The researchers took a simple community of microbes from a pink slick on the floor of an abandoned mine, ground them up, and shotgun sequenced the lot. As they put the pieces of DNA back together, the snippets fell easily into five distinct genomes, four of them unknown until now.
"This is the first recovery of a genome from an environmental sample," said Jillian F. Banfield, professor of earth and planetary science and of environmental science, policy and management at UC Berkeley. "This ushers in a whole new way of exploring and understanding our environment, allowing us to determine how organisms work as individuals and together, and how they contribute to geochemical processes."
Banfield and graduate student Gene W. Tyson from UC Berkeley's Department of Environmental Science, Policy and Management, with colleagues from UC Berkeley and the U.S. Department of Energy's Joint Genome Institute (JGI) in Walnut Creek, Calif., report their feat this week in the Advance Online Publication of the journal Nature.
Banfield and her students, post docs and colleagues are primarily interested in how the microbes, obtained from the Richmond Mine in Iron Mountain, Calif., one of the largest Superfund sites in the country, interact with minerals to produce acid mine drainage.
"Acid mine drainage is one of the most pressing long-term environmental problems worldwide, and it's caused by microbial processes," Banfield said. "This study has dramatically improved our understanding of the microorganisms involved and has opened the way for development of much more highly refined models of acid mine drainage systems."