Kram Karin E, Geiger Christopher, Ismail Wazim Mohammed, Lee Heewook, Tang Haixu, Foster Patricia L, Finkel Steven E
Department of Biology, California State University, Dominguez Hills, Carson, California, USA.
Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California, USA.
mSystems. 2017 Mar 7;2(2). doi: 10.1128/mSystems.00192-16. eCollection 2017 Mar-Apr.
Experimental evolution of bacterial populations in the laboratory has led to identification of several themes, including parallel evolution of populations adapting to carbon starvation, heat stress, and pH stress. However, most of these experiments study growth in defined and/or constant environments. We hypothesized that while there would likely continue to be parallelism in more complex and changing environments, there would also be more variation in what types of mutations would benefit the cells. In order to test our hypothesis, we serially passaged in a complex medium (Luria-Bertani broth) throughout the five phases of bacterial growth. This passaging scheme allowed cells to experience a wide variety of stresses, including nutrient limitation, oxidative stress, and pH variation, and therefore allowed them to adapt to several conditions. After every ~30 generations of growth, for a total of ~300 generations, we compared both the growth phenotypes and genotypes of aged populations to the parent population. After as few as 30 generations, populations exhibit changes in growth phenotype and accumulate potentially adaptive mutations. There were many genes with mutant alleles in different populations, indicating potential parallel evolution. We examined 8 of these alleles by constructing the point mutations in the parental genetic background and competed those cells with the parent population; five of these alleles were found to be adaptive. The variety and swiftness of adaptive mutations arising in the populations indicate that the cells are adapting to a complex set of stresses, while the parallel nature of several of the mutations indicates that this behavior may be generalized to bacterial evolution. With a growing body of work directed toward understanding the mechanisms of evolution using experimental systems, it is crucial to decipher what effects the experimental setup has on the outcome. If the goal of experimental laboratory evolution is to elucidate underlying evolutionary mechanisms and trends, these must be demonstrated in a variety of systems and environments. Here, we perform experimental evolution in a complex medium allowing the cells to transition through all five phases of growth, including death phase and long-term stationary phase. We show that the swiftness of selection and the specific targets of adaptive evolution are different in this system compared to others. We also observe parallel evolution where different mutations in the same genes are under positive natural selection. Together, these data show that while some outcomes of microbial evolution experiments may be generalizable, many outcomes will be environment or system specific.
实验室中细菌群体的实验进化已导致确定了几个主题，包括适应碳饥饿、热应激和pH应激的群体的平行进化。然而，这些实验大多研究在确定的和/或恒定的环境中的生长情况。我们推测，虽然在更复杂和不断变化的环境中可能会继续存在平行性，但有益细胞的突变类型也会有更多变化。为了验证我们的假设，我们在细菌生长的五个阶段全程在复杂培养基（Luria-Bertani肉汤）中连续传代。这种传代方案使细胞经历了多种应激，包括营养限制、氧化应激和pH变化，因此使它们能够适应多种条件。在每大约30代生长后，总共约300代，我们将老化群体的生长表型和基因型与亲代群体进行了比较。仅30代后，群体就表现出生长表型的变化并积累了潜在的适应性突变。不同群体中有许多带有突变等位基因的基因，表明存在潜在的平行进化。我们通过在亲代遗传背景中构建点突变并将这些细胞与亲代群体竞争，对其中8个等位基因进行了检测；发现其中5个等位基因具有适应性。群体中出现的适应性突变的多样性和迅速性表明细胞正在适应一组复杂的应激，而几个突变的平行性质表明这种行为可能普遍适用于细菌进化。随着越来越多的工作致力于使用实验系统理解进化机制，解读实验设置对结果有何影响至关重要。如果实验性实验室进化的目标是阐明潜在的进化机制和趋势，那么这些必须在各种系统和环境中得到证明。在这里，我们在复杂培养基中进行实验进化，使细胞能够经历生长的所有五个阶段，包括死亡阶段和长期稳定期。我们表明，与其他系统相比，该系统中选择的迅速性和适应性进化的特定目标有所不同。我们还观察到平行进化，即同一基因中的不同突变受到正自然选择。总之，这些数据表明，虽然微生物进化实验的一些结果可能具有普遍性，但许多结果将是特定于环境或系统的。
