduced by-products. By simultaneously considering oxygen as well as anaerobic respiration accepting processes, this study demonstrates that oxygen does not function as the ultimate oxidant in coastal marine sediments due to precipitation and burial of reduced species. Furthermore, the biogeochemistry of coastal sediments is typically investigated ex situ after collection of sediment cores. However, coastal sediments are subject to complex subsurface hydrological forcing that cannot be accounted for with ex situ measurements. Consequently, in situ approaches are required to better understand the impact of physical processes on sediment biogeochemistry, and two novel in situ voltammetric systems were developed as part of this research. First, a new autonomous benthic lander equipped with a benthic chamber to measure TOU fluxes with a high temporal resolution and a potentiostat and micromanipulator to simultaneously acquire voltammetric depth profiles of the main redox species in pore waters was deployed in a pristine river-fed estuary to characterize the seasonal variability of coastal sediment biogeochemistry and examine the impact of riverine discharge on carbon remineralization processes. Simultaneously, a new electrochemical analyzer equipped with a solar and wind power charging system to ensure continuous monitoring capability and a VHF radio to transmit data was operated remotely via the internet from the Georgia Tech campus to investigate the dynamic coupling between hydrological, chemical, and biological processes in intertidal marsh sediments. Finally, new microelectrodes were deployed in microbial mats to examine the chemical and biological oxidation of sulfide with submillimeter resolution. Typically, only biological processes are considered to oxidize sulfide in these environments. Depth profiles during diel studies were able to demonstrate the formation of thiosulfate as an intermediate oxidation product of sulfide oxidation, suggesting that the chemical oxidation of sulfide is much more prevalent than previously recognized when compared to biological oxidation. Overall, using a novel in situ sampling technique with high temporal resolution, these studies confirm that biogeochemical processes in coastal sediments vary seasonally. More importantly, these studies also reveal that estuarine sediments are significantly influenced by riverine discharge, demonstrate that the biogeochemical response of these sediments to natural perturbations is rapid, and indicate that respiration processes in continental shelf sediments are controlled by a combination of temperature, supply of inorganic and organic substrates, and hydrological processes, which has important implications regarding the effect of climate change on the biogeochemical cycling of carbon in these environments.