Evolution of a cross-feeding interaction following a key innovation in a long-term evolution experiment with Escherichia coli

The evolution of a novel trait can profoundly change an organism's effects on its environment, which can in turn affect the further evolution of that organism and any coexisting organisms. We examine these effects and feedbacks following the evolution of a novel function in the Long-Term Evolution Experiment (LTEE) with Escherichia coli. A characteristic feature of E. coli is its inability to grow aerobically on citrate (Cit(-)). Nonetheless, a Cit(+) variant with this capacity evolved in one LTEE population after 31000 generations. The Cit(+) clade then coexisted stably with another clade that retained the ancestral Cit(-) phenotype. This coexistence was shaped by the evolution of a cross-feeding relationship based on C-4-dicarboxylic acids, particularly succinate, fumarate, and malate, that the Cit(+) variants release into the medium. Both the Cit(-) and Cit(+) cells evolved to grow on these excreted resources. The evolution of aerobic growth on citrate thus led to a transition from an ecosystem based on a single limiting resource, glucose, to one with at least five resources that were either shared or partitioned between the two coexisting clades. Our findings show that evolutionary novelties can change environmental conditions in ways that facilitate diversity by altering ecosystem structure and the evolutionary trajectories of coexisting lineages.