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Shotgun sequencing finds nanoorganisms

quite a lot of organisms."

Banfield, Baker and their UC Berkeley and University of Queensland, Australia, colleagues report their findings in the Dec. 22 issue of Science.

Banfield noted that the bacteria and newfound Archaea living in the highly acidic mine drainage are archetypes of the kind of life that could exist on other planets, such as in the iron- and sulfur-rich soil of Mars.

"This community of microbes is relevant to probing potential strategies for life on other planets, especially the life likely to exist on Mars," she said.

The organisms in the mine drainage, which live in a pink slick on pools of acidic green water, obtain energy by oxidizing iron - that is, generating rust -- and in the process create sulfuric acid and dissolve pyrite (iron sulfide or fool's gold) to release more iron and sulfur. This self-sustaining process creates the acidic drainage that pollutes creeks and rivers, including those around the researchers' study site, the Richmond Mine at Iron Mountain, Calif. The mine is one of the largest Superfund sites in the country.

Banfield has been trying to understand how the extremophiles - microbes that live in extreme environments - live together and generate the acid drainage that makes such mines toxic hazards. The green runoff from the mine, captured and treated by the Environmental Protection Agency, is a hot 108 degrees Fahrenheit, as acidic as battery acid, and loaded with toxic metals - zinc, iron, copper and arsenic.

In 2004, Banfield collaborated with the Department of Energy's Joint Genome Institute to shotgun sequence a drop of the slime. This type of sequencing involves homogenizing the organisms in the sample, isolating the combined DNA and breaking it into lots of random strands. Each strand is then sequenced, and a powerful computer is used to find overlaps so that the pieces can be properly reordered.

This process identified five separate genomes that
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Contact: Robert Sanders
rsanders@berkeley.edu
510-643-6998
University of California - Berkeley
21-Dec-2006


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