Date of Award

Summer 2012

Document Type


Degree Name

Doctor of Philosophy (PhD)


Civil, Construction, and Environmental Engineering

First Advisor

Zitomer, Daniel H

Second Advisor

Maki, James

Third Advisor

Seston, Sherry


A deeper understanding of how microbial community structure relates to process function would help improve anaerobic digester design. This dissertation describes both qualitative and quantitative relationships between anaerobic digester function and microbial community structure. Community structure was characterized using banding pattern intensities from denaturing gradient gel electrophoresis (DGGE) for the mcrA gene of methanogenic Archaea. The first project compared a single-stage continuously mixed stirred tank reactor (CSTR) and staging with an acidogenic CSTR followed by a methanogenic CSTR. After seeding with the same biomass, these unique process configurations exhibited different function and qualitatively different methanogen communities. Compared to a single-stage CSTR, staging increased the maximum rate of methane production by 41, 26, and 57% with propionate, acetate, and hydrogen, respectively. Additionally, the staged digester produced 10% more methane and achieved 10% greater volatile solids (VS) destruction. The second project also provided a qualitative relationship: methanogen community structure impacted digester function upon bioaugmentation. Specific methanogenic activity (SMA) with propionate statistically increased (up to 57%) in six of nine bioaugmented anaerobic cultures. These increases correlated to methanogen community structure above the 98% level (rs = 0.770) using Spearman’s Rank Correlation Coefficient (two-tailed). In the third project, a quantitative structure-activity relationship (QSAR) was established between methanogen community structure and two activities using multiple linear regression (MLR). Two different QSARs were predictive of SMA values with propionate (q2 = 0.52) and with glucose (q2 = 0.56), respectively. A MLR model may be applicable to other biological communities when trophic redundancy and a ubiquitous gene are present and when a linear model is appropriate. Greater understanding of anaerobic digester microbial communities is possible using these QSARs. This research serves as a template that can be used to construct additional QSARs for other complex microbial communities in engineered systems.