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Anaerobic digestion (AD) is a sustainable waste management technology that primarily generates two products: biogas and digestate. The technology relies on the microorganisms' activity, which depends on several operational factors, such as pH, temperature, solid contents, and ammonia levels. Ammonia is an inorganic form of nitrogen resulting from the biodegradation of organic nitrogen. It is considered one of the major concerns for AD operations due to its inhibitory effects on some microorganisms, particularly methanogens. A common feedstock characterized by high nitrogen content is poultry manure (PM). PM is often avoided in anaerobic digesters due to the anticipated inhibition resulting from its high ammonia levels. However, since poultry manure is one of the most widely available organic wastes, researchers have extensively investigated ways to include PM as a primary feedstock for AD. One possible way to treat high ammonia levels in digestate is ammonia stripping, the physio-chemical separation of ammonia from a solution by introducing a stripping (carrier) gas. There are a few approaches to performing ammonia stripping in AD applications; the most commonly discussed in the literature are pre-hydrolysis and side-stream ammonia stripping. Pre-hydrolysis ammonia stripping is performed on raw feedstock after increasing pH and temperature and is usually not restricted in selecting the gas carrier. On the other hand, side-stream ammonia stripping is when a portion of the digester's working volume is filtered, and the filtrate is sent to a unit where pH and temperature are increased. The carrier gas in these systems is often limited to anaerobic gases such as biogas or steam. The third and most novel approach is post-hydrolysis ammonia stripping, conducted at an intermediate stage between hydrolysis and methanogenesis in a two-stage AD process. This configuration would address the shortcomings of the other two systems. However, there is minimal information on the feasibility and potential of this approach in the literature. This study aims to comprehensively investigate the post-hydrolysis ammonia stripping approach through the following four phases: Phase I) Proof of Concept; Phase II) Optimization; Phase III) Assessment of Alternative Carrier Gases; and Phase IV: Comparison of Different Ammonia Stripping Configurations. Phase I provided the proof of concept under the batch mode and compared the performance of post-hydrolysis ammonia stripping with two-stage AD and co-digestion to improve poultry manure's methane potential as the primary substrate. It was observed that ammonia stripping successfully improved methane potential by up to 150%, whereas improvements due to two-stage AD and co-digestion were limited to 41 and 9%, respectively. Phase II provided more insight into optimizing the ammonia stripping process. Different stripping conditions were tested (pH 7.8 (unadjusted), 9 and 10, temperature 25 (unadjusted), 40 and 55 °C, and flow rate 300 L/L/hour). The results showed that higher pH and temperature lead to higher removal efficiency. However, it was concluded that optimal conditions ultimately depend on the initial and target ammonia levels. Moreover, Analysis of Variance showed that pH and temperature were significant factors affecting the ammonia removal efficiency. In addition, it was observed that higher stripping temperatures (55 °C) enhanced the digestibility of PM and increased its methane potential more than stripping at 40 °C. It was concluded that the optimum stripping conditions were pH 9.5, temperature 40 or 55 °C, and flowrate of 100 L/L/hour to collectively increase ammonia removal while reducing the associated costs and material handling. In Phase III, renewable natural gas (RNG) was evaluated as a stripping medium in batch testing as a potential replacement for biogas and air. Ammonia stripping with RNG yielded promising results comparable to the application of air in terms of ammonia removal and enhancing biogas production from PM (60 and 69% ammonia removal for RNG and air, respectively). In addition, a metagenomic shotgun analysis showed that most biogas production was conducted through hydrogenotrophic methanogens instead of acetoclastic methanogens, which are more susceptible to high ammonia levels. Phase IV assessed the semi-continuous flow two-stage operation of mesophilic AD reactors coupled with different ammonia stripping configurations. Post-hydrolysis ammonia stripping successfully achieved a stable operation of PM mono-digestion at ammonia levels of 1700 and 2400 mg NH₃-N/L in the cases of stripping with air and RNG, respectively. In addition, post-hydrolysis ammonia stripping in semi-continuous flow mode may have promoted acetoclastic methanogens growth since volatile fatty acid concentrations were reduced in the digesters. Phase IV also proved that the performance of post-hydrolysis ammonia stripping is superior over pre-hydrolysis and side-stream ammonia stripping. In the semi-continuous flow