Adam Arkin inspects samples at the Microbial Characterization Facility

Adam Arkin:

Seeking a Microbe With an Appetite for Biofuels    

Microbial systems fascinate UC Berkeley systems biologist Adam Arkin. They are evolved to survive in nearly every niche that supports life. They express many strategies to tolerate inclement conditions. They metabolize substrates to enable growth and produce many natural products, including molecules useful for biofuels.

And they can be very stubborn, resistant to reengineering for optimal production of molecules for human use. So Arkin and his lab have spent years developing the computational and experimental approaches to dissect the operation of microbial pathways at a genome scale. Recently, they began to use these tools to design new behaviors in bugs.

“There are few natural bacterial systems that hold the promise of efficient conversion of biomass to fuel, but Zymomonas mobilis is one of them,” said Arkin. “While the ultimate fuel produced may not be ethanol, Zymomonas, a genetically tractable and industrially honed organism, provides an excellent platform for both study and application.” 

Zymomonas is the only bacterium that commercially makes ethanol from sugars.  The organism does its best work in a “flocculant” state, when it clusters together and has relatively high tolerance to the ethanol product.  No one knows exactly why or how this all works. But if he could understand all of the factors affecting its metabolism, including its tolerance or sensitivity to factors coming from the feedstock or to its biofuel products, Arkin believes Z. mobilis or a mutant form of the bacterium could be optimized for commercial biofuel production.

That’s what his Microbial Characterization Facility is designed to do for EBI – develop an experimental and computational pipeline for discovering and engineering the stress response and metabolic pathways that affect the ability of microbes to make biofuels. Starting with Zymomonas as the model, Arkin’s team will develop high throughput partially automated systems to make libraries of microbial mutants, all possessing slightly altered arrangements of the bacteria’s 2,000 genes, and expose them to different fuel types and inhibitors present in feedstocks. That way, the group can determine central pathways that are important to biomass production and fermentation in biofuels. To do that, he and a dozen researchers will have to develop functional genomic screening and analysis technologies on a scale and sensitivity heretofore unknown in this area.

“What systems affect the bacteria’s ability to produce fuels?” he asks. “What genes are determining growth and tolerance, and how does it break down the food product, take some fraction of the carbon, and direct it to the synthesis of molecules that are useful as fuels? The idea is to be able to reduce the cycle time for optimizing design of both feedstock and microbial pathways for biofuel production and industrial scale-up.”

Arkin’s long-standing interest in optimizing microbes for human application has been growing since he and collaborators initiated projects to understand how microbes could remediate heavy-metal waste and how bacteria and viruses could be engineered for therapeutic purposes. As part of the Department of Energy-sponsored remediation project, his lab established the “Microbes Online” website, a publicly available resource that features tools to enable genomic comparisons of genes and genomes of microbes. In the past year alone, the site received 30,000 individual hits.

Bacteria possess the remarkable ability to degrade a variety of organic compounds in waste processing and bioremediation. Bacteria capable of digesting the hydrocarbons in petroleum are often used to clean up oil spills. If Arkin and his team are successful, they will employ these ubiquitous one-celled organisms to replace oil rather than just break it down.