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Cataloguing invisible life: Microbe genome emerges from lake sediment
Date:8/17/2008

When entrepreneurial geneticist Craig Venter sailed around the world on his yacht sequencing samples of seawater, it was an ambitious project to use genetics to understand invisible ecological communities. But his scientific legacy was disappointing a jumble of mystery DNA fragments belonging to thousands of unknown organisms.

Now a team led by a University of Washington scientist has studied lake mud, which contains microbial communities even more complex than those in seawater, and homed in on bacteria that perform the ecological task of eating methane. The study, published Sunday (Aug. 17) in the journal Nature Biotechnology, shows a way to sequence unidentified life.

"This work demonstrates that we can get a complete genome for a totally unknown organism," said lead author Ludmila Chistoserdova, a UW research scientist in chemical engineering. "We extracted a complete genome from a very complex community, and this is something novel."

Only 1 percent of microbes survive in the laboratory, Chistoserdova said, and the remaining 99 percent are undiscovered. Genetics can bypass the laboratory to help reveal microscopic communities, but most genetic tools use short stretches of known genetic code. Researchers look for these short stretches and copy, or amplify, them from the environment.

"You can only use amplification when you know what you're trying to get. And that's the problem," Chistoserdova said. "When you want to discover something unknown, amplification is a very deficient technique because you keep discovering the things you already know. So how can you discover the unknown?"

The researchers targeted a particular ecological function, in this case eating single-carbon compounds such as methane. First they collected samples of mud from the bottom of Lake Washington, a typical freshwater lake of moderate temperature and average levels of compounds such as methane, produced by decomposing
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Contact: Hannah Hickey
hickeyh@u.washington.edu
206-543-2580
University of Washington
Source:Eurekalert  

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