Date of Award

Summer 2011

Document Type


Degree Name

Doctor of Philosophy (PhD)


Biological Sciences

First Advisor

Maki, James S.

Second Advisor

Zitomer, Daniel

Third Advisor

Noel, Dale


Anaerobic wastewater treatment is an environmentally and economically beneficial biotechnology in which the degradation of organic compounds in industrial and municipal wastewaters results in the production of methane, an alternative energy source. The degradation of organic waste is carried out by an interdependent microbial community; and the Archaea known as the methanogens complete one of the final steps, producing methane. However, the contribution of methanogens and the community ecology of anaerobic digesters are just beginning to be understood. Specifically, links between methanogen community structure and the successful transformation of organic pollutants to methane have not been clearly defined. In order to examine the relationship between anaerobic digester function and methanogen community structure, anaerobic biomass samples were obtained from anaerobic hydrogen/carbon dioxide enrichment cultures, lab-scale anaerobic digesters, and industrial-scale digesters. DNA and cDNA clone libraries using the methanogen-specific gene mcrA were generated from the enrichment cultures and two industrial digester samples, and quantitative polymerase chain reaction (qPCR) was used to quantify the mcrA genes and transcripts in all of the biomass samples. Phylogenetic analysis of the mcrA sequences found in the clone libraries showed differences in the methanogen communities from different anaerobic biomass samples, even from enrichment cultures started with the same seed sludge. Furthermore, comparison of mcrA genes and transcripts from the enrichment cultures revealed that some methanogens were more active than others. However, no direct links were found between methanogen diversity and digester function. Tandem qPCR and specific methanogenic activity (SMA) assays showed positive correlation between mcrA gene copy number and methane production rates against specific substrates. This result indicates a relationship between the number of methanogens and digester function. Positive correlation was determined between mcrA transcript number and SMA only under certain conditions. This study represents the establishment of a direct link between the microbial community in anaerobic biomass and digester function. The data obtained from these studies provides a better understanding of methanogen communities in digesters which can be applied to develop better assays for monitoring the function of anaerobic biomass, and to engineer better microbial communities that produce more methane for use as renewable fuel.

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