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Determining the Microbial Community Dynamics of Anaerobic Digestion Using Metagenomics

Nicholls, Henry (2015) Determining the Microbial Community Dynamics of Anaerobic Digestion Using Metagenomics. PhD thesis, University of York.

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Abstract

Anaerobic Digestion (AD) is a biologically mediated technology that is used as a method for managing and obtaining energy from organic waste materials. Through the biological action of Bacteria, Fungi and Archaea, in the absence of oxygen, the organic waste is converted to biogas, mainly methane, which can be used as a fuel source. This gas can be burned to generate electricity, heat, injected into the grid or used to fuel vehicles. I have developed a single stage, lab scale anaerobic digester that is a reflection of full-scale process systems. This model reactor facilitates the collection of samples for metagenomic sequencing, along with process data, providing an insight to the AD process. Three experiments were carried out (using the lab model) to determine (i) the dynamic changes that occur in microbial AD communities, (ii) the rate at which these communities change and (iii) if the observed changes are comparable between numerous systems run under the same conditions. The use of amplicon sequencing appears to be a common method used to study the composition of microbial communities, especially in AD, but this method is prone to inaccuracies and so alternative methods were developed, as described in this thesis. By applying the use of shotgun metagenomic sequencing, combined with various contig assemblers and a custom clustering method, more detail on the microbes present and their functions in AD is obtained compared to targeted sequencing. Pipelines to interpret large datasets generated through Next Generation Sequencing (NGS) have been developed and utilised in this project. We have identified microbes that are present within the AD system, and the time-scale of the dynamic changes. This method has also revealed novel methanogens that are important in the AD process.

Item Type: Thesis (PhD)
Academic Units: The University of York > Biology (York)
Depositing User: Mr Henry Nicholls
Date Deposited: 24 May 2016 09:44
Last Modified: 24 May 2016 09:44
URI: http://etheses.whiterose.ac.uk/id/eprint/13154

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