Background Light-driven consortia, which consist of sucrose-secreting cyanobacteria and heterotrophic species, have attracted considerable attention due to their capability for the sustainable production of valuable chemicals directly from CO2. In a previous study, we achieved a one-step conversion of sucrose secreted from cyanobacteria to fine chemicals by constructing an artificial coculture system consisting of sucrose-secreting Synechococcus elongateus cscB+ and 3-hydroxypropionic acid (3-HP) producing Escherichia coli ABKm. Analyses of the coculture system showed that the cyanobacterial cells grew better than their corresponding axenic cultures. To explore the underlying mechanism and to identify the metabolic nodes with the potential to further improve the coculture system, we conducted integrated transcriptomic, proteomic and metabolomic analyses. Results We first explored how the relieved oxidative stress affected cyanobacterial cell growth in a coculture system by supplementing additional ascorbic acid to CoBG-11 medium. We found that the cell growth of cyanobacteria was clearly improved with an additional 1 mM ascorbic acid under axenic culture; however, its growth was still slower than that in the coculture system, suggesting that the improved growth of Synechococcus cscB+ may be caused by multiple factors, including reduced oxidative stress. To further explore the cellular responses of cyanobacteria in the system, quantitative transcriptomics, proteomics and metabolomics were applied to Synechococcus cscB+. Analyses of differentially regulated genes/proteins and the abundance change of metabolites in the photosystems revealed that the photosynthesis of the cocultured Synechococcus cscB+ was enhanced. The decreased expression of the CO2 transporter suggested that the heterotrophic partner in the system might supplement additional CO2 to support the cell growth of Synechococcus cscB+. In addition, the differentially regulated genes and proteins involved in the nitrogen and phosphate assimilation pathways suggested that the supply of phosphate and nitrogen in the Co-BG11 medium might be insufficient. Conclusion An artificial coculture system capable of converting CO2 to fine chemicals was established and then analysed by integrated omics analysis, which demonstrated that in the coculture system, the relieved oxidative stress and increased CO2 availability improved the cell growth of cyanobacteria. In addition, the results also showed that the supply of phosphate and nitrogen in the Co-BG11 medium might be insufficient, which paves a new path towards the optimization of the coculture system in the future. Taken together, these results from the multiple omics analyses provide strong evidence that beneficial interactions can be achieved from cross-feeding and competition between phototrophs and prokaryotic heterotrophs and new guidelines for engineering more intelligent artificial consortia in the future.

Synthetic microbial consortia represent a new frontier for synthetic biology given that they can solve more complex problems than monocultures. However, most attempts to co-cultivate these artificial communities fail because of the winner-takes-all in nutrients competition. In soil, multiple species can coexist with a spatial organization. Inspired by nature, here we show that an engineered spatial segregation method can assemble stable consortia with both flexibility and precision. We create microbial swarmbot consortia (MSBC) by encapsulating subpopulations with polymeric microcapsules. The crosslinked structure of microcapsules fences microbes, but allows the transport of small molecules and proteins. MSBC method enables the assembly of various synthetic communities and the precise control over the subpopulations. These capabilities can readily modulate the division of labor and communication. Our work integrates the synthetic biology and material science to offer insights into consortia assembly and serve as foundation to diverse applications from biomanufacturing to engineered photosynthesis.

Background: The light-driven consortia consisted of sucrose-secreting cyanobacteria and heterotrophic species capable of producing valuable chemicals have recently attracted significant attention, and are considered as a promising strategy for green biomanufacturing. In a previous study (Zhang et al, 2020, Biotechnol Biofuel, 13:82), we achieved a one-step conversion of CO2 through sucrose derived from cyanobacteria to fine chemicals by constructing an artificial co-culture system consisting of sucrose-secreting Synechococcus elongateus cscB+ and 3-hydroxypropionic acid (3-HP) producing Escherichia coli ABKm. Analysis of the co-culture system showed that cyanobacterial cells were growing better than its corresponding axenic culture. To explore the underlaid mechanism and to identify the metabolic modules to further improve the co-culture system, an integrated metabolomics, transcriptomic and proteomic analysis was conducted.Results: We first explored the effect of reactive oxygen species (ROS) on cyanobacterial cell growth under co-culture system by supplementing additional ascorbic acid to scavenge ROS in CoBG-11 medium. The result showed cyanobacterial growth was obviously improved with additional 1 mM ascorbic acid under pure culture; however, cyanobacterial growth was still slower than that in the co-culture with E. coli, suggesting that the better growth of Synechococcus cscB+ might be caused by other factors more than just ROS quenching. We then investigated the intracellular metabolite levels in cyanobacteria using LC-MS based metabolomics analysis. The results showed that metabolites involved in central carbon metabolism were increased, suggesting more carbon sources were utilized by cyanobacteria in the co-culture system, which illuminating that enhanced photosynthesis attributes to the higher CO2 availability produced from co-cultivated heterotrophic partner. To further explore the interaction based on cross-feeding and metabolite exchange, quantitative transcriptomics and proteomics were applied to Synechococcus cscB+. Analysis of differentially regulated genes/proteins showed that the higher availability of carbon, nitrogen, phosphate, calcium, Cu2+, Fe3+ and co-factors was observed in co-cultivated Synechococcus cscB+ during co-cultivation, suggesting the heterotrophic partner in the system might be involved in supplementing CO2 and improving essential micronutrients necessary to maintain high photosynthetic growth of Synechococcus cscB+. Conclusion: Integrated omics analysis of the interaction mechanism between S. elongateus and E. coli showed metabolic changes such as enhanced photosynthesis, oxidative phosphorylation, essential micronutrients, and the ROS scavenging occurred at multiple levels of genes, proteins and metabolites, which might be together contributing to the better cell growth of Synechococcus cscB+ in co-cultivation. In addition, the results implicated that the co-culture system could be further improved by engineering the modules related to the ROS quenching, carbon metabolism, nitrogen metabolism, Pi transport, metal transport and co-factors biosynthesis. Finally, the light condition, which may influence the cross-feeding metabolites between phototrophic and heterotrophic species, and also affect the oxidative pressure on the E. coli strains due to the photosynthesis, could be further optimized to improve cell growth in the co-culture system, eventually leading to high productivity of value-added products.