LTREB Renewal: The Long-Term Evolution Experiment with Escherichia coli

细菌在许多环境过程、人类健康和疾病以及生物技术中发挥着关键作用。因此，重要的是要了解细菌随时间变化的过程，并测量其基因，生理功能和生态性能的实际变化率。这两个研究小组将繁殖和分析12个大肠杆菌种群，因为它们在受控的实验室环境中进化了数千代细菌。为了测量适应性，研究人员将把后代的细菌与祖先的菌株进行竞争，祖先的菌株已被储存在深冻中，并将被复活用于这些测定。为了量化遗传变化，研究人员将在不同时间点对来自进化种群的细菌基因组进行测序，并将其与祖先的DNA序列进行比较。这些分析将提供有关细菌进化的速率、机制、影响和可预测性的独特信息。所获得的知识将有利于科学和社会，因为细菌对环境，健康和生物技术至关重要，并且因为它们的持续进化可以影响这些重要系统。这项长期的研究引起了公众的极大兴趣，研究人员将继续与公众和其他科学家交流他们的发现。 这个长期的研究项目提供了一个独特的细菌进化研究，通过从12个重复种群中产生一个非常长的时间序列的样本，所有这些样本都来自同一个E.大肠杆菌，并在相同的环境中维持数十年。研究小组将通过每天将它们转移到新鲜培养基中来繁殖种群;每500代，样本将被冷冻储存，在那里它们仍然可以存活并可用于研究。在接下来的五年里，实验将超过85，000代。冷冻样本将用于分析自然选择的适应动力学，表型和基因组进化的耦合以及进化变化的可重复性。其中一个需要解决的问题是：细菌相对于它们共同祖先的适应性是否会继续增加？相对适应度和基因组进化的轨迹是否具有相似的曲率，或者它们是不一致的？在复制种群中，适应性增益和基因组变化的可重复性如何？该项目生成的生物样本和数据集将与科学界共享。该奖项反映了NSF的法定使命，并且通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

Bacteria play critical roles in many environmental processes, in human health and disease, and in biotechnology. Therefore, it is important to understand the processes by which bacteria change over time, and to measure the actual rates of change in their genes, physiological functions, and ecological performance. The two research teams will propagate and analyze 12 populations of Escherichia coli as they evolve in a controlled laboratory environment for thousands of bacterial generations. To measure adaptation, the researchers will place the bacteria from later generations in competition with the ancestral strain, which has been stored in a deep freeze, and which will be revived for these assays. To quantify genetic change, the researchers will sequence the genomes of bacteria from the evolving populations at different time points and compare them to the ancestor’s DNA sequence. These analyses will provide unique information about the rates, mechanisms, effects, and predictability of bacterial evolution. The knowledge gained will benefit science and society because bacteria are essential to the environment, health, and biotechnology, and because their on-going evolution can impact these vital systems. This long-running study has attracted substantial public interest, and the investigators will continue to communicate their findings with the public as well as with other scientists. This long-term research project provides a unique study of bacterial evolution by generating an exceptionally long time-series of samples from 12 replicate populations, all of them founded from the same ancestral strain of E. coli and maintained for decades in identical environments. The research teams will propagate the populations by transferring them daily into fresh medium; every 500 generations, samples will be stored frozen, where they remain viable and available for study. During the next five years, the experiment should surpass 85,000 generations. The frozen samples will be used to analyze the dynamics of adaptation by natural selection, the coupling of phenotypic and genomic evolution, and the repeatability of evolutionary changes. Among the questions to be addressed: Will the fitness of the bacteria relative to their common ancestor continue to increase? Do the trajectories for relative fitness and genomic evolution have similar curvatures, or are they discordant? How repeatable are the fitness gains and genomic changes across the replicate populations? The biological samples and datasets generated in this project will be shared with the scientific community.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.