Deciphering The Genetic And Molecular Underpinnings Of Carbohydrate-Degrading Systems In Ruminal Bacteria
A major thrust of the DOE’s current research portfolio is to develop advanced biofuels like ethanol. In particular, 36 billion gallons of biofuels is mandated to be produced annually by 2022; 16 billion is expected to come from cellulosic material. Currently, our ethanol output is 10 billion gallons/year, primarily in the form of grain ethanol. Plant biomass contains the largest reservoir of terrestrial organic carbon in the form of cellulose, and the ability to tap into this source promises to be sustainable and renewable. However, our current ability to convert cellulose into simple sugars, which can then be fermented into ethanol, is inefficient. To address this, highly cellulolytic microbes and their enzymes must be characterized. One approach is to study microbes from natural communities proficient at degrading plant biomass. The focus of this project was to investigate microbes found within the rumen of cows, which are highly optimized for the degradation of cellulolytic material. Specifically, we studied three highly-cellulolytic bacteria including Cellulomonas gilvus, Fibrobacter succinogenes, and Ruminococcus albus. Capitalizing on their available genome sequences, we used a combination of genome-scale approaches including transcriptomics, functional genomics, and enzyme characterization to not only understand how these microbes degrade and utilize cellulose-containing plant biomass, but also for identifying novel enzymes useful for polysaccharide degradation. Importantly, our work uncovered specific novel mechanisms by which all three microbes degrade cellulose, each of which are unique within the diversity of cellulolytic bacteria. These findings help to explain the different rates at which each microbe degrades cellulose, and provides further insight into their efficiency, with F. succinogenes specializing and utilizing only cellulose, while C. gilvus and R. albus are polysaccharide generalists capable of degrading and utilizing multiple different types of sugars. Finally, our work also identified and characterized a number of novel cellulases and xylanases with synergistic properties that may be useful for industrial applications requiring degradation of plant polysaccharides. Taken together, our work not only advance our understanding of the fundamental process through which microbes deconstruct plant biomass, but also provides novel leads for industrially-attractive enzymes.