reactors, post-hydrolysis ammonia stripping with air achieved on average 831 L biogas/ kg VS at an organic loading rate (OLR) of 2.6 g VS/L/day, whereas side-stream ammonia stripping resulted in average of 700 L biogas/ kg VS at OLR of 1.8 g VS/L/day and higher ammonia stripping requirements. Having said that, the base scenario (no ammonia stripping) was inhibited, indicating that both ammonia stripping configurations were considered successful in alleviating inhibitory effects of ammonia from poultry manure. Phase IV results also proved that air stripping repeatedly outperformed RNG as stripping mediums by having higher ammonia removal efficiencies resulting in higher methane production. However, stripping with RNG is believed to have more practical advantages than air due to avoiding the risk of oxygen infiltration into the reactor. Moreover, renewable natural gas has proven to be an efficient stripping medium that is available on-site. The final stage of Phase IV tested pre-hydrolysis ammonia stripping using air in batch mode and compared it with post-hydrolysis ammonia stripping. Pre-hydrolysis ammonia stripping provided little to no improvement to the methane potential of PM in batch mode and therefore was excluded from the semi-continuous flow experiment. The four phases of this study demonstrated the flexibility and the superiority of post-hydrolysis ammonia stripping over the other pre-hydrolysis and side-stream ammonia stripping. In addition, post-hydrolysis ammonia stripping was proven efficient and feasible for ammonia removal and enabling the mono- or co-digestion of poultry manure. The study also showed that using RNG instead of biogas can significantly reduce the operational costs of the treatment.

The efficient use of resources and sustainable recovery of various materials are important to minimize the anthropogenic impact on the climate and environment. One such resource is the phosphorus present in manure and sewage sludge. Various technologies are currently being developed to recover the phosphorus for the use of fertilizers in agricultural applications. Thermochemical conversion presents an opportunity to recover energy from these materials. At the same time, elements can be recovered in ash fractions, potentially harmful organic substances can be destroyed and heavy metals fractionated from the P. Mono-combustion of sewage sludge mainly produce apatite, which is not plant available and useful for fertilization. Co-combustion/-gasification with other fuels enables modification of ash transformation pathways and also remedy potential problems, such as bed agglomeration, associated with e.g. agricultural residues used as fuels. This thesis aims to increase the current knowledge in ash transformation of phosphorus-rich materials in cocombustion/-gasification with woody and agricultural fuels in process temperatures relevant for fluidized bed systems. The work focuses on i) possibility for formation of plant-available K-bearing phosphates ii) the effect of fuel ash composition and chemical association of P in the fuel on the distribution and speciation of P and iii) interaction of P-rich ash with bed material in fluidized beds. Experiments were carried out in bench-scale bubbling fluidized bed (BFB), macro-TGA (thermogravimetric analysis) combustion reactors and a dual fluidized bed (DFB) gasification reactor. Fuels studied were mixtures of chicken litter together with wheat straw and bark, and mixtures of digested sewage sludge combined with wheat straw and sunflower husk. Ash fraction and bed materials were collected and analyzed using ICP-OES/MS, SEM-EDS and XRD techniques. For the mixture of chicken litter and K- and Si-rich wheat straw, combusted in BFB, P and Si together with K and Ca formed homogeneous ash particles with large amounts of potentially amorphous iv content. A similar behavior was observed in sewage sludge and wheat straw mixtures where P and Si were likely present in a melt that is amorphous after extraction. In addition to these particles, P was also found in crystalline compounds such as hydroxyapatite, whitlockite and CaKPO4. For mixtures with Ca-rich bark, most of the phosphate formed was in the form of hydroxyapatite. In the interaction of ash with bed material, P captures Ca and K in phosphates, decreasing the interactions of these elements with the bed material, and thus can decrease the risk for bed agglomeration. The findings show that it is possible to modify the ash transformation of P towards K-bearing phosphates by co-combustion. Furthermore, they suggest that it is possible to recover most of the phosphorus in coarse ash fractions through co-combustion of P-rich materials with agricultural fuels. This means that P and volatile heavy metals can be separated into different ash fractions. This also increases the possibility of utilizing existing boilers for recovery of P as well as increased their flexibility to different fuels. To further validate the agricultural value of the produced ashes, plant growth studies have to be performed.

