WALNUT CREEK, CAToday's powerful sequencing machines can rapidly read the genomes of entire communities of microbes, but the challenge is to extract meaningful information from the jumbled reams of data. In a paper appearing in Nature Biotechnology August 17, a collaboration headed by researchers at the University of Washington and the U.S. Department of Energy Joint Genome Institute (DOE JGI) describes a novel approach for extracting single genomes and discerning specific microbial capabilities from mixed community ("metagenomic") sequence data.
For the first time, using an enrichment technique applied to microbial community samples, the research team explored the sediments in Lake Washington, bordering Seattle, WA and characterized biochemical pathways associated with nitrogen cycling and methane utilization, important for understanding methane generation and consumption by microbes. Methane is both a greenhouse gas and a potential energy source.
"Even if you have lots of sequence, for complex communities it still doesn't tell you which organism is responsible for which function," said the paper's senior author Ludmila Chistoserdova, a microbiologist at the University of Washington. "This publication presents an approach, via simplification and targeted metagenomic sequencing, of how you can go after the function in the environment."
Chistoserdova and colleagues study microbes that oxidize single-carbon compounds such as methane, methanol and methylated amines, which are compounds contributing to the greenhouse effect and are part of the global carbon cycle.
"To utilize these single-carbon compounds, organisms employ very specialized metabolism," said Chistoserdova. "We suspect that in the environment, there are novel versions of this metabolism, and possibly completely novel pathways."
Most of the microbes that oxidize single-carbon compounds are unculturable and therefore unknown, as are the vast majorit
|Contact: David Gilbert|
DOE/Joint Genome Institute