UC Santa Barbara

Waste management and sustainable energy production are two major concerns of modern society. The use of microbial consortia for waste treatment has the potential to address both of these concerns simultaneously, since consortia possess the ability to convert crude biomass into biofuels and bio-based chemicals. The organic fraction of municipal solid waste (OFMSW) or food waste is an abundant and inexpensive carbon substrate that can be utilized by microbial systems to generate useful products. Anaerobic consortia containing fungi, bacteria, protozoa, and methanogenic archaea capable of converting wet waste materials into valuable substances already exist in nature and have been isolated from the guts of herbivores. Although bioreactors utilizing undefined natural consortia to digest wet waste and generate biogas have been constructed, the failure rate is high due to instability and death of the microbial community. The development of biotechnology capable of handling variable input, recovering from environmental disturbances, and producing consistent products is dependent upon engineering stability and robustness among consortia members. To achieve this, it is necessary to understand the genomic basis for stable interaction between members of these microbial communities.In this work, transcriptional and metabolic changes induced by methanogen co-culture were evaluated in the anaerobic fungal strain C. churrovis across a variety of substrates to identify mechanisms that impact biomass breakdown and sugar uptake. Co-culture with the methanogen increased overall transcription of carbohydrate active enzymes (CAZymes), carbohydrate binding modules, and dockerin domains in co-cultures grown on both lignocellulose and cellulose. Next, a system for simultaneous and sequential co-cultivation of the anaerobic fungus Anaeromyces robustus and the anaerobic bacterium C. acetobutylicum was established based on lactate cross-feeding to produce butyrate and butanol from lignocellulose. Higher levels of butyrate and butanol in fungal and C. acetobutylicum cultures reveal that creating consortia that include these two microbes could be a promising future avenue of industrial bio-butyrate and biobutanol production. Finally, a method to extract high-quality RNA from anaerobic fungi at multiple timepoints in the fungal growth phase was developed to fully characterize differential expression in both fungal monocultures and fungal-methanogen co-cultures. The fungal strain Anaeromyces robustus co-cultivated with the methanogen Methanobacterium bryantii upregulates genes encoding fungal carbohydrate active enzymes and other cellulosome components relative to fungal monocultures when grown on a cellulose substrate, but expression patterns changed at 24-hour intervals throughout the fungal growth phase. Overall, this work indicates that anaerobic fungi can be successfully combined with non-native microbes in consortia capable of converting low-cost biomass substrates into value-added products.