Engineering Stable Anaerobic Consortia by Understanding the Genomic Basis for Stable Interaction
Anaerobic consortia containing fungi, bacteria, protozoa, and methanogenic archaea capable of converting wet waste materials into valuable substances 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, failure rates are high due to the instability 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. This defense will discuss three topics explored in my project:
1. The transcriptional effect of substrate availability and strain variation in a fungal-methanogen co-culture
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.
2. The co-cultivation of an anaerobic fungus with bacteria to bolster bacterial production of value-added chemicals
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 bio-butanol production.
3. The establishment of an optimal range for high-quality RNA extraction from anaerobic fungi
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.