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Antibiotics and antibiotic resistance genes from animal manure applied to soil as fertilizer are now among the most concerned contaminants in soil. The widespread use of antibiotics in livestock might amplify the risk of developing antibiotic resistance, causing once treatable diseases to turn deadly. The World Health Organization declared antibiotic resistance as "one of the biggest threats to global health, food security, and development". The goal of this dissertation was to develop best manure management practices by understanding the behavior of manure-associated antibiotics in manure, water, and soil. In particular, my research focused on the effects of manure application methods, on-site manure treatment methods, manure application seasons, and manure-rainfall time gaps on antibiotic surface runoff losses, antibiotic distribution and movement in soil, antibiotic dissipation in soil, and development of antibiotic resistance. Rainfall simulation field-scale and soil incubation lab studies were combined to find the best manure management practices. My research has shown for the first time that using the manure soil subsurface injection method, especially during spring application season due to moist soil, applying manure at least 3 days before a subsequent rainfall, and using composted manure, can significantly reduce the quantity of antibiotic loss with runoff from manure-applied fields to the surrounding environment. The majority of applied antibiotics remained in soil. All antibiotics showed a similar dissipation pattern with fastest kinetics during the first 14 d before slowing down. The effect of two manure application methods on antibiotic dissipation kinetics varied with different antibiotics. Although the half-life of tested antibiotics in soil was short (<21 days), some remained detectable even at 6 months after a single manure application. Results also showed that compared to the surface application, the subsurface injection slits acted as a "hot zone" with a higher amount of antibiotics, manure microbes, and antibiotic resistance. The results provide information for policy makers, manure managers, and farmers to develop better manure management practices that can use manure as fertilizer while minimizing the spread of antibiotics to surrounding water, soil, and plants. / Doctor of Philosophy / There is growing concern about antibiotic resistance as a serious human health threat because a resistant infection may kill, can spread, and increases health costs. Every year in the United States, there are 2 million people infected with antibiotic resistant bacteria, 23,000 people die as a direct result of these infections, and $55 billion is lost due to increased hospital stay and lost work days. Although bacteria naturally develop the ability to resist antibiotics, the problem is the length between antibiotic introduction and resistance development is shortening because of the widespread and overuse of antibiotics, especially in the livestock industry. The goal of this study was to develop the best manure management practices balancing the benefits of antibiotics in livestock and animal manure and their impact on the environment. In particular, we monitored, using field-scale and laboratory studies, the effects of manure application methods, on-site manure treatment methods, manure application seasons, and manure-rainfall time gaps on antibiotic loss through surface runoff, antibiotic distribution and movement in soil, antibiotic dissipation in soil, and development of antibiotic resistance. In order to reduce the amount of antibiotic loss with surface runoff from manure-applied fields to the surrounding environment, farmers are recommended to 1) compost manure before application, 2) watch the forecast to apply manure at least 3 days before a subsequent rainfall, and 3) use the subsurface injection method, especially when the soil is wet (spring season). The majority of applied antibiotics remained in soil. All tested antibiotics showed a similar dissipation pattern with the fastest rate during the first two weeks after manure application, then slowing down. Although the half-life of tested antibiotics in soil was short (<21 days), some remained detectable even at 6 months after a single manure application. Besides, the subsurface injection slits acted as a hot zone with a concentrated amount of antibiotics, manure microbes, and antibiotic resistance. The results provide recommendations for policy makers, manure managers, and farmers to maximize benefits of manure as fertilizer while minimizing the spread of manure-associated antibiotics to surrounding water, soil, and plants.

