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Analysis of Lake Washington microbes shows the power of metagenomic approaches
Date:8/17/2008

y of microbes on Earth. To find species of interest, the researchers sequenced microbial communities from Lake Washington sediment samples, Chistoserdova said, because lake sediment is known to be a site of high methane consumption. However, these sediment samples contained over 5,000 species of microbes performing a complex, interconnected array of biochemical tasks.

To enrich the samples for the microbes of interest, the researchers adapted a technique called stable isotope probing. This is the first time the technique has been used on a microbial community, Chistoserdova said. The researchers used five different single-carbon compounds labeled with a heavy isotope of carbon, and fed each compound to a separate sediment sample. The microbes that could consume the compound incorporated the labeled carbon into their DNA, Chistoserdova said, while organisms that couldn't use the compound did not incorporate the label. The labeled DNA was then separated out and sequenced. In this way, microbial "subsamples" were produced that were highly enriched for organisms that could metabolize methane, methanol, methylated amines, formaldehyde and formate.

The functionally enriched samples contained far fewer microbes than the total sample, Chistoserdova said. The sample that was fed methylated amines was simple enough that the group was able to extract the entire genome of a novel microbe, Methylotenera mobilis, that normally comprises less than half a percent of the community, but appears to be a first responder to methylated amines in the environment. The researchers were able to construct much of M. mobilis' biochemistry, and predict that it is also involved in nitrogen cycling, demonstrating the utility of metagenomic analysis.

The DOE JGI performed the sequencing and assembly of these complex metagenomic data sets. The complexity of the community's sequence samples created new challenges for genome assembly. "It is very important for metagenomic
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Contact: David Gilbert
degilbert@lbl.gov
925-296-5643
DOE/Joint Genome Institute
Source:Eurekalert

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