abstract: The potential of using bio-geo-chemical processes for applications in geotechnical engineering has been widely explored in order to overcome the limitation of traditional ground improvement techniques. Biomineralization via urea hydrolysis, referred to as Microbial or Enzymatic Induced Carbonate Precipitation (MICP/EICP), has been shown to increase soil strength by stimulating precipitation of calcium carbonate minerals, bonding soil particles and filling the pores. Microbial Induced Desaturation and Precipitation (MIDP) via denitrification has also been studied for its potential to stabilize soils through mineral precipitation, but also through production of biogas, which can mitigate earthquake induced liquefaction by desaturation of the soil. Empirical relationships have been established, which relate the amount of products of these biochemical processes to the engineering properties of treated soils. However, these engineering properties may vary significantly depending on the biomineral and biogas formation mechanism and distribution patterns at pore-scale. This research focused on the pore-scale characterization of biomineral and biogas formations in porous media. The pore-scale characteristics of calcium carbonate precipitation via EICP and biogenic gas formation via MIDP were explored by visual observation in a transparent porous media using a microfluidic chip. For this purpose, an imaging system was designed and image processing algorithms were developed to analyze the experimental images and detect the nucleation and growth of precipitated minerals and formation and migration mechanisms of gas bubbles within the microfluidic chip. Statistical analysis was performed based on the processed images to assess the evolution of biomineral size distribution, the number of precipitated minerals and the porosity reduction in time. The resulting images from the biomineralization study were used in a numerical simulation to investigate the relation between the mineral distribution, porosity-permeability relationships and process efficiency. By comparing biogenic gas production with abiotic gas production experiments, it was found that the gas formation significantly affects the gas distribution and resulting degree of saturation. The experimental results and image analysis provide insight in the kinetics of the precipitation and gas formation processes and their resulting distribution and related engineering properties. / Dissertation/Thesis / Doctoral Dissertation Civil, Environmental and Sustainable Engineering 2019

abstract: There is a growing consensus that photodegradation accelerates litter decomposition in drylands, but the mechanisms are not well understood. In a previous field study examining how exposure to solar radiation affects decomposition of 12 leaf litter types over 34 months in the Sonoran Desert, litter exposed to UV/blue wavebands of solar radiation decayed faster. The concentration of water-soluble compounds was higher in decayed litter than in new (recently senesced) litter, and higher in decayed litter exposed to solar radiation than other decayed litter. Microbial respiration of litter incubated in high relative humidity for 1 day was greater in decayed litter than new litter and greatest in decayed litter exposed to solar radiation. Respiration rates were strongly correlated with decay rates and water-soluble concentrations of litter. The objective of the current study was to determine why respiration rates were higher in decayed litter and why this effect was magnified in litter exposed to solar radiation. First, I evaluated whether photodegradation enhanced the quantity of dissolved organic carbon (DOC) in litter by comparing DOC concentrations of photodegraded litter to new litter. Second, I evaluated whether photodegradation increased the quality of DOC for microbial utilization by measuring respiration of leachates with equal DOC concentrations after applying them to a soil inoculum. I hypothesized that water vapor sorption may explain differences in respiration among litter age or sunlight exposure treatments. Therefore, I assessed water vapor sorption of litter over an 8-day incubation in high relative humidity. Water vapor sorption rates over 1 and 8 days were slower in decayed than new litter and not faster in photodegraded than other decayed litter. However, I found that 49-78% of the variation in respiration could be explained by the relative amount of water litter absorbed over 1 day compared to 8 days, a measure referred to as relative water content. Decayed and photodegraded litter had higher relative water content after 1 day because it had a lower water-holding capacity. Higher respiration rates of decayed and photodegraded litter were attributed to faster microbial activation due to greater relative water content of that litter. / Dissertation/Thesis / Masters Thesis Biology 2019

