CAREER: Designing Synthetic Anaerobic Consortia for Bioproduction

University Of California-Santa Barbara, Santa Barbara CA

Investigators

Abstract

Microbes work together in complex, dynamic communities that recycle carbon throughout the Earth, from animal guts to landfills and compost piles. In order to better understand rumen (animal stomach) microbial communities which live in the absence of oxygen, new "synthetic" partnerships between microbes will be constructed that are inspired by nature, which will enable sustainable chemical production from plant waste materials. New isolation and culture techniques will be developed which will likely lead to the isolation of novel microorganisms and the construction of novel communities with desirable attributes from nature. Undergraduate and graduate students, a postdoctoral fellow, K-12 students and the public will be integrated into the studies through coursework, laboratory research, outreach in collaboration with the Santa Barbara Zoo, and a science program for economically disadvantaged Hispanic students. This project has far reaching impacts on plant biomass breakdown, climate change, sustainability, and carbon capture in the environment. This research will build synthetic microbial consortia based on the natural syntrophy between rumen anaerobes. The rumen microbiome within large herbivores consists of four interdependent microbial populations (bacteria, protozoans, fungi, and methanogens) that work together to drive crude biomass into sugars and fermentation waste products, including carbon dioxide and methane. However, the interdependency of these microbes and their impact on microbial metabolism are difficult to characterize due to their recalcitrance to culture. Recently, these challenges have been overcome through the isolation of fungi with dependent methanogens from herbivore fecal materials, creating a simplified system to model their syntrophy. Robust fungal-methanogen syntrophs from herbivores will be screened to study how pairs are matched by nature, and how co-culture accelerates biomass breakdown. Stable fungal-methanogen pairs will be used to generate a metabolism model for gut fungi, and the model will be curated with experimental data. Finally, interdependent communities containing non-native microbes (acetotrophic methanogens and facultative anaerobes) will be designed and optimized using a bottom up approach to compartmentalize biomass-degradation and bioproduct formation. This research will serve as the focal point to establish a new educational partnership with the Santa Barbara Zoo that exposes the broader public to the importance of microbes in our environment.