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.

进化创新使种群能够占据新的生态位。我们此前报道，在适应含柠檬酸（citrate）的最低葡萄糖培养基（DM25）过程中，大肠杆菌（Escherichia coli）种群进化出了利用柠檬酸进行有氧生长的能力（Cit+）。Cit+变体还能在仅含柠檬酸的培养基（DM0）中生长，这对大肠杆菌而言是一种全新环境。为研究对这一生态位的适应机制，我们建立了两组Cit+种群，并使其在DM0或DM25中进化2500代。进化后的谱系获得了大量平行突变，其中许多由转座元件（transposable elements）介导。部分谱系还进化出了含maeA基因区域的扩增。意外的是，部分进化后的种群和克隆体表现出明显的适合度（fitness）下降。我们还发现Cit+克隆体中存在大量细胞死亡的证据。因此，我们的结果表明，大肠杆菌对新柠檬酸生态位表现出快速的性状优化与适应能力，同时也揭示其生理机制与柠檬酸生长环境之间存在难以调和的矛盾。