Caught in the act: Team discovers microbes speciating

Not that long ago in a hot spring in Kamchatka, Russia, two groups of genetically indistinguishable microbes parted ways. They began evolving into different species – despite the fact that they still encountered one another in their acidic, boiling habitat and even continued exchanging some genes, researchers report. It is one of the first examples of ecological speciation in a microorganism. This new study, led by Rachel Whitaker, is published 21 February in the online, open-access journal PLoS Biology.

"One of the big questions, from Darwin on, is how do species diverge if they are living together?" Whitaker said. "That question really hasn't been answered very well, even in the macro-organisms that we've studied for hundreds of years."

"Bacteria, and their distantly-related microbial cousins the archaea, are even more difficult to study because they have so many different ways of sharing genetic information," Whitaker said. Even with new sequencing technologies, the task of studying microbial evolution is daunting.

The team focused on Sulfolobus islandicus, a heat-loving archaea species, because it is one of few microorganisms that live in distinct "island" populations created by geothermal hot springs. The researchers sequenced the genomes of twelve strains of S. islandicus from a hot spring in the Mutnovsky Volcano region of Kamchatka. By comparing sequences at multiple sites on the microbes' single (circular) chromosome, the researchers were able to reconstruct the genetic history of each of the strains.

The analysis revealed two distinct groups of S. islandicus among the twelve strains. The microbes were swapping genes with members of their own group more than expected, but sharing genes with the other group less than expected. And the exchange of genetic material between the two groups was decreasing over time.

This indicates that the two groups are already separate species, even though they share the same habitat, Whitaker said. The differences between the two groups were slight, but speciation was clearly underway, she said.

Looking more closely at the chromosome, the researchers saw vast "continents" of variation and smaller "islands" of stability. Those islands likely represent regions that have low recombination, Whitaker said; this combined with selection reduces variation in these regions. The variable regions are more fluid, with genes coming and going (a process called 'recombination'), increasing diversity.

"This study provides a glimpse of the profound genetic diversity that likely occurs everywhere in wild microbial populations," Whitaker said.

"What we see as two different species are 0.35 percent different across the chromosome; that's about one-third of the distance between human and chimp," she said. The two distinct groups of microbes are "orders of magnitude" more similar to each other than groups normally considered separate species, she said.

"That means there are orders of magnitude more species of microbes than we ever thought there were," she said. "And that's kind of mind-boggling."

Source: Public Library of Science