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

Evolutionary innovations allow populations to colonize new ecological
niches. We previously reported that aerobic growth on citrate (Cit+)
evolved in an Escherichia coli population during adaptation to a minimal
glucose medium containing citrate (DM25). Cit+ variants can also grow in
citrate-only medium (DM0), a novel environment for E. coli. To study
adaptation to this niche, we founded two sets of Cit+ populations and
evolved them for 2500 generations in DM0 or DM25. The evolved lineages
acquired numerous parallel mutations, many mediated by transposable
elements. Several also evolved amplifications of regions containing the
maeA gene. Unexpectedly, some evolved populations and clones show apparent
declines in fitness. We also found evidence of substantial cell death in
Cit+ clones. Our results thus demonstrate rapid trait refinement and
adaptation to the new citrate niche, while also suggesting a recalcitrant
mismatch between E. coli physiology and growth on citrate.