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Thermophilic aerobic digestion was investigated as a potential waste treatment technology for biodegradable wastes generated in a long-term closed eco-system. The overall objectives of this research were to contribute to a regenerable closed-loop system for food production and water, air and waste treatment, while also minimizing the mass, volume, power, cooling and crewtime needs of the overall system. Biological treatment becomes more feasible due to resupply constraints with longer mission scenarios. The primary objectives of this research included the evaluation of the system, including effects of influent solids loadings, hydraulic retention time, oxygen transfer, and the influence of operational parameters such as pH, ORP, and temperature. Investigation into the effect of mechanical changes in the system on oxygen transfer was evaluated.