Cradle of creation: Evolution shapes up new ecosystem in the lab

• by Michael Le Page

Long run: lab evolution takes place in flasks like these (Image: Michigan State University)

The longest running evolutionary lab experiment has reproduced yet another aspect of the natural world, showing how a major change in one creature can transform its environment, and alter the evolutionary trajectory of all the creatures inhabiting that space.

The Long-term Experimental Evolution Project began in 1988. Richard Lenskiat Michigan State University took a single strain of the E. coli bacterium and set up 12 cultures.

Every day since then, a sample of each culture has been transferred to fresh growth medium, containing glucose as the main nutrient. The bacteria have now undergone more than 60,000 generations since the experiment began.

Evolutionary experiments in the lab are now routine. Many biologists are also studying evolution in the wild and some think that rapid evolution may be the norm rather than the exception.

But Lenski's experiment has allowed us to witness evolution in unprecedented detail. Because samples are frozen every 75 days, the team can go back and identify the precise genetic mutations underlying the changes they see.

The experiment has become a poster child for evolution, causing consternation among creationists trying to explain away its compelling evidence.

The biggest evolutionary shift occurred after about the 31,500 generation, when one line in one of the 12 populations evolved the ability to feed on citrate, another chemical in the growth medium. Now, Caroline Turner and other members of Lenski's team have described some of the consequences of this change in a paper posted on a preprint server.

Revolving door solution

E. coli don't normally feed on citrate because they can't carry it into their cells. But a mutation in the citrate-eaters allowed them to make an "antiporter" protein, CitT, that allows citrate to cross the membrane and enter the cell. The gene for this protein already existed, but it's usually switched off when oxygen is present.

The antiporter is a kind of revolving door. It allows one molecule to be swapped for another. In this case, the citrate is imported into the cell in exchange for one of three smaller, less-valuable molecules: succinate, fumarate or malate.

Once this ability to feed on citrate evolved the population boomed because the same growth medium could now sustain more cells.

Those citrate feeders soon became dominant, outcompeting all but one other strain of E. coli, which in turn evolved to exploit the changed environment – which now contained the three exported molecules.

It did this by making more of a transporter protein called DctA, which imports - at a small energy cost - succinate and other molecules exported by the citrate-eating strain.

But things did not stop there. The citrate-eaters then also started making more DctA to try to claw back some of the succinate and other molecules they were losing in the process of acquiring citrate.

The work is a neat example of how evolution and ecosystems are inextricably linked. "Our findings show how evolutionary novelties can change environmental conditions, thereby facilitating diversity and altering both the structure of an ecosystem and the evolutionary trajectories of coexisting organisms," the paper says.

The researchers compare this to the evolution of photosynthetic bacteria some 2.4 billion years ago: just as oxygen excreted by the first photosynthesiserstransformed Earth and changed the course of evolution, so the appearance of citrate eaters altered the growth medium and changed the evolutionary path of all the bacteria living in it.

It's just what biologists expect to happen, but thanks to this experiment and others like it we can now watch evolution in action.

Turner's findings are also yet another example of the mindlessness of evolution. The best solution would be to use a little energy to import citrate directly, rather than swapping it for succinate and then spending energy to try to get that succinate back before other bacteria can feed on it.

"The evolution of citrate consumption is an example of how evolutionary innovation frequently involves jury-rigging, reusing existing parts," Turner says. "Our work shows how that jury-rigging can have important consequences for the ecology of the system and for future evolution."

Journal reference: bioRxiv, DOI: 10.1101/020958