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2013

Watching Bacteria Evolve, With Predictable Results
New York Times, August 15, 2013
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If we could somehow rewind the history of life to the dawn of the animal kingdom, it would be unlikely that we humans would ever evolve, the evolutionary biologist Stephen Jay Gould argued. The history of life was shaped by too many flukes and contingencies to repeat its course.

Scientists can’t turn back the clock 700 million years, so we can’t know for sure whether Dr. Gould was right on that particular point. But in experiments using bacteria and other fast-breeding organisms, scientists can replay evolution many times over in their labs. And the results of a new experiment published Thursday in the journal Cell Reports demonstrate — with movies — that evolution can be astoundingly predictable.

The experiment was carried out by Joao Xavier of Memorial Sloan-Kettering Cancer Center and his colleagues. They studied a common species of bacteria called Pseudomonas aeruginosa. These microbes live pretty much everywhere — in dirt, in water, on our skin. Under certain conditions, they also invade our bodies and cause dangerous infections. People with cystic fibrosis, for example, can get P. aeruginosa infections in their lungs, which are often impossible to eradicate.

To better understand the biology of this pathogen, Dr. Xavier began to study how it searches for food. In a process called swarming, the bacteria spray out gooey molecules that form a slippery carpet; they can then slither over it by whipping their tails, devouring food they encounter along the way.

“I just wondered why nobody had filmed them before, because the pattern is so striking,” said Dr. Xavier. He dropped a few hundred microbes in the middle of a petri dish laced with sugar and switched on a camera overhead.

To better understand how the bacteria swarm, Dr. Xavier and his colleagues allowed them to evolve. They seeded petri dishes with a few hundred microbes and gave them a day to swarm and reproduce. The next day, they drew a small sample of the bacteria from the dishes and used them to seed new ones.

The scientists reasoned that, with each generation, new mutations would arise from time to time. If a mutation helped bacteria thrive in this new environment, it might become more common because of natural selection.

And so it did.

Within a few days, the evolution of the bacteria took a dramatic turn. The bacteria became 25 percent faster than their ancestors — Dr. Xavier dubbed them “hyperswarmers.” A movie of hyperswarmers starkly illustrates how different they had become, able to fill up the entire dish.

“We thought, ‘Something weird has happened,'” said Dr. Xavier.

The hyperswarmers emerged in three lines of bacteria overseen by Dr. Xavier’s post-doctoral researcher Dave van Ditmarsch. Dr. Xavier and another lab member, Jen Oyler, each ran the experiment again. “I wanted to make sure this wasn’t just due to Dave’s magic fingers,” said Dr. Xavier.

But no matter who applied their fingers to the task, the result was the same. Out of 27 lines of bacteria, 27 evolved into hyperswarmers.

When the scientists put the hyperswarmers under a microscope, they could see what had changed. An ordinary P. aeruginosa sports a single tail. The hyperswarmers had evolved so that they had as many as half a dozen tails. Those extra tails gave the bacteria more speed.

To determine how the bacteria had gained their tails, Dr. Xavier and his colleagues sequenced the DNA of 24 lines of hyperswarmers. In 24 out of 24 cases, they discovered that they have gained a mutation in the same gene, called FleN.

FleN encodes a protein that controls other genes involved in building tails. Somehow — Dr. Xavier doesn’t yet know how — the mutations cause FleN to produce a multitude of tails, all of which are fully functional.

Using their many tails, the hyperswarmers were able to get out in front of ordinary bacteria and reach fresh food first. They could then reproduce faster, leaving behind more offspring. As a result, each population of the bacteria rapidly turned into pure hyperswarmers.

Hyperswarmers evolved so reliably in Dr. Xavier’s experiments that he began to wonder why they had never been seen before. He speculated that, in his lab, the bacteria gained an ability to swim fast at the expense of some other trait that they need in nature.

Swarming, after all, is not the only essential task that P. aeruginosa must carry out. When the bacteria find a place that’s good for settling down, they anchor themselves to a surface — on a leaf, for example, or inside a human lung. They form a rubber sheet known as a biofilm.

Dr. Xavier and his colleagues found that the hyperswarmers are bad at making biofilms on their own. They then mixed hyperswarmers with normal bacteria and allowed the two types of microbes to make biofilms together. When the biofilm formed, the scientists tallied up how many bacteria in it were ordinary microbes and how many were hyperswarmers.

In a video showing the 3-D structure of one of these biofilms, the ordinary bacteria win, and the hyperswarmers have practically gone extinct — confirming that the ability to make microfilms is more important to the bacteria’s survival than being speedier consumers of food.

Dr. Xavier’s discovery could help doctors who are struggling to fight P. aeruginosa. In hospitals around the world, the bacteria are evolving resistance to many antibiotics, and biofilms provide some of their protection by acting like a shield. If scientists could find a way to coax ordinary P. aeruginosa to behave more like hyperswarmers, they might lose their ability to make biofilms.

But Dr. Xavier’s research also provides a scientific thrill in itself: the chance to see evolution in action — over and over again.

And if there’s one thing Dr. Xavier can now be sure of, it’s that his bacteria will end up as hyperswarmers, thanks to mutations to the same gene.

“In this case, it could be that there are only a few solutions in the evolutionary space,” he said.

Copyright 2013 The New York Times Company. Reproduced with permission.
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