Evolution Under A Microscope

The longest-running and most celebrated of modern evolution experiments is the appropriately named Long-Term Evolution Experiment (LTEE). Started by Richard Lenski in 1988 at the University of California, Irvine, and continuing in the hands of Jeffrey Barrick at the University of Texas at Austin, the LTEE has been running nearly continuously for 80,000 generations of E. coli over nearly 40 years. This is equivalent to two million years of human evolution.

The experiment began when 12 genetically identical populations of E. coli were grown in liquid medium. Every day since then, one percent of the previous day’s culture has been transferred into fresh medium. The medium is a dilute sugary solution limited in glucose, which E. coli uses as its primary carbon source. After about seven generations the glucose runs out and the bacteria stop growing until the next day, when they are transferred into fresh medium. Like Dallinger’s warm water, glucose-limited media is a selective pressure on the microbes, spurring the evolution of adaptations that compensate for a lack of their preferred food source.

Every 75 days (about 500 generations), a portion of LTEE’s cloudy soup of bacteria is stored in a minus-80-degree-centigrade freezer. These remain as frozen fossil records that can be used for direct comparison to their descendants.

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The LTEE has shed light on many unanswered questions about the dynamics of evolution, and experimentally validated long-running speculations. Do species improve indefinitely in a constant environment or will they stop at some maximum level? By comparing evolved E. coli with their ancestors, LTEE found that the rate of adaptation to the environment slows over time, but doesn’t plateau. Even after tens of thousands of generations in a stable laboratory environment, natural selection seems to be able to continuously eke out improvements.

Another major finding was that not all replicate populations follow the same evolutionary trajectory. In one replicate, named Ara-2, the population diverged into two coexisting lineages: one that rapidly consumes glucose and afnother that feeds on a byproduct of glucose metabolism called acetate. From a single population came a community of two.

But the most surprising finding was the observation that after about 31,000 generations, a different replicate, Ara-3, gained the ability to grow on citrate. Natural E. coli can’t metabolize citrate—in fact, it’s one of the defining features of the species—so the emergence of a strain which thrives on this carbon source could represent an entirely new species.

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Today, labs around the world are running evolution experiments of all shapes and sizes, each using microbes to understand a specific facet of evolution. Some study predation by mixing predator and prey species, and observing how each adapts to the other. Other groups have studied starvation by growing bacteria for long periods of time without the addition of any nutrients, nor the removal of dead cells. And by selecting yeasts for increased size, others have directed the evolution of macroscopic multicellularity from single-celled ancestors.

Evolution by its nature takes time. With microbes we’ve been able to condense it down to more manageable timescales, but even 80,000 generations is a blip on the evolutionary clock. As these experiments continue to run, the more we’re sure to learn from them.

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