abstract: Soil organic carbon (SOC) is a critical component of the global carbon (C) cycle, accounting for more C than the biotic and atmospheric pools combined. Microbes play an important role in soil C cycling, with abiotic conditions such as soil moisture and temperature governing microbial activity and subsequent soil C processes. Predictions for future climate include warmer temperatures and altered precipitation regimes, suggesting impacts on future soil C cycling. However, it is uncertain how soil microbial communities and subsequent soil organic carbon pools will respond to these changes, particularly in dryland ecosystems. A knowledge gap exists in soil microbial community responses to short- versus long-term precipitation alteration in dryland systems. Assessing soil C cycle processes and microbial community responses under current and altered precipitation patterns will aid in understanding how C pools and cycling might be altered by climate change. This study investigates how soil microbial communities are influenced by established climate regimes and extreme changes in short-term precipitation patterns across a 1000 m elevation gradient in northern Arizona, where precipitation increases with elevation. Precipitation was manipulated (50% addition and 50% exclusion of ambient rainfall) for two summer rainy seasons at five sites across the elevation gradient. In situ and ex situ soil CO2 flux, microbial biomass C, extracellular enzyme activity, and SOC were measured in precipitation treatments in all sites. Soil CO2 flux, microbial biomass C, extracellular enzyme activity, and SOC were highest at the three highest elevation sites compared to the two lowest elevation sites. Within sites, precipitation treatments did not change microbial biomass C, extracellular enzyme activity, and SOC. Soil CO2 flux was greater under precipitation addition treatments than exclusion treatments at both the highest elevation site and second lowest elevation site. Ex situ respiration differed among the precipitation treatments only at the lowest elevation site, where respiration was enhanced in the precipitation addition plots. These results suggest soil C cycling will respond to long-term changes in precipitation, but pools and fluxes of carbon will likely show site-specific sensitivities to short-term precipitation patterns that are also expected with climate change. / Dissertation/Thesis / Masters Thesis Biology 2019

Storing almost a third of the global soil carbon pool, wetlands are an essential component of the carbon cycle, and carbon-rich peat soil accumulates when carbon input through primary productivity exceeds output through decomposition. However, woody shrub encroachment in herbaceous wetlands can alter soil carbon processes, potentially diminishing stored carbon. To examine the effects of shrub encroachment on soil carbon, I compared soil carbon input through litterfall and fine root production, output through decomposition, and below-canopy microclimate conditions between Carolina willow shrub (Salix caroliniana) and herbaceous sawgrass (Cladium jamaicense) in the Blue Cypress Marsh Conservation Area (BCMCA), FL. To assess the level of production and its response to water level, I compared aboveground green biomass by measuring normalized difference vegetation index (NDVI) and photosynthetic stress by measuring photochemical reflectance index (PRI) between sawgrass and willow. I collected willow litterfall using litter traps and measured sawgrass and willow fine root production with fine root ingrowth bags. Litter decomposition was measured with decomposition bags deployed using a reciprocal litter placement design at BCMCA and incubated in a greenhouse to examine the effects of char and water level on decomposition. Above and belowground microclimate conditions were measured using sensors installed within sawgrass and willow canopies. Despite experiencing more photosynthetic stress, willow produced more green biomass than sawgrass. However, willow produced fewer fine roots than sawgrass and these roots were deeper within the soil. Willow litter decomposed faster even though sawgrass decomposition increased under drier conditions. Compared to the sawgrass canopy, the willow canopy had greater light availability, lower evaporative demand plus warmer and drier soils; however, litter decomposition did not differ between the canopies. These results suggest that willow encroachment can reduce the amount and alter the distribution of carbon within an herbaceous wetland, likely resulting in a net loss of soil carbon. Although willow encroachment may increase aboveground biomass carbon stocks, these stocks will likely be offset by a loss of soil carbon due to reduced fine root production and increased decomposition. Therefore, the transition from herbaceous wetland to shrub wetland will likely result in a loss of stored soil carbon. / Includes bibliography. / Dissertation (Ph.D.)--Florida Atlantic University, 2020. / FAU Electronic Theses and Dissertations Collection

In natural ecosystems, like deciduous and coniferous forests, soil CO2 flux or soil respiration is highly variable and influenced by multiple factors including temperature, precipitation, dissolved soil organic carbon (DOC), dissolved organic matter (DOM), and bacterial and fungal biomass and diversity. However, as the human population continues to grow rapidly, so too do urbanized landscapes with unknown consequences to soil respiration. To determine the extent urbanization influences seasonal shifts in microorganisms and environmental drivers alter soil respiration, we evaluated bacterial and fungal communities, soil physiochemical characteristics, and respiration in forested and urbanizing ecosystems in three watersheds across northern Utah, USA. Based on the next-generation sequencing of the 16s DNA and RNA, we found that montane bacteria were predominantly structured by season while urban bacteria were influenced by degree of urbanization. There was no apparent effect of season on montane fungi, but urban fungal communities followed patterns similar to urban bacterial communities. Bacterial diversity was sensitive to seasonality, especially in montane ecosystems, declining 21-34% from spring to summer and staying relatively low into fall, and fungal diversity was generally depressed in spring. Urban bacterial communities were differentiated by substantially more bacterial taxa with 62 unique OTUs within families structing phylogenetic differences compared with only 18 taxa differentiating montane communities. Similar to bacteria and fungi, DOC and ammonium concentrations fluctuated predominantly by season while these same parameters where highly variable among urban soils among the three watersheds. Structural components of DOM via parallel factor analysis (PARAFAC) of fluorescence excitation-emission matrices show varying patterns between montane and urban systems with humic substance resistance to biodegradability found more dominantly in montane systems. Incorporating all soil chemical parameters, daily temperature and moisture, and fungal and bacterial diversity and richness in mixed linear effects models describing daily CO2 over all seasons, we found that a single model best described montane soil respiration, while individual watershed models best described urban respiration. Montane respiration was related to the availability of DOC, different DOM components, and rRNA-based bacterial diversity . Alternatively, urban respiration was influenced by either bacterial diversity and richness in our rapidly urbanizing environment, DOM characteristics and soil O2 in the more agricultural urban soils, or the DOM parameter humification index (HIX) in highly urbanized soils. Our results suggest that urbanization creates distinct bacterial and fungal communities with a single soil biotic or chemical parameter structuring soil respiration, while montane ecosystems select for similar bacterial and fungal communities with respiration sensitive to fluctuations in soil moisture, bacteria and the recalcitrance of carbon (C) resources.

