Investigating Biological Approaches for Monitoring and Manipulating Microbial Communities in Anaerobic Digestion

Anaerobic digestion (AD) is green technology used to treat anthropogenic biological wastes while simultaneously generating renewable energy. Our understanding of the composition of the mixed microbial communities that underpin AD has increased substantially in recent years thanks largely to metagenomic sequencing efforts, yet our ability to monitor and manipulate them in a controlled and predictable manner has not kept pace. The objective of this project was to investigate biological approaches at the whole organism level through which this might be achieved. Methods aimed at improving AD whole cell biosensors through integration of volatile reporter genes were investigated. Genetic techniques were used to exogenously express a recently discovered anaerobic ethylene synthesis pathway, with results demonstrating preliminary evidence of successful synthesis of this valuable chemical precursor in an engineered bacterial system. Proof of principle work was used to demonstrate the potential of targeted microbial isolation techniques and directed evolution for AD chassis organism improvement, resulting in the successful generation of bacterial strains with increased fitness in anaerobic conditions, accompanied by sequencing data revealing possible causative genetic changes. Culturomics and a custom isolate identification strategy were also successfully applied to AD microorganisms. It is hoped that the results and ideas presented in this thesis will facilitate further development of targeted AD monitoring and manipulation approaches in the future.