bacteria

Evolution details revealed through 21-year E. coli experiment

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Evolution details revealed through 21-year E. coli experiment

In 1988 an associate professor started growing cultures of Escherichia coli. Twenty-one years and 40,000 generations of bacteria later, Richard Lenski, who is now a professor of microbial ecology at Michigan State University, reveals new details about the differences between adaptive and random genetic changes during evolution.

Sequencing genomes of various generations of the bacteria, which had been frozen periodically over the years, Lenski and his team found that adaptive and random genomic changes don’t necessarily follow the same patterns. Rather than a plodding equilibrium, even in a consistent environment, the interplay between these two kinds of genomic changes “is complex and can be counterintuitive,” Lenski said in a prepared statement.

Early changes in the bacteria appeared to be largely adaptive, helping them be more successful in their environment. “The genome was evolving along at a surprisingly constant rate, even as the adaptation of the bacteria slowed down,” he noted. “But then suddenly the mutation rate jumped way up, and a new dynamic relationship was established.”

By generation 20,000, for example, the group found that some 45 genetic mutations had occurred, but 6,000 generations later a genetic mutation in the metabolism arose and sparked a rapid increase in the number of mutations so that by generation 40,000, some 653 mutations had occurred. Unlike the earlier changes, many of these later mutations appeared to be more random and neutral.

The long-awaited findings show that calculating rates and types of evolutionary change may be even more difficult to do without a rich data set. “The fluid and complex coupling observed between the rates of genomic evolution and adaptation even in this simplistic system cautions against categorical interpretations about rates of genomic evolution in nature without specific knowledge of molecular and population-genetic processes,” the paper authors wrote.

Such detailed pictures of mutation rates have been made possible since the advent of rapid genome sequencing. “It’s extra nice now to be able to show precisely how selection has changed the genomes of these bacteria, step by step over tens of thousands of generations,” Lenski said.

The new data “beautifully emphasize the succession of mutational events that allowed these organisms to climb toward higher and higher efficiency in their environment,” Dominique Schneider of the Université Joseph Fourier in Grenoble, France, and a coauthor on the paper, said in a prepared statement. The paper, published online today in Nature, also happens to come 150 years after Charles Darwin published his Origin of Species. (Scientific American is a part of the Nature Publishing Group.)

The findings might eventually help scientists better understand mutations in human diseases and infections. “Cancer progression is a fundamentally similar evolutionary process,” Jeffery Barrick, a postdoctoral researcher at the lab and lead author of the paper, said in a prepared statement. And although the research team will continue to study the progress of the minute bacteria in search for more answers, he added: “We know an astounding amount about the details of evolution in these little Erlenmeyer flasks.”

Thanks to JT. Hundley for this one.

Bacteria make major evolutionary shift in the lab

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Bacteria make major evolutionary shift in the lab

A major evolutionary innovation has unfurled right in front of researchers’ eyes. It’s the first time evolution has been caught in the act of making such a rare and complex new trait.

And because the species in question is a bacterium, scientists have been able to replay history to show how this evolutionary novelty grew from the accumulation of unpredictable, chance events.

Twenty years ago, evolutionary biologist Richard Lenski of Michigan State University in East Lansing, US, took a single Escherichia coli bacterium and used its descendants to found 12 laboratory populations.

The 12 have been growing ever since, gradually accumulating mutations and evolving for more than 44,000 generations, while Lenski watches what happens.

Profound change

Mostly, the patterns Lenski saw were similar in each separate population. All 12 evolved larger cells, for example, as well as faster growth rates on the glucose they were fed, and lower peak population densities.

But sometime around the 31,500th generation, something dramatic happened in just one of the populations – the bacteria suddenly acquired the ability to metabolise citrate, a second nutrient in their culture medium that E. coli normally cannot use.

Indeed, the inability to use citrate is one of the traits by which bacteriologists distinguish E. coli from other species. The citrate-using mutants increased in population size and diversity.

“It’s the most profound change we have seen during the experiment. This was clearly something quite different for them, and it’s outside what was normally considered the bounds of E. coli as a species, which makes it especially interesting,” says Lenski.