Experimental Evolution with Microorganisms



Most of our knowledge about evolution comes from a retrospective view of past events such as by analysis of the fossil record. As an alternative, the discipline of experimental evolution aims at directly observing evolution as it unfolds in the laboratory. This “real-time” perspective of evolution is especially facilitated by propagating bacteria and unicellular eukaryotes (protists) which can multiply for hundreds or thousands of generations in a few months or years. That advantage is epitomized by Richard Lenski’s experiment in which 12 lines of Escherichia coli have been evolving in the lab for over 60,000 generations (27 years). The results of this experiment and many others not only corroborate conventional tenets of evolution by natural selection, but are also providing new powerful insights into the dynamics of evolution in action.


Usually in experimental evolution with microorganisms, a single genotype (such as a single colony on solid medium) is chosen as a progenitor (ancestor) to establish an evolving population. This is propagated in a chemostat or by serial dilutions in a designed culture medium representing a challenging environment (such as nutritional, thermal, or osmotic stress). With no other interference imposed by the investigator, any adaptation to the environment is the result of natural selection. Such adaptations can be measured by comparing relative growth rates of the evolving population to the progenitor. Higher growth rates than the ancestral indicate increased “fitness” of the evolving line. It is also possible to directly compare and contrast different populations evolving in parallel, such as sexual versus asexual lines as proposed here. Another marked advantage of cultivating microorganisms is the ability to store under cryogenic conditions cells collected at any time point of the experiment. By thawing a sample, one can “resurrect” and analyze an evolutionarily transitional form. Finally, modern next-generation sequencing (NGS) allows fast resequencing of the small genomes characteristic of microorganisms, facilitating discovery of DNA mutations underlying evolution. By genetic transformation, those evolved alleles can be inserted into the ancestral genotype to further confirm their individual contributions to the population’s fitness. More than ever before, microorganisms represent powerful resources for probing real-time evolution. This project takes advantage of modern experimental protocols with microorganisms to tackle one of the most important problems in evolutionary biology. Learn more about our Project Goals...



Further reading:

Elena, S.F. & Lenski, R.E. Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nat Rev Genet 4, 457-69 (2003).

Buckling, A., Craig Maclean, R., Brockhurst, M.A. & Colegrave, N. The Beagle in a bottle. Nature 457, 824-9 (2009).

Brockhurst, M.A., Colegrave, N. & Rozen, D.E. Next-generation sequencing as a tool to study microbial evolution. Mol Ecol 20, 972-80 (2010).

Barrick, J.E. et al. Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461, 1243-7 (2009).

Blount, Z.D., Barrick, J.E., Davidson, C.J. & Lenski, R.E. Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature (2012).

Conrad, T.M., Lewis, N.E. & Palsson, B.O. Microbial laboratory evolution in the era of genome-scale science. Mol Syst Biol 7, 509 (2011).