Despite significant vector control advancements in the past years, the current malaria trends suggest that new control strategies are urgently required. These new approaches should address the current frontline intervention challenges like increasing insecticide resistance in mosquitoes and residual transmission issues. Insecticide-treated livestock (ITL) is one of the novel potential strategies to overcome the above challenges. ITL involves treating livestock near humans with an insecticide like ivermectin (IVM) to kill zoophagic malaria vectors. However, ivermectin pharmacokinetics data suggests that most IVM-administered drugs remain intact, and more than 90 % of this drug is eliminated in feces. Biological metabolites: 3′′-O-demethylivermectin (3DI) and 24-hydroxymethyl ivermectin (24OHI) are also excreted in feces. Therefore, using manure from treated cattle as fertilizers contaminates the soil, ground, and surface water with IVM or its metabolites through leaching and hydraulic water flow affecting the soil and aquatic ecosystems. Contemplating the contamination impacts, these drugs' environmental fate and effects could be regarded before massive IVM applications. Many researchers have tried to address this subject in temperate regions compared to the tropics, where IVM is urgently needed. Regional discrepancies such as soil types and climate can independently and dependently determine the fate and impact of ivermectin. Our research investigates the environmental fate of IVM and its primary biological metabolites. Laboratory and field studies in Tanzania and Virginia were conducted to simulate the difference between tropical and temperate climates. Soil and soil-manure mixture spiked with IVM were layered into two 5 mm layers in columns exposed to natural sunlight. The remaining IVM and its primary metabolite were quantified using Liquid Chromatography with a tandem mass spectrometry detector (LC-MS/MS. These compounds degraded up to 1.5 times faster in Tanzania than in Virginia, depending on temperature, soil depths and type, organic matter, and soil moisture. When IVM is subcutaneously injected into cattle, drug residues and metabolites: 3DI and 24OHI are excreted in feces following a positive skewed Poisson distribution profile. IVM, 3DI, and 24OH were found to degrade rapidly when cattle pats when exposed to the field. Since we conducted our study in the Summer, no IVM or its metabolites leached into the soil beneath. The obtained half-lives suggest that ivermectin's massive drug administration has little to worry about, primarily when the dung from treated cattle is spread into the field in thin layers in the Summer before farm application. / Doctor of Philosophy / Despite significant vector control advancements in the past years, the current malaria trends suggest that new control strategies are urgently required. These new approaches should address the current frontline intervention challenges like increasing drug resistance in mosquitoes and residual transmission issues. Treating cattle with ivermectin is one of the novel potential strategies to overcome the above challenges. This strategy is effective because the amount of ivermectin (IVM) found in the blood of treated cattle is enough to kill malaria vectors feeding on them. However, the literature suggests that most IVM-administered drugs remain intact, and more than 90 % of this drug is eliminated in feces. Metabolite bioproducts: 3″-O-demethylivermectin (3DI) and 24-hydroxymethyl ivermectin (24OHI) are also excreted in feces. Therefore, using manure from treated cattle as fertilizers contaminates the soil, ground, and surface water with IVM or its metabolites through leaching and hydraulic water flow affecting the soil and aqua ecosystems. Contemplating the contamination impacts, these drugs' environmental fate and effects could be regarded before massive IVM applications. Many researchers have tried to address this subject in temperate regions compared to the tropics, where IVM is more needed. Regional discrepancies such as soil types and climate can independently and dependently determine the fate and impact of ivermectin. Our research investigates the environmental fate of IVM and its primary bioproducts. Laboratory and field studies in Tanzania and Virginia were conducted to simulate the difference between tropical and temperate climates. Soil and soil-manure mixture spiked with IVM were layered into two 5 mm layers in columns exposed to natural sunlight. The remaining IVM and its primary metabolite were quantified on the appropriate instrument. These compounds degraded up to 1.5 times faster in Tanzania than in Virginia, depending on temperature, soil depths and type, organic matter, and soil moisture. When IVM drug is injected into cattle, the intact drug and its bioproducts: 3DI and 24OHI, are eliminated in feces following a favorable skewed normal distribution profile. IVM, 3DI, and 24OH were found to degrade rapidly when cattle pats when exposed to the field. Since we conducted our study in the Summer, no IVM or its bioproducts leached into the soil beneath. The obtained data suggest that ivermectin's massive drug administration has little to worry about, primarily when the dung from treated cattle is spread into the field in thin layers in the Summer before farm application.