This dissertation analyzed the effect of biologic and hydrologic processes on water quality in urban, semi-arid watersheds. In the first chapter, we analyzed bacterioplankton and water quality along elevation and urbanization gradients in three Wasatch Mountain watersheds across three seasons. We found that trace metals correlated with bacterioplankton composition and that the typical dispersal of bacteria from headwater sources (soil or groundwater) along the longitudinal pathway was drastically disrupted by the presence of large reservoirs. In the second chapter, we used high-frequency sensor data collected in streams above and below the urban center in the three watersheds to estimate the relative contribution of biologic, hydrologic, and anthropogenic processes to changes in nitrate concentration. In-stream metabolism correlated with less than 38% of diel fluctuations in nitrate, but diel nitrate concentration only represented 10% of the total nitrate variability, demonstrating how in-stream uptake can easily be overwhelmed by nutrient loading in even moderately modified watersheds. A majority of the nitrate was associated with hydrologic variables, specifically discharge and specific conductivity, with pulses of nitrate corresponding to anthropogenic activity that far exceeded the capability of the system to remove or process the nitrogen. In the third chapter, we used citizen science to collect synoptic solute data to analyze the catchment hydrology in one of the Wasatch watersheds (Provo River and Utah Lake). Unlike previous research from humid and temperate catchments, we did not observe a systematic decrease in spatial variability with watershed size in this semi-arid, endorheic basin. Our results demonstrate the value of combining participatory science with modern ecohydrological methods to determine catchment chemistry and hydrology. This dissertation shows how hydrology, and anthrophenic changes to watersheds that affect hydrology, are largely responsible for determining water quality in urbanizing, semi-arid watersheds.

Lake Macquarie is the largest estuarine lake in New South Wales and is located on the eastern seaboard of Australia, approximately 85 km north of Sydney.The study of heavy metal concentrations in surficial sediments, sediment cores, seagrasses and fish conducted by the New South Wales Department of Mines in 1974 revealed that significant heavy metal contamination of Lake Macquarie has occurred. The metalloid selenium was found in elevated concentrations in 1987. Selenium has a complex chemistry and is both an important nutrient and in high concentrations toxic. This review describes briefly the Lake Macquarie environment and suggests some approaches of modelling the remobilisation and cycling of selenium in sediment. The biogeochemical cycling of selenium in an estuarine environment is exceedingly complex. Factors include Eh, pH, ligand complexing ability, solubility of selenium containing minerals, sediment/soil characteristics, microbially-mediated reactions and physical reworking by biota (bioturbation). The goal of the model will be to be able to estimate the transport rates from a calculated value of Se concentration in sediment pore water resulting in a Se flux value for the interface between sediment and overlaying water. / www.ima.kth.se

