Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

2023 Abstracts

Developing, Understanding, and Harnessing Modular Carbon/Nitrogen-fixing Tripartite Microbial Consortia for Versatile Production of Biofuel and Platform Chemicals


Yanmeng Liu1, David Carruthers1, Yi Dai1, Josie Mcquillan2, Maciek Antoniewicz1, Sujit Datta3, Jagroop Pandhal2, Andrew Allman1, and Xiaoxia “Nina” Lin1* ([email protected])


1University of Michigan; 2University of Sheffield; and 3Princeton University


The overall goal of this project is to design, construct, analyze and optimize a synthetic microbial consortium system consisting of three closely interacting members: a CO2-fixing photosynthetic specialist, a N2-fixing specialist, and a third specialist that can convert organic carbon and nitrogen generated by the first two specialists to synthesize a desired product. By integrating complimentary expertise from multiple research laboratories at three institutions, researchers are pursuing three specific objectives: i) Develop tripartite microbial consortia for carbon/nitrogen fixation and production of bio-molecules with various nitrogen/carbon ratios; ii) Investigate molecular and cellular mechanisms governing the tripartite consortia via omics study and predictive modeling; and iii) Explore alternative spatial configurations and develop scalable design principles.


Microbial communities are ubiquitous in nature, exhibiting incredibly versatile metabolic capabilities and remarkable robustness. Inspired by these synergistic microbial ecosystems, rationally designed synthetic microbial consortia is emerging as a new paradigm for bioprocessing and offers tremendous potential for solving some of the biggest challenges society faces. In this project, the team focuses on a tripartite consortium consisting of a CO2-fixing photosynthetic specialist, a N2-fixing specialist, and a third specialist that can convert organic carbon and nitrogen generated by the first two specialists to synthesize a desired product. In addition to CO2 fixation, a noteworthy feature of this design is the elimination of the requirement for nitrogen fertilizer, which has been produced through ammonia synthesis using the Haber-Bosch process and accounts for an estimated 2% of global energy expenditure. Researchers aim to develop a modular and flexible model system capable of producing diverse bio-molecules (varying C:N ratio) as advanced biofuel or platform chemicals, to dissect this complex ecosystem using a spectrum of cutting-edge systems approaches, and to ultimately derive scalable and broadly applicable design principles for maximizing the system performance.

The first prototype tripartite consortium employs genetically modified strains of photosynthetic cyanobacterium Synechococcus elongatus that secretes sucrose (Abramson et al. 2016) and nitrogen-fixing bacterium Azotobacter vinelandii that secretes ammonia (Barney et al. 2015). respectively, to form a symbiotic foundation for supporting a third producer member. Researchers demonstrated supported growth for a range of producer strain candidates, including a sucrose-metabolizing Escherichia coli K-12 derivative strain, Corynebacterium glutamicum, and Bacillus subtilis, using a multi-chamber bioreactor system under continuous culture conditions (Carruthers et al. in preparation).

On-going investigation include: i) development of predictive mathematical models of the tri-culture system to systematically explore the parameter space to understand how different biological parameters and operating strategies impact the system performance such as yield and productivity; and ii) omics analysis of monocultures and cocultures under controlled yet suboptimal/stressed conditions to identify the molecular bottlenecks limiting the performance of each member and hence the overall tri-culture.


Abramson, B. W., et al. 2016. “Increased Photochemical Efficiency in Cyanobacteria via an Engineered Sucrose ” Plant and Cell Physiology, 57(12), 2451–60.

Barney, B. M., et al. 2015. “Gene Deletions Resulting in Increased Nitrogen Release by Azotobacter vinelandii: Application of a Novel Nitrogen Biosensor.” Applied and Environmental Microbiology 81(13), 4316–28.

Carruthers, D., et al. In preparation. “Engineering Modular Carbon- and Nitrogen-Fixing Microbial Consortia for Sustainable Biochemical Production.”

Funding Information

This research was supported by the DOE Office of Science, Office of Biological and Environmental Research (BER), grant no. DE-SC0022136.