Using High-Throughput Gene Surveys to Investigate the Stability of Anaerobic Digestion and Fermentation Processes

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In the carboxylate platform, undefined mixed cultures of anaerobic microbes can be used to convert organic wastes to fuels or valuable industrial chemicals. Anaerobic digestion is an established carboxylate platform technology in which a diverse consortia of microbes break down organic wastes to ultimately produce the gaseous end-product methane. More recently under the carboxylate platform umbrella, researchers have examined directing the anaerobic reactor microbiome toward producing medium-chain carboxylic acids instead of methane, by lowering the reactor pH and utilizing product extraction. The process by which these carboxylic acids are produced is called biological chain elongation. These medium-chain carboxylic acids, such as n-caproic and n-caprylic acid, can be used as antimicrobials in animal feed, in fragrances and flavors, or potentially be upgraded to diesel and aviation fuel. In this dissertation, I will present three studies which looked at the stability of carboxylate platform processes. In the first study, the effect of the dairy antibiotic monensin on the anaerobic digestion of cow manure was investigated. Monensin altered the anaerobic digestion microbiome and decreased methane production, though the digesters were able to adapt during the operating period. In the second study, the effect of changing substrate ratios of ethanol to acetate on the production of medium-chain carboxylic acids and the anaerobic reactor microbiome was investigated. The study found that higher substrate ratios of ethanol to acetate led to increased selectivity for n-caprylic acid production. In the third study, differences in the microbial communities of anaerobic fermenters that were producing medium-chain carboxylates from ethanol and acetate were investigated using Illumina 16S rRNA gene sequencing, shotgun metagenomics, and metaproteomics. In both the second and third studies, I observed that shaping the anaerobic reactor microbiome for medium-chain carboxylate production led to a relatively uneven community, which was dominated by relatively few microbes. This work points toward the need to further improve the stability of the biological chain-elongation process.

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Environmental engineering


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Union Local


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Angenent, Largus

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Werner, Jeffrey J.
Gossett, James Michael

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Biological and Environmental Engineering

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Ph. D., Biological and Environmental Engineering

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Doctor of Philosophy

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dissertation or thesis

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