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There is an ongoing need to develop more sustainable systems for producing energy and treating wastes. Anaerobic digestion is one type of technology that can meet this need. The sustainability and microbial community dynamics of ambient temperature anaerobic digesters was evaluated by this research. An emergy analysis of the EARTH University Taiwanese model anaerobic digesters was performed, and the results were compared to other forms of energy production. The results of this analysis indicate that the EARTH University digester was a more sustainable system than traditional sources of energy production such as oil and natural gas. The success of the EARTH University digesters was due, in part, to the tropical climate of Costa Rica that provides favorable ambient temperature year round for anaerobic digestion. The remainder of this dissertation focused on the analysis of the microbial community dynamics in variable temperature anaerobic digesters. The results of the microbial community analysis of the Waterman fixed-dome digester showed that there are significant shifts in the structure of the both the Archaeal and Bacterial communities tha