Fertilized croplands unintentionally export large amounts of reactive nitrogen (N), which degrades water and air quality and contributes to climate change. In this dissertation, I focus on how these reactive N losses are likely to change in the near future as agriculture intensifies in the tropics, and ecological intensification strategies to mitigate N losses are more widely adopted. I use a combination of empirical field measurements in Mato Grosso, Brazil and Skåne, Sweden, literature review, and statistical models to quantify trends. In chapter one, I quantified emissions of nitric oxide (N₂O) and nitrous oxide (N₂O) in forest, single cropped soybean, and N-fertilized double-cropped soybean-maize at three nitrogen fertilizer levels within the largest area of recent cropland expansion on earth, in the Amazon and Cerrado biomes in Mato Grosso, Brazil. I found that NO emissions do not increase when forests are converted to croplands under current fertilization levels, and that NO will respond more strongly than N₂O fluxes to increases in fertilizer applications. In chapter two, I investigated anion exchange capacity and soil nitrate (NO₃¯) pools in deep soils in Mato Grosso, Brazil in the southern Amazon. I found that soil NO₃¯ pools in the top 8 m increased from 143 kg N ha¯¹ in forest to 1,052 and 1,161 kg N ha¯¹ in soybean and soybean-maize croplands. This NO₃¯ accumulation in croplands compared with forest soils matched the estimated amount of surplus N from the croplands, and could be explained by the soil’s positive charge through its anion exchange capacity. In chapter three, I conducted a meta-analysis of the effects of fertilization amount on of NO₃¯ leaching, N₂O emissions, NO emissions, and ammonia (NH₃) volatilization, totaling over 1,000 observations. I found that the relationship between N inputs and losses differed little between temperate and tropical croplands, although total NO losses were higher in the tropics. Among the potential drivers I studied, the N input rate controlled all N losses, but soil texture and water inputs also controlled NO₃¯ leaching losses. In chapter four, I explored the differences in NO₃¯ leaching, fertilizer N use efficiency, and soil N cycling in perennial wheat, which is being domesticated as a more sustainable alternative to annual crops, and annual wheat at a long-term experimental site in Skåne, Sweden. I found that NO₃ leaching was more than two orders of magnitude lower in perennial wheat, overall ecosystem recovery of fertilizer was quite high and not significantly different between perennial and annual wheat after the first growing season, and that measures of soil N cycling were largely the same between both crops. Together, these chapters highlight that reactive N losses will remain a critical global challenge in the coming decades, but that there are also key opportunities to reduce N losses by increasing the use of perennial crops and focusing tropical agricultural intensification on Oxisol soils which buffer against NO₃¯ leaching.

The arctic tundra has been warming disproportionately faster than the global mean. Although the tundra has historically been a carbon sink, the current state of its carbon balance is highly uncertain. Large warming induced changes to tundra ecosystems complicate our ability to model tundra carbon cycling. In this dissertation I explore the impact of herbivores on dry heath vegetation and carbon flux, herbivore impact on dry heath tundra canopy, and lastly, the impact higher vegetation has on the conditions under which the tundra transitions from a carbon sink to a carbon source. Chapter 1 presents a study on the impact long term herbivore absence has on dry heath tundra. I measured vegetation cover, abundances of plant growth forms and carbon flux. I demonstrate the herbivore exclusion in this tundra ecosystem results in higher vegetation abundance and greater carbon uptake. Moreover, under average environmental conditions during the measurement period, I show that excluding herbivores resulted in net carbon uptake under average temperature and light conditions during the measurement period. In chapter 2 I build upon my result from chapter 1. I quantify differences in canopy structure due to herbivore exclusion and integrate this into carbon flux estimates. I show that that different herbivore assemblages have significantly different effect on carbon fluxes. Specifically, exclusion of large herbivores results in higher carbon uptake compared to exclusion of large and small herbivores. I also demonstrate that incorporating canopy structure results in significantly lower carbon uptake during morning and evening hours than carbon flux estimates based on my results from chapter 1 would suggest. In chapter 3 I quantify the conditions under which tussock tundra transitions from a carbon sink to source and how that is impacted by increasing vegetation abundance. I show that under low light, tundra with higher vegetation abundance must surpass higher temperatures to become carbon sources compared to tundra with lower vegetation abundance. However, under high light, the conditions are reversed, and tundra with higher vegetation abundance become carbon sources at lower temperatures than tundra with lower vegetation.

Hydrological drought at high latitudes represents a rising environmental hazard induced byglobal climate change. Yet, we still know little about how drought events influence thebiogeochemistry of boreal streams. Here, I used 15 years of data from eight streams withinthe Krycklan Catchment to test how interannual variability in summer low flows influencesstream water chemistry. My analysis focused several key biogeochemical indicators in thesestreams, including concentrations of dissolved organic carbon (DOC), dissolved organicnitrogen (DON), nitrate (NO3) and ammonium (NH4), as well as the total C/N and NH4/NO3ratios. Overall, results revealed widespread declines in summer average DOC concentrationsand C/N ratios with greater drought severity. These responses likely reflect shifts in thebiogeochemical properties of soils that feed streams during high- versus low-flow summers.By comparison, nitrogen-based parameters were less clearly influenced by drought, exceptfor in mire-dominated headwaters, where NH4 and DON both increased during the lowestflow periods. Overall, the strong effects of flow variability drove a high degree of interannualsynchrony for DOC and C/N across all sites in the drainage system. This synchrony was morevariable overall for nitrogen-based parameters, with several sites having unique year-to-yearchanges in concentrations and ratios. However, strong temporal coherence for NH4 acrossforested streams suggest other broad-scale factors (e.g., related to forest processes) mayregulate interannual patterns for this nutrient. Collectively, results provide insight into howincreases in drought frequency and severity may alter boreal streams and rivers in the future.