During anaerobic digestion (AD) of high-nitrogen wastes, organically bound nitrogen is released as ammonia. If ammonia concentrations are too high, ammonia toxicity may occur and contribute to reactor failure. To avoid ammonia toxicity, operators often blend low and high nitrogen wastes to achieve lower ammonia concentrations. However, if better AD performance and process stability can be achieved when ammonia is high, then feedstock blending would be unnecessary and the ammonia released could be harvested at high concentrations as a fertilizer or energy source. The goal of the research described in this dissertation was to enrich and identify ammonia tolerant microorganisms from different anaerobic waste treatment systems including: landfill leachate obtained from a bioreactor landfill in New Jersey and a traditional landfill in Thailand; an anaerobic digester treating swine waste; and a municipal wastewater treatment plant sludge digester. Total ammonia nitrogen (TAN) concentrations of up to 12.5 g TAN/L were imposed on reactors inoculated from the different treatment systems and were fed glutamate as a model nitrogen-containing substrate. A longer start-up phase, decreased methane production, and accumulation of volatile fatty acids (VFAs) generally occurred at high TAN concentrations. Microbial community shifts were evident and were related to different TAN concentrations, fluctuations in VFA concentrations, and methane production. The Thailand reactors appeared to have the greatest intrinsic ammonia resistance. Compared to the other inocula, little reactor instability was observed in Thailand leachate enrichments, even at the highest TAN concentrations. In constrast, the municipal anaerobic digester sludge had no instrinsic capacity to adapt to ammonia stress. Divalent cation effects (Ca2+ and Mg2+) to counteract ammonia toxicity were also investigated in the swine waste digestate reactors. The presence of counter ions was related to enhanced tolerance by certain microbial strains to ammonia. Microbial community analysis of 16S rRNA genes using denaturing gradient gel electrophoresis (DGGE) and 454 pyrosequencing, revealed that phylotypes related to Tepidanaerobacter acetatoxydans, an anaerobic, syntrophic acetate-oxidizing bacterium, in the phylum Firmicutes was dominant in reactors inoculated with landfill leachate (both Thailand and New Jersey) and swine waste digestate (including Ca2+-amended reactors). In contrast, phylotypes matching Thermanaerovibrio acidaminovoran, a moderately thermophilic, syntrophic, glutamate-degrading bacterium, was detected at low TAN concentrations, mainly in reactors inoculated with wastewater sludge digestate. Archaeal community analysis revealed that phylotypes matching Methanosarcina spp. in the phylum Euryarchaeota were dominant in reactors inoculated with Thailand landfill leachate, swine waste digestate (target 0.5 to 5 g TAN/L) and swine waste digestate with divalent cation addition—all of which exhibited relatively stable operation. The presence of Methanosarcina spp. at higher TAN concentrations thus suggested that its presence may impart reactor resistance at high TAN concentrations. In contrast, reactors from New Jersey landfill leachate, second generation reactors from swine waste digestate (target 5 to 12.5 g TAN/L), and reactors from the municipal wastewater treatment plant sludge digester had phylotypes matching Methanoculleus spp. as the dominant methanogens. These reactors generally excibited greater reactor instability as indicated by VFA accumulation and decreased methane production. Overall, this study provides important information about ammonia tolerant microorganisms from different anaerobic waste treatment systems. Different systems had very different capacities for adapting to ammonia stress. Knowledge of inoculum sources containing ammonia-tolerant microbial communities could aid in developing bioaugmentation strategies for more rapid adaptation of AD systems treating high nitrogen wastes.Ph.D.Includes bibliographical referencesby Sunirat Rattan