Biofuels, such as ethanol made from whole plants – stalks, leaves, and all – could have a significant impact on reducing both carbon dioxide emissions and the country’s dependence on foreign oil. In theory, the same amount of carbon released when the biofuel is burned in vehicles’ engines would be sucked up by the next year’s fuel crop. What’s more, fermenting bacteria and yeast could make ethanol from agricultural waste and weeds such as switchgrass that could be grown on land unsuitable for food crops.

Despite all their attractive benefits, however, biofuels have not been an economically competitive alternative to fossil fuels in the United States because the cost of the processing needed to break down plant starches is not offset by the amount of ethanol produced in the end. Now a group of researchers led by MIT’s Gregory Stephanopoulos, a chemical engineering professor, are working to improve the productivity and robustness of the microbes that convert treated biomass into ethanol. Stephanopoulos has developed a new technology that enables researchers to introduce complex traits into bacteria and yeast – such as the ability to continuously convert sugar into ethanol – and hopes the technology will help turn things around for biofuels.

About a year ago, the Department of Energy released a study (large .pdf file) suggesting that the United States could sustainably produce 1.38 billion tons of biomass annually for conversion into fuels. “If all of the sugar from this biomass is utilized, it could supply 40 billion gallons of fuel a year,” says Stephanopoulos. Even if the DOE number is inflated, he says, biofuels could make a major difference in the United States, which currently consumes 110 billion gallons of liquid fuel each year.

Stephanopoulos says the best way to begin the process of turning biomass into fuel using microbes is with a simple physical method. Plant matter is chopped up into small pieces that are then treated with enzymes to break down complex molecules like cellulose into simple sugars that microbes can digest. Bacteria or yeast are introduced to the sugar solution, which they convert to ethanol. But the microbes can only convert so much of the sugar, and they have a relatively low ethanol tolerance. Thus, as the amount of ethanol in solution goes up, the microbes slow down.

Stephanopoulos is engineering E. coli and yeast with higher ethanol production and tolerance. Stephanopoulos takes a systems approach to genetic engineering, attempting to take into account networks of reactions in a cell. “The production of ethanol is a property of the whole organism, not the manifestation of a single gene,” he says. “When you think about all the things you have to do in order to change many genes at the same time the problem becomes really enormous.”

Nonetheless, Stephanopoulos says he has suceeded in increasing E. coli and yeasts’ ethanol production. He has also introduced a complex yeast trait – tolerance to higher amounts of ethanol – to E. coli cells. Stephanopoulos has created a technology he calls global Transcriptional Machinery Engineering (gTME). It “allows us to simultaneously modify multiple genes and introduce important new [traits],” he says.

Stephanopoulos says biofuels have not been successful in the past – but their time is coming. “I feel bullish about applying these methods for energy production. We now have an idea of how much biomass is in the U.S. The prospect of getting cheap products from it is on the horizon.” Using his technique, Stephanopoulos says he “can easily see the possibility of engineering organisms to produce liquid fuels.”

Given sky-high crude oil prices, “ethanol biomass fuels look like they could be a decent alternative to oil, as long as you don’t use a lot of fossil fuels in the process,” says John Reilly, associate research director of MIT’s Joint Program on Climate Change. Reilly points to the success of “flex-cars” in Brazil, which can run on ethanol from sugar cane, gasoline, or a combination of both. “It provides an easy way to put whatever’s cheaper in the tank,” he says.