Date of Award

Summer 2016

Document Type


Degree Name

Doctor of Philosophy (PhD)


Civil and Environmental Engineering

First Advisor

Zitomer, Daniel

Second Advisor

Hristova, Krassimira

Third Advisor

Switzenbaum, Michael

Fourth Advisor

Maki, James


This dissertation describes two research projects on anaerobic digestion (AD) that investigated the relationship between microbial community structure and digester function. Both archaeal and bacterial communities were characterized using high-throughput (Illumina) sequencing technology with universal 16S rRNA gene primers. In the first project, bioaugmentation using a methanogenic, aerotolerant propionate enrichment culture was investigated as a possible method to increase digester methane production. Nine anaerobic digesters, seeded with different biomass, were operated identically and their quasi steady state function was compared. Before bioaugmentation, different seed biomass resulted in different quasi steady state function, with digesters clustering into high, medium or low methane (CH4) production groups. High CH4 production correlated with neutral pH and high Methanosarcina abundance, whereas low CH4 production correlated to low pH and high Methanobacterium and DHVEG-6 family abundance. After bioaugmentation, CH4 production from the high CH4-producing digesters transiently increased by 11±3% relative to non-bioaugmented controls (p <0.05, n=3), whereas no functional changes were observed for medium and low CH4 producing digesters. The CH4 production increase after bioaugmentation was correlated to increased relative abundance of Methanosaeta and Methanospirillum originating from the bioaugment culture. In conclusion, different anaerobic digester seed biomass can result in different quasi steady state function. The bioaugmentation employed can result in a period of increased methane production. In the second project, a quantitative structure activity relationship (QSAR) between anaerobic microorganism relative abundance values and digester methane production rate was developed using 150 lab-scale anaerobic digesters seeded with 50 biomass samples obtained from 49 US states. Although all digesters were operated identically for a minimum of 5 retention cycles, their quasi steady-state performance varied significantly, with the average daily methane production rate ranging from 0.09±0.004 to 0.98±0.05 L-CH4/LR-day (average ± standard deviation). Analysis of over 4.1 million-sequence reads revealed approximately 1300 operation taxonomical units (OTUs) at the genus level across all digesters, with each digester having 158±27 OTUs (mean ± standard deviation). Using Spearman’s rank correlation, 10 OTUs, which included one archaeal OTU, were found to significantly correlate to digester methane production rate. The relative abundance values of the 10 OTUs were used as descriptors to develop a MLR equation, with good statistical prediction of the digester methane production rates. The results are encouraging and provide an initial step for further research to develop more robust QSAR models to predict the function of anaerobic and other bioprocesses using microbial community descriptors.