Systems Biology of Autotrophic-Heterotrophic Symbionts for Bioenergy (Final Report)

Microbial consortia composed of autotrophic and heterotrophic species abound in nature and represent an extremely stable and self-supporting symbiosis. To establish a platform for sustainable bioenergy production, an artificial symbiosis was studied through combining the metabolic capability of photoautotrophs to capture carbon dioxide and then channeling the resulting organic carbon directly to a partner heterotroph for producing biofuels precursors. We first utilized a model cyanobacterium, Synechococcus elongatus PCC 7942, that had been modified to secrete some of the carbon it fixes as sucrose, a carbohydrate that can be utilized by many other microbes. Then, we tested the capability of sucrose-secreting cyanobacteria to act as a flexible platform for the construction of synthetic, light-driven consortia by pairing them with heterotrophs for bioproducts. The comparison of these different co-culture dyads reveals general design principles for the construction of robust autotroph/heterotroph consortia. We observed heterotrophic growth dependent upon cyanobacterial photosynthate in each co-culture pair. Furthermore, these synthetic consortia could be stabilized over the long-term (weeks to months) and both species could persist when challenged with specific perturbations. Stability and productivity of autotroph/heterotroph co-cultures was dependent on heterotroph sucrose utilization, as well as other species-independent interactions that we observed across all dyads. One destabilizing interaction we observed was that non-sucrose byproducts of oxygenic photosynthesis negatively impacted heterotroph growth. Conversely, inoculation of each heterotrophic species enhanced cyanobacterial growth in comparison to axenic cultures. Finally, these consortia can be flexibly programmed for photoproduction of target compounds and proteins; by changing the heterotroph in co-culture to specialized strains of Bacillus subtilis, Escherichia coli or Rhodotorula glutinis we demonstrate production of alpha-amylase, polyhydroxybutyrate and fatty acids respectively. Moreover, co-cultures of S. elongatus and R. glutinis were sustained over 1 month in both batch and in semi-continuous culture, with the final biomass and overall lipid yields in the batch co-culture 40 to 60% higher compared to batch mono-cultures of S. elongatus. Finally, we demonstrated the exchanged metabolites, including NH4, amino acids and sugars, between symbiotic partners through simulation with reconstructing community models and identification with metabolomics. The pairing of a cyanobacterium and eukaryotic heterotroph in the artificial lichen of this project demonstrates the importance of mutual interactions between phototrophs and heterotrophs, e.g., phototrophs provide a carbon source to heterotrophs, and heterotrophs assist phototrophic growth and survival by removing/eliminating oxidative stress. Our results establish a potential stable production platform that combines the metabolic capability of photoautotrophs to capture inorganic carbon with the channeling of the resulting organic carbon directly to a robust heterotroph partner for producing biofuel and other chemical precursors.