Genomics of Cellulose Fermentation for Process Optimization

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The use of biotechniology and microorganisms for production of value-added bioproducts is of great importance to industry. Chemical and process engineering methods are used to optimize growth of microorganisms and product yields. However, engineering approaches alone do not take into consideration the genomic basis of microbial metabolism and physiology. Deeper insight into how different growth conditions influence microbial metabolism and physiology may be obtained by understanding the relationships between genome content, gene and gene product expression, metabolic pathway utilization, and end-product synthesis patterns. The current NSERC Discovery grant seeks to understand how changes in process parameters influence microbial metabolism and physiology at the genomic level so that rational, evidence-based strategies for fermentation process optimization may be established. My research is multidisciplinary and applies the tools of genome science (bioinformatics, genomics, transcriptomics, and proteomics) to elucidate changes in gene and gene product expression levels in two model organisms that can utilize cellulose directly as a carbon source: the mesophilic bacterium Clostridium termiditis, and the thermophilic bacterium Clostridium thermocellum. These bacteria will be grown on cellulosic substrates in different types of reactions vessels (sealed tube or bottle reactors without pH control, versus open bioreactor systems with pH control), and with different fermentation processes (batch versus fed-batch versus semi-continuous-feed systems). The short-term objectives of the research are to: 1) investigate the efficiency of cellulose conversion by C. thermocellum and C. termiditis to cell mass and fermentation end-products in batch, fed-batch, and semi-continuous fermentation reactions; 2) identify the biosynthetic mechanisms associated with efficient fermentation systems using transcriptomics and proteomics; and 3) develop a model to predict fermentation end-product synthesis patterns using a mass-spectrometry-based, on-line monitoring system. This research will enable the development of scaled-up processes for direct conversion of cellulose to biofuels via consolidated bioprocessing by i) providing an approach to understanding the mechanisms of fermentation processes at the genomic level; ii) linking process engineering and end-product synthesis outcomes to genomic events; and iii) providing tools for online monitoring of complex fermentation reactions. Through my multidisciplinary research program, 3 PhD, 2 MSc, and 5 undergraduate students will acquire a range of skills that are essential to the growing industrial biotechnology sector of the Canadian economy.