Evolving Microbial Communities for Biofuel Production

Plant lignocellulose is the most abundant raw material on the planet and a promising substrate for biofuel production. While this complex polymer is efficiently degraded by a range of naturally occurring microbial communities, cost- and energy-efficient industrial use is hampered by its recalcitrance to degradation. By gaining a better understanding of how microbial lignocellulose degrading communities function we may be able to improve industrial processes. In this thesis, I used a combination of ecological and evolutionary approaches to uncover the species and functional traits that drive lignocellulolytic microbial community productivity. I found that the presence of key highly active cellulolytic bacteria increased the productivity of microbial consortia. Specifically, we identified two species, Cellulomonas sp. D13 and Paenibacillus sp. A8, with a range of cellulase and hemicellulase enzymes that have potential for application in industrial processes. Experimental evolution revealed that the rate of phenotypic adaptation of a focal bacterial species, Stenotrophomonas sp. D12, to growth on wheat straw was accelerated by the presence of other competing species. The trajectory of focal species evolution was determined by both the identity and the ecological and evolutionary responses of the competing species. Genome sequencing of evolved clones suggested that genetic adaptation by the focal species to degrade wheat straw involved mutations targeting regulatory genes involved in catabolite repression and carbon storage, two systems that may represent promising targets for the improvement of industrial strains. Overall these results suggest the ecological and evolutionary approaches can be used to design and improve microbial consortia for lignocellulose bioconversion.