While most attempts to engineer biofuel-producing microbes have focused on well-known organisms such as yeasts and E. coli, scientists also hope to co-opt the unique metabolic functions of some of the microbial world's less-studied creatures. Anthony Sinskey and his team at MIT have been cataloguing the genomic secrets of Rhodococcus bacteria, soil-dwelling microbes known to eat a variety of toxic compounds. The goal is to make a biodiesel-producing organism that can use a variety of sources as fuel. "We have done a lot of the basic chemistry and biology," says Sinskey. "Now we need to figure out how to maximize yields."

The strain of bacteria that Sinskey is working on, Rhodococcus opacus, is related to the type that causes tuberculosis, but it has two particularly appealing qualities. The bacteria have a flexible appetite, with the ability to eat a number of sugars and toxic compounds--in fact, the microbes were originally isolated from contaminated soil, where they were breaking down petroleum waste products. In addition, R. opacus are one of just a few types of bacteria that naturally produce a type of lipid called tryacylglycerols, which can be chemically converted into biodiesel. "Its life is focused around lipid metabolism, eating weird lipids and making more of them," says Jason Holder, a postdoctoral researcher in Sinskey's lab. "The trick is to engineer them to make it more efficiently, using waste streams of carbon."

The research is part of a larger effort to develop biofuels that, unlike ethanol made from corn or sugarcane, do not rely on food sources or agricultural land. Some companies, such as Synthetic Genomics, Amyris, LS9, and Joule Biotechnologies, are using synthetic biology techniques to engineer bacteria to more efficiently produce desirable metabolic products that can be used for biofuels.

Sinskey's team has recently sequenced R. opacus's genome and mapped its 9,000 genes into various metabolic pathways. Understanding these pathways allows scientists to boost or inhibit specific reactions, which can in turn increase the microbe's efficiency at creating a particular fuel or end product. The researchers have also developed a microarray for Rhodococcus--a genomics tool that allows scientists to quickly assess patterns of gene expression--and are using it to study these metabolicnetworks. "It will allow us to predict other bacteria that might do the same thing," says Sinskey, "and it will help us identify genes important in the assembly process." They plan to publish the genome soon.