Genomic and phenotypic evolution ofEscherichia coliin a novel citrate-only resource environment

ABSTRACT Evolutionary innovations allow populations to colonize new, previously inaccessible ecological niches. We previously reported that aerobic growth on citrate (Cit + ) evolved in a population of Escherichia coli during adaptation to a minimal glucose medium containing citrate (DM25). Cit + can grow in citrate-only medium (DM0), which is a novel environment for E. coli . To study adaptation to this new niche, we evolved one set of Cit + populations for 2,500 generations in DM0 and a control set in DM25. We identified numerous parallel mutations, many mediated by transposable elements. Several lineages evolved multi-copy amplifications containing the maeA gene, constituting up to ∼15% of the genome. We also found substantial cell death in ancestral and evolved clones. Our results demonstrate the importance of copy-number variation and transposable elements in the refinement of the Cit + trait. However, the observed mortality suggests a persistent evolutionary mismatch between E. coli physiology and a citrate-only environment.