The effect of global warming on methane (CH₄) and nitrous oxide (N₂O) emissions from agriculture was investigated and simulated from a soil warming experiment. Experiments were designed and installed in a temperature controlled greenhouse. The relationships between elevated temperatures and CH₄ and N₂O emissions were determined and calculated as the Q₁₀s of production, emission and oxidation. A study of the populations of methanogens and methanotrophs at a range of soil temperatures was performed based on soil molecular DNA analysis. This study showed that global warming would increase CH₄ emissions from rice agriculture and that the resultant emissions will be potentially large enough to cause changes in the present atmospheric concentrations. This research also showed that this increase was most evident for soil temperatures below 30⁰C, above which emissions decreased with increasing temperature. The seasonal average Q₁₀s of CH₄ emission, production, oxidation, methanogen and methanotroph populations were found to be 1.7, 2.6 and 2.2, 2.6 and 3.8, respectively, over a temperature of 20-32⁰C. Considering that the processes of CH₄ production and emission are similar to those in natural wetlands, which is the largest source of atmospheric CH₄, the contribution of this feedback is likely to cause a significant increase to the present CH₄ atmospheric budget if the current global warming trend persists over the next century. The Q₁₀s of N₂O emissions and production were 0.5-3.3 and 0.4-2.9, respectively. The low Q₁₀ values found for N₂O suggest that although global warming will have a direct impact on the production and emission rates. Nevertheless, the magnitude of the impact of global on both CH₄ and N₂O emissions from agriculture is likely to vary from one region to another due to the spatial variations in agricultural soil temperatures and the likely changes in the global regional distribution of water resources (water tables, rainfall patterns), water management practices and the responses of terrestrial CH₄ and N₂O sources such as natural wetlands and plants.

This doctoral research provides an advanced molecular approach for the investigation of microbial structure and function in response to operational conditions of biological nitrogen removal (BNR) processes, including those leading to direct production of a major greenhouse gas, nitrous oxide (N₂O). The wastewater treatment sector is estimated to account with 3% of total anthropogenic N₂O emissions. Nevertheless, the contribution from wastewater treatment plants (WWTPs) is considered underestimated due to several limitations on the estimation methodology approach suggested by the Intergovernmental Panel on Climate Change (IPCC). Although for the past years efforts have been made to characterize the production of N₂O from these systems, there are still several limitations on fundamental knowledge and operational applications. Those include lack of information of N₂O production pathways associated with control of aeration, supplemental organic carbon sources and adaptation of the microbial community to the repeated operational conditions, among others. The components of this thesis, lab-scale investigations and full-scale monitoring of N₂O production pathways and emissions in conjunction with meta-omics approach, have a combined role in addressing such limitations. Lab-scale experiments imposing short-term anoxic-aerobic cycling on partial- and full-nitrification based processes were conducted to investigate the microbial response to N₂O production. Interestingly, it was determined that full-nitrification systems could be a higher contributor to N₂O production and emissions than partial-nitrification. While it has been reported in the literature a higher contribution from the latter when the microbial community is not subjected to oxygen cycling conditions. Following the knowledge obtained with a single anoxic-aerobic cycle imposed to nitrifying communities, long-term adaptation of the microbial community to continued anoxic-aerobic cycling and its impact on N₂O production were investigated through a meta-omics approach. Long-term studies are particularly significant regarding engineered systems, where the microorganisms are continually subjected to cycling conditions again and again. A microbial adaptation at the RNA level was identified on both autotroph and heterotroph organisms. The transcripts of the metabolic pathways related to NO and N₂O production (nir, nor) and consumption (nor, nos) were initially induced followed by a gradual decline, leading to a parallel reduction in gaseous emissions over time. Other pathways not typically interrogated in conjunction with the nitrogen metabolism, such as electron transport chain and carbon fixation were also investigated and revealed a mechanism to overcome the imbalance in electron flow and generation of proton motive force (increased transcription of terminal oxidase genes, cco and cox) to uphold carbon fixation during continued cycling. The second part of this thesis focuses on full-scale WWTPs, where it is crucial to determine specific nuances of the systems’ dynamics and of the different types of treatment that may contribute to increased production and emissions of N₂O. For that purpose, two distinct BNR systems not usually considered and studied in terms of N₂O production and emissions were chosen. First, a separate centrate treatment (SCT) process employing glycerol as the supplemental carbon source was monitored. Significantly, this system was found to have one of the highest levels of N₂O production and emission report thus far. Glycerol revealed to foster a microbial community (i.e. Burkholderiales, Rhodobacterales and Sphingomonadales) that stores internal carbon and promote partial denitrification, leading to accumulation of nitrite and N₂O [7-11]. Second, both fixed- and moving-bed biofilm BNR systems were investigated. The overall N₂O emission fractions for the Integrated Fixed-Film Activated Sludge (IFAS)(0.09 – 1.1% infl-TKN) and denitrification filters (0.11 – 1.4% infl-TN) were similar to the reported emissions from suspended growth activated sludge systems [4-6]. For the IFAS system, aqueous and gaseous N₂O profiles paralleled the diurnal variability on influent nitrogen load. The production of N₂O was significantly correlated with ammonia concentration (p<0.05, r=0.91), suggesting the production through hydroxylamine oxidation pathway. Denitrification filters displayed a very peculiar pattern on N₂O emissions associated with intermittent operational cycles (i.e. nitrogen release cycle and backwash). These intrinsic operations of the denitrification filters contributed to transient oxygen conditions and nearly the entire N₂O emissions through gaseous stripping and production by inhibition of denitrification. Similarly to suspended growth systems, process design and operations demonstrated to also play an important role in N₂O emissions from attached growth processes. Finally, aeration strategies for energy efficient conventional nitrification based on the microbial community development and its associated performance was investigated in lab-scale. It was demonstrated that using the same air supply rate, continuous and intermittent aeration resulted in completely different microbial structure. Consequently, distinct kinetics and nitrification performance were observed. The aeration rate could be minimized (resulting in reduction in energy consumption) for high ammonia removal efficiency and lower N₂O emissions, as long as the process is designed accordingly to the microbial ecology developed in such conditions. In sum, the microbial structure, function and connection of metabolic pathways of complex engineered microbial communities as applicable to BNR systems and its operations were investigated in detail. From an engineering perspective, this dissertation provides an advancement on the molecular approach to characterize structure and function of microbial responses to engineered operations beyond the business-as-usual target genes, which can eventually result in better design and control of engineered BNR processes. This study offers more than an improved scientific understanding of the complex microbial environment and direct engineering applications. It connects sanitation with water quality and the greenhouse gas effect by prioritizing concurrent enhanced biological nitrogen removal and mitigation of N₂O production and emission. Ultimately the implications of the result presented herein can provide economical, environmental, health benefits for the society.

Atmospheric nitrous acid (HONO) is a significant and sometimes dominant OH source at polar region. An improved method of detecting HONO is developed using photo-fragmentation and laser-induced fluorescence (LIF). The detection limit of this method is 2-3 pptv for ten-minute integration time with 35% uncertainty. The abundance of laser-induced fluorescence (LIF) HONO measurements during ANTCI (Antarctic troposphere chemistry investigation) 2003 exceeds the pure gas phase model predictions by a factor of 1.92±0.67, which implies snow emission of HONO. A 1D air-snowpack model of HONO was developed and constrained by observed chemistry and meteology data. The 1D model includes pure gas phase chemical mechanisms, molecular diffusion and mechanical dispersion, windpumping in snow, gas phase to quasi-liquid layer phase HONO transfer and quasi-liquid layer nitrate photolysis. Based on the air-snowpack model, snow emission of HONO is highly likely and will be transported to place of the measurements. The pH, thickness of quasi liquid layer and contineous nitrite measurement are key factors to calibrate and validate the air snowpack model.

Nitrogen (N)-fixing trees can both mitigate climate change, by relieving N limitation of plant growth which promotes carbon dioxide (CO²) sequestration in plant biomass, and exacerbate climate change, by stimulating nitrification and denitrification which promotes nitrous oxide (N²O) emissions from soils. The balance between the negative radiative forcing (CO² sequestration in plant biomass) and positive radiative forcing (N²O emissions from soils) of N-fixing trees is unresolved. In this thesis I use a sequence of theoretical and empirical approaches to investigate the influence of N-fixing trees on CO² sequestration by forests and N²O emissions from forest soils, i.e., the net CO²-N²O effect of forests. The first chapter establishes a basis for the N²O effect of N-fixing trees with a meta-analysis, to accompany existing meta-analyses of the CO² effect of N-fixing trees. Chapter one demonstrates that N- fixing trees significantly increase N²O emissions from forest soils relative to non-fixing trees. The second chapter explores the controls and potential global importance of the net CO²-N²O effect of N-fixing trees using a theoretical ecosystem model. The third chapter explores the net CO²-N²O effect of N-fixing trees under manipulations of these controls with a field experiment paired with a modified version of the theoretical ecosystem model from the second chapter. Together, chapters two and three suggest that the net CO²-N²O effect of N-fixing trees is controlled by N limitation of plant growth and the extent to which N-fixing trees can regulate N fixation: N-fixing trees mitigate climate change relative to non-fixing trees under N limitation of plant growth, but N-fixing trees that cannot regulate N fixation exacerbate climate change relative to non-fixing trees under non-N limitation of plant growth. The fourth chapter represents the ecological mechanisms studied in chapters one, two and three in a land model: LM4.1-BNF is a novel representation of biological N fixation (BNF) and an updated representation of N cycling in the Geophysical Fluid Dynamics Laboratory Land Model 4.1 (LM4.1). LM4.1-BNF includes a mechanistic representation of asymbiotic BNF by soil microbes, the competitive dynamics between N-fixing and non-fixing plants, N limitation of plant growth, and N2O emissions from soils. Together these chapters elucidate the influence of N-fixing trees on the capacity of forests to mitigate and exacerbate climate change and establish a framework to analyse and project the trajectory of the net CO²-N²O effect of forests under global change.

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Agricultural systems are known to emit nitrous oxide (N2O)---a potent greenhouse gas. The roving flux tower measuring system of Agriculture and Agri-Food Canada was used to make continuous measurements of N2O fluxes in an edible pea field in Western Quebec in 2003-04 and then in an alfalfa-timothy forage field in Eastern Ontario in 2004-05. The experiment was designed to capture, at the field scale, the expected large N2O emissions occurring as a result of fertilizer application for a year, in relation to both large precipitation events and spring thaw. / Growing season N2O emissions averaged 0.5 to 5 mg N2 O-N m-2 d-1 with peaks following snow melt (between 5 and 8 mg N2O-N m-2 d-1) and manure applications (8 to 37 mg N2O-N m-2 d -1). Although generally small (&lt;0.25 mg N2O-N m -2 d-1), emissions were detectable during the fall and winter, indicating the importance of including them in annual emission totals. / The measurements were used to verify the performance of the simulation model DNDC (DeNitrification-DeComposition) in estimating N2O emissions from legumes and in response to dairy manure application. Sensitivity tests were also carried out in which baseline input values were modified. Results suggest that the current model version (DNDC8.9) requires further modification prior to application for estimating greenhouse gas emissions in national accounting systems.