Evolutionary contingency’s impact on laboratory evolution of Escherichia coli under fluctuating environments

Abstract

1The adaptation of biological organisms to fluctuating environments is one major determinant of their structural and dynamical complexity. Organisms have evolved devoted adaptations to ensure the robust performance of physiological functions under environmental fluctuations. To further our understanding of particular adaptation strategies to different environmental fluctuations, we perform laboratory evolution experiments of Escherichia coli under three temperature fluctuation regimes alternating between 15{degrees}C and 43{degrees}C. Two of these regimes are determined by the populations growth, while the third regime switches stochastically. To address evolutionary contingencies, the experiments are performed on two lineages departing from different genetic backgrounds. The two lineages display distinct evolutionary trajectories, demonstrating dependency on the starting strains genetic background. Several genes exhibit a high degree of parallelism, suggesting their potential adaptive nature. The growth increase of the representative clones from each final population relative to their ancestor at 15{degrees}C and 43{degrees}C demonstrated no correlation between both temperatures, insinuating an absence of a strong trade-off between these two temperatures. Some had a growth rate decrease at 15{degrees}C unless exposed to a 43{degrees}C epoch, indicating some degree of internalization of the structure of the environment fluctuations. The phenotypic response of the evolved clones at 15{degrees}C and 43{degrees}C was assessed by a phenotype array method. The resulting responses reveal a general tendency to move closer to the phenotypic response of our starting strains at the optimum of 37{degrees}C. This observation expands the documented restorative responses, even when facing complex environmental conditions.\n\n2 Author SummaryLaboratory evolution experiments have been widely employed to test hypotheses from evolutionary theory. To assess the dynamics of adaptation under environmental fluctuations, we evolved 24 Escherichia coli populations under different regimes of temperature switching between 15{degrees}C and 43{degrees}C for about 600 generations. At the final point of the evolution experiment, the evolved populations were genome sequenced and clones were isolated and sequenced for phenotypic characterization. Fitness measurements revealed adaptation to both environmental conditions and some strains internalized the environmental fluctuation. Array phenotypic measurements showed that the majority of evolved strains tended to restore the phenotypic signature of the perturbed environments to that of the optimal temperature condition. This observation expands the documented restorative responses, even when facing complex environmental conditions.