Harvard Medical School
For most of the species we see, evolution is a slow process, taking generations to show its effects. But the species we can’t see – bacteria and other microbes – can go through dozens of generations in a single day. For them, evolution can be a rapid process, as antibiotic resistance has made us painfully aware of.
Therefore, researchers often use bacteria to study evolutionary processes. In perhaps the best-known experiment, a single lab has now sent E coli competing for limited resources through tens of thousands of generations and has tracked the resulting changes at the DNA level.
But evolution is not always a constant competition of everyone against everyone, as happens in these experiments. Instead, you get migrations and exploitation of new habitats, allowing rare founders to spawn entire populations. Now a research team has come up with a fun way to study founder dynamics in a bacterial culture, and thereby made it possible to view the branching of evolutionary lineages like a movie.
The work was based on what the creators call MEGA, the arena for microbial evolution and growth. MEGA is essentially a giant rectangular Petri dish, 4 feet long, set up a bit like an American football field. The two ends have nothing but food for bacteria, but conditions change along a series of stripes that lead to the center of the field. As you get closer to the center, the concentration of an antibiotic increases so that by the time you reach MEGA’s midfield, there is 3000 times as much antibiotic as there is E coli can tolerate.
The bottom of the plate contains a high concentration of gelling agent, creating a semi-solid area where the bacteria remain in place. But above that is a thin layer with much less gelling agent, creating a semi-liquid for the bacteria to swim through and migrate to new habitats.
Bacteria were seeded at the ends and quickly spread through the antibiotic-free zone, stopping at the edge of the area where the concentration of the drug was three times what the bacteria could tolerate. However, three days later, the first mutants had developed a tolerance to this level of the drug and spread to the new zone from a single starting point. The process repeated at each of the borders with higher drug levels until the bacteria finally spread to the zone with the highest antibiotic levels.
Because of the way the experiment was set up, it was like watching an evolutionary tree expand over time. Each new drug tolerant line could be watched as it entered a new zone, fanned out, and then began to compete with other lines. It resulted in a compelling film.
Evolution, the movie.
As with other experiments, the authors sequenced the genomes of different lineages to determine how the bacteria changed over time. A feature that has evolved multiple times is a high rate of mutations, caused by mutations in the error correction region of the enzyme that copies DNA. Essentially, the bacteria had evolved to generate more mutations, which are the raw material for further evolution. Strangely enough, however, these ‘mutator’ strains didn’t seem to adapt faster than some of their peers.
Many of the mutations that allowed the bacteria to tolerate antibiotics came at a cost: slower growth. Still, slower growth was beneficial because it allowed these bacteria to expand into what was uninhabited habitat. In many cases, further mutations elsewhere later restored normal growth rates.
In many cases, by the time these beneficial mutations occurred it was too late; fast-migrating bacteria had now left their healthier peers in the dust, moving to a crowded, competitive region of the MEGA plate. When the authors restarted the experiment and seeded it with these well-adapted species, they outsmarted the competition. But as the researchers describe it, “population fitness is not determined by the strongest mutants, but rather by those who are both sufficiently fit and sufficiently close to the advancing front.”
This is probably a useful evolutionary model, given that growing populations often occur in nature, including in our own species’ past as we expanded out of Africa. MEGA complements the multi-year evolution experiment in many ways; both types of competition exist in the wild, and each can help us understand its dynamics and test some of our theoretical models.
But in terms of an evolution movie, MEGA clearly has the edge.
Science2016. DOI: 10.1126/science.aag0822 (About DOIs).