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DOE Joint BioEnergy Institute and LS9 Collaboration Develops Microbe That Produces Biodiesel, Alcohols and Waxes Directly From Biomass

Electron micrograph shows rod-shaped E. coli secreting oil droplets containing biodiesel fuel, along with fatty acids and alcohol. (Image by Jonathan Remis, JBEI) Click to enlarge.

A collaboration led by researchers with the US Department of Energy’s Joint BioEnergy Institute (JBEI) has developed a microbe that can produce an advanced biofuel directly from biomass. Deploying the tools of synthetic biology, the JBEI researchers engineered a strain of Escherichia coli bacteria to produce biodiesel fuel and other important chemicals derived from fatty acids.

Jay Keasling, the Chief Executive Officer for JBEI, and a leading scientific authority on synthetic biology led the collaboration, which was made up of a team from JBEI’s Fuels Synthesis Division that included Eric Steen, Yisheng Kang and Gregory Bokinsky, and a team from LS9, a privately-held industrial biotechnology firm based in South San Francisco.

The LS9 team was headed by Stephen del Cardayre and included Zhihao Hu, Andreas Schirmer and Amy McClure. The collaboration has published the results of their research in the 28 January 2010 edition of the journal Nature.

The fact that our microbes can produce a diesel fuel directly from biomass with no additional chemical modifications is exciting and important. Given that the costs of recovering biodiesel are nowhere near the costs required to distill ethanol, we believe our results can significantly contribute to the ultimate goal of producing scalable and cost effective advanced biofuels and renewable chemicals.

—Jay Keasling

Fuels and chemicals have been produced from the fatty acids in plant and animal oils for more than a century. These oils now serve as the raw materials not only for biodiesel fuel, but also for a wide range of important chemical products including surfactants, solvents and lubricants.

The increased demand and limited supply of these oils has resulted in competition with food, higher prices, questionable land-use practices and environmental concerns associated with their production. A more scalable, controllable, and economic alternative route to these fuels and chemicals would be through the microbial conversion of renewable feedstocks, such as biomass-derived carbohydrates.

—Jay Keasling

E. coli is a well-studied microorganism whose natural ability to synthesize fatty acids and exceptional amenability to genetic manipulation make it an ideal target for biofuels research. The combination of E. coli with new biochemical reactions realized through synthetic biology, enabled Keasling, Steen and their colleagues to produce structurally tailored fatty esters (biodiesel), alcohols and waxes directly from simple sugars.

Biosynthesis of microbial fatty acids produces fatty acids bound to a carrier protein, the accumulation of which inhibits the making of additional fatty acids. Normally E. coli doesn’t waste energy making excess fat, but by cleaving fatty acids from their carrier proteins, we’re able to unlock the natural regulation and make an abundance of fatty acids that can be converted into a number of valuable products. Further, we engineered our E. coli to no longer eat fatty acids or use them for energy.

—Eric Steen

After successfully diverting fatty acid metabolism toward the production of fuels and other chemicals from glucose, the JBEI researchers engineered their new strain of E. coli to produce hemicellulases—enzymes that are able to ferment hemicellulose, the complex sugars that are a major constituent of cellulosic biomass and a prime repository for the energy locked within plant cell walls.

Engineering E. coli to produce hemicellulases enables the microbes to produce fuels directly from the biomass of plants that are not used as food for humans or feed for animals. Currently, biochemical processing of cellulosic biomass requires costly enzymes for sugar liberation. By giving the E. coli the capacity to ferment both cellulose and hemicellulose without the addition of expensive enzymes, we can improve the economics of cellulosic biofuels.

—Eric Steen

The JBEI team is now working on maximizing the efficiency and the speed by which their engineered strain of E. coli can directly convert biomass into biodiesel. They are also looking into ways of maximizing the total amount of biodiesel that can be produced from a single fermentation. Productivity, titer and efficient conversion of feedstock into fuel are the three most important factors for engineering microbes that can produce biofuels on an industrial scale, Steen says. “There is still much more research to do before this process becomes commercially feasible.

This research was supported by funds from LS9, Inc., and the UC Discovery Grant program. LS9 is using synthetic biology techniques to develop patent-pending UltraClean fuels and sustainable chemicals. The UC Discovery Grant program is a three-way partnership between the University of California, private industry and the state of California that is aimed at strengthening and expanding California’s economy through targeted fields of research.

JBEI is one of three Bioenergy Research Centers funded by the US Department of Energy to advance the development of the next generation of biofuels. Headquartered in Emeryville, California, JBEI is a scientific partnership led by Lawrence Berkeley National Laboratory (Berkeley Lab) and including the Sandia National Laboratories, the University of California (UC) campuses of Berkeley and Davis, the Carnegie Institution for Science (located on the campus of Stanford University), and the Lawrence Livermore National Laboratory.


  • Eric J. Steen, Yisheng Kang, Gregory Bokinsky, Zhihao Hu, Andreas Schirmer, Amy McClure, Stephen B. del Cardayre, Jay D. Keasling (2010) Microbial production of fatty-acid-derived fuels and chemicals from plant biomass. Nature 463, 559-562 doi: 10.1038/nature08721

  • Keasling Lab


Henry Gibson

Again it must be said that there is not enough biomass production capability in the US to provide for the oil needs. Over two-hundred years ago Britain exhausted its biomass and the US did it a hundred years later.

Now let them engineer one that eats coal and makes diesel. Or plug the bacteria directly into electrical sources from solar cells and wind generators to have them produce diesel directly from water and CO2, Escherichia-coli-electro-dieseli. Just figure out how many acres of wind-turbines it would take to produce the oil required by the US; it would be better to use the electricity for plug in hybrids. ..HG..


these bacteria don't make the fuels out of oil seeds, but out of any biomass. We could start by converting any organic waste to fuel. This part of the biochemistry would already result in enormous production capacities. The other part of the biochemistry (to start using H2 in addition and convert every carbon atom into fuel) will be the next add-on, but the werk presented here is a first and essential step.
It is useless to start building installations to convert H2 and CO2 to fuel, while at the same time we let billions of tons of organic waste rot on the fields. Especially at a moment where there are still power stations burning coal. Once all electricity is green or nuclear, and there is still not enough biomass to produce the fuels we need, this would become logic.

Once this technology is mature, addition of H2 will probably be the next step (this will increase the amount of fuel produced from a given amount of organic waste). A third step will