Washington, August 18 : A research team has developed a novel approach for extracting single genomes and discerning specific microbial capabilities from mixed community ("metagenomic") sequence data, which may help understand methane generation and consumption by microbes.
The team is headed by researchers at the University of Washington and the US Department of Energy Joint Genome Institute (DOE JGI), whose report has been published in a paper in Nature Biotechnology.
Today'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.
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," she added.
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," she added.
Most of the microbes that oxidize single-carbon compounds are unculturable and therefore unknown, as are the vast majority of microbes on Earth.
To find species of interest, the researchers sequenced microbial communities from Lake Washington sediment samples, 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.
The researchers used five different single-carbon compounds labeled with a heavy isotope of carbon, and fed each compound to a separate sediment sample.
According to Chistoserdova, the microbes that could consume the compound incorporated the labeled carbon into their DNA, 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.