Enhanced metabolic entanglement emerges during the evolution of an interkingdom microbial community

Metabolic interactions are common in microbial communities and are believed to be a key factor in the emergence of complex life forms. However, while different stages of mutualism can be observed in nature, the dynamics and mechanisms underlying the gradual erosion of independence of the initially autonomous organisms are not yet fully understood. In this study, we conducted the laboratory evolution of an engineered microbial community and were able to reproduce and molecularly track its stepwise progression towards enhanced partner entanglement. The evolution of the community both strengthened the existing metabolic interactions and led to the emergence of de novo interdependence between partners for nitrogen metabolism, which is a common feature of natural symbiotic interactions. Selection for enhanced metabolic entanglement repeatedly occurred indirectly, via pleiotropies and trade-offs within cellular regulatory networks. This indicates that indirect selection may be a common but overlooked mechanism that drives the evolution of mutualistic communities.