Date of Award

Fall 2012

Document Type


Degree Name

Master of Science (MS)


Biological Sciences

First Advisor

Maki, James S.

Second Advisor

Noel, Dale K.

Third Advisor

Zitomer, Daniel H.


Methanogens are integral to carbon cycling, catalyzing the production of methane and carbon dioxide, both potent greenhouse gases. Methane is produced in a wide variety of highly reduced anaerobic environments, as well as by degradation of organic compounds in industrial and municipal wastewater. This process is carried out by the concerted activity of an interdependent microbial community, composed of Bacteria and Archaea, the later including methanogens which complete the final step and produce methane and carbon dioxide. Methanogenesis is often the rate limiting step and is sensitive to processing imbalances. Therefore, an understanding of the microbial community structure and dynamics in anaerobic process is a basic requirement to optimize anaerobic digestion for increased renewable energy production. To examine the relationship between methane production and methanogen community structure, quantitative polymerase chain reaction (qPCR) was used to quantify the total methanogen community (mcrA gene) as well as specific genera (16S rRNA gene) in biomass from industrial scale digesters. Results from this study revealed that there was a positive correlation between methane production and mcrA and Methanospirillum transcripts. It was also found that reactors not dominated by any particular genus, but those that had a balanced community of hydrogenotrophic and aceticlastic methanogens had a higher capacity to resist organic overload and produce methane. One of the major problems faced in anaerobic digestion process is its inherent instability and sensitivity to frequent exposure to oxygen. qPCR analyses of 16S rRNA revealed that Methanoculleus had significantly lower activity, while Methanospirillum and Methanosaeta had significantly higher activity at higher oxygen concentrations. Finally, this study also presents the use of freeze drying as a viable method for preserving anaerobic methanogenic biomass. qPCR with 16S rRNA genus specific primers revealed that methanogens varied in their ability to tolerate the process of freeze drying. Methanospirillum had the highest 16S rRNA transcripts before and after drying, followed by Methanosaeta and Methanoculleus. Therefore, the data obtained from this study helps to determine the identity of desirable organisms and community architecture in relation to digester performance, exposure to oxygen and low temperature desiccation encountered during preservation by freeze drying.

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Microbiology Commons