Anaerobic bioreactors are useful for neutralizing wastes while simultaneously generating energy in the form of methane. These reactors are widely used at municipal wastewater treatment plants to reduce biosolids and generate on-site power. With the potential to yield net energy, this technology is a sustainable method of waste treatment, and may eventually replace tradiational aerobic reactors. Its popularity continues to grow and is now commonly applied for the treatment of various agricultural, industrial, manufacturing, and landfill wastes.

Anaerobic Digesters have been used for over 100 years to neutralize waste and produce energy-rich biogas, but operated with minimal understanding of their complex biochemistry. Anaerobic digestion proceeds as a biochemical cascade; various microbial groups degrade initially complex substrates to produce carbon dioxide, methane, and undigested residuals. The process fails in a bioreactor when conditions become inhospitable to its microbes. A thorough understanding of what conditions are favorable to anaerobic digestion requires that both the quantity of microbes and their metabolic activity be quantified. The difficulty of accurately measuring anaerobes led previous research to focus mostly on metabolic activity. Quantitative Polymerase Chain Reaction (qPCR) presents new opportunities to measure the quantity of the various organisms that dynamically interact in anaerobic digesters and better understand how these groups are affected by operating conditions. Accurate measurements of organism concentration may improve the predictive power of wastewater models, leading to informed digester operation optimized for energy production and reactor stability. Within this thesis are two papers where qPCR measurements were used to study the microbiology of full-scale and laboratory-scale digesters. A third paper describes a new method to quantify the efficiency of DNA extractions that precede qPCR.

Automated and continuous measurements of biogas flow rates are useful for studying the kinetics of anaerobic digestion. Respirometers are commercially available to accurately measure the low gas flow rates produced by laboratory-scale digesters, but their cost may be prohibitive, and many only measure one gas. The fourth chapter of this thesis describes an economical respirometer that was designed, built, and used for the continuous measurement of biogas flow and composition.