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.

Indiana University-Purdue University Indianapolis (IUPUI) / Riparian buffers have well documented capacity to remove nitrate (NO3-) from runoff and subsurface flow paths, but information on field-scale N2O emission from these buffers is lacking. This study monitored N2O fluxes at two agricultural riparian buffers in the White River watershed (Indiana) from December 2009 to May 2011 to assess the impact of landscape and hydrogeomorphologic factors on emission. Soil chemical and biochemical properties were measured and environmental variables (soil temperature and moisture) were monitored in an attempt to identify key drivers of N2O emission. The study sites included a mature riparian forest (WR) and a riparian grass buffer (LWD); adjacent corn fields were also monitored for land-use comparison. With the exception of net N mineralization, most soil properties (particle size, bulk density, pH, denitrification potential, organic carbon, C:N) showed little correlation with N2O emission. Analysis of variance (ANOVA) identified season, land-use (riparian buffer vs. crop field), and site geomorphology as major drivers of N2O emission. At both study sites, N2O emission showed strong seasonal variability; the largest emission peaks in the riparian buffers (up to 1,300 % increase) and crop fields (up to 3,500 % increase) occurred in late spring/early summer as a result of flooding, elevated soil moisture and N-fertilization. Nitrous oxide emission was found to be significantly higher in crop fields than in riparian buffers at both LWD (mean: 1.72 and 0.18 mg N2O-N m-2 d-1) and WR (mean: 0.72 and 1.26 mg N2O-N m-2 d-1, respectively). Significant difference (p=0.02) in N2O emission between the riparian buffers was detected, and this effect was attributed to site geomorphology and the greater potential for flooding at the WR site (no flooding occurred at LWD). More than previously expected, the study results demonstrate that N2O emission in riparian buffers is largely driven by landscape geomorphology and land-stream connection (flood potential).