Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment

Evolutionary innovations allow populations to colonize open ecological niches. However, successful establishment may also often depend on subsequent adaptation to a new niche. We previously reported the evolution of aerobic growth on citrate (Cit+) in a population of Escherichia coli after ~31,000 generations of adaptation to a minimal glucose medium that also contains citrate (DM25). The Cit+ variants can also grow aerobically in citrate-only medium (DM0), which is a novel environment for E. coli. To investigate the capacity of the Cit+ ecotype to adapt to this environment, we founded a set of new populations using three early Cit+ clones and evolved them for 2,500 generations in DM0. We also evolved a second, control set of populations in DM25. We then assessed the populations' evolution at the phenotypic, genomic, and transcriptomic levels. Our genomic analysis of clones identified numerous parallel, and likely adaptive, mutations across replicate populations, including many mediated by transposable elements.