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ASM Session Highlights Microbe-Based Biofuel Development

PHILADELPHIA (GenomeWeb News) – Microbes and microbial metabolism are paving the way for alternative energy sources, attendees at the American Society for Microbiology meeting heard here yesterday — and a variety of genomics-based approaches are helping to unlock the bugs' secrets for producing energy and extracting it from plants.

At a session, called "Plugging Microbial Activities and Genomes into the Energy Grid," researchers involved in biofuel production projects across the country outlined their efforts to create new energy sources using microbes.

Oak Ridge National Laboratory researcher Martin Keller described research in his own lab as well as work being done by the Oak Ridge-led BioEnergy Science Center, a group of 300 researchers from 17 institutions working on understanding and modifying plant resistance to breakdown. Keller, who is heading BESC, said multi-disciplinary approaches to biofuels research have yielded remarkable progress in the field over the past year-and-a-half.

By tweaking biomass processing to exploit the hard-to-access sugars in the inedible parts of plants, BESC hopes to spur the production of cellulosic biofuels — fuels based on the unpalatable plant parts. But because these bits are resistant to breakdown, researchers are turning to the microbes that do similar breakdown jobs in nature.

BESC is working on consolidated bioprocessing, a one-step process for converting plant mass into ethanol, Keller explained, and exploring ways to employ microbial enzymes for plant breakdown. They're also developing a knowledgebase for integrating and making sense of SNPs, genes, and other genome sequence data related to microbes' ability to dismantle plants.

In Keller's own lab, meanwhile, researchers have been evaluating both sides of the equation, looking at the variation in poplar trees and tackling microbial genetics in order to better understand how certain bugs convert cellulose to sugars.

Since the poplar is sequenced and grows quickly, Keller noted, it may be useful as a biofuel source. So far the team has sampled more than 1,000 poplar trees on the west coast of North America — from California to Canada — and applied a pipeline approach, including high-throughput sequencing and genetic marker mapping, to identify enhanced tree characteristics linked to high sugar release.

In collaboration with researchers at the US Department of Energy's Joint Genome Institute, Keller added, the researchers are in the process of sequencing many more microbes thought to contain valuable plant-degrading enzymes.

In the same session, University of Wisconsin at Madison chemical and biological engineering researcher Jennifer Reed described her group's computational approach to creating microbes specialized for biofuel production.

Using analytical tools such as MoMA, ROOM, OptKnock, and variations of OptKnock to predict the effects of knocking out one or more genes, they are identifying mutations that could eventually be used to engineer microbes for better biofuel production.

Reed offered an example of how such approaches have uncovered Escherichia coli mutations that increase ethanol production. And, she said, similar analyses can be done for other cellulosic substrates as well, using any microbe with a genome annotation.

Andreas Schirmer, a researcher from a renewable petroleum replacement development company called LS9, discussed his company's efforts to create a diesel fuel replacement compatible with the existing fuel infrastructure.

The company — founded by Harvard University geneticist George Church, University of California at Berkeley plant and microbial biology researcher Chris Somerville, and others — is focusing their efforts on microbial fatty acid metabolism using several approaches, including genome mining to find fatty acid conversion pathways. Schirmer said LS9 plans to produce this "ultra-clean diesel" on a commercial scale by 2013.

University of California at Los Angeles researcher James Liao, associate director of the US DOE's genomics and proteomics, spoke about his group's efforts to produce high energy, long-chain alcohols in microbes using chemistry gleaned from microbial metabolism.

But not everyone is focusing on creating carbon-based products. University of Wisconsin bacteriologist Timothy Donohue, director of the US Department of Energy's Great Lakes Bioenergy Research Center, explained that his group is working on creating hydrogen-based re-usable fuel sources. They're currently using gene expression profiling, among other techniques, to understand how photosynthetic microbes produce hydrogen.

"Microbes are the master chemists of the planet," Donohue told reporters during a news conference yesterday. As such, he explained, it's not surprising that researchers are turning to them for clues about energy production as they move to reduce our reliance on fossil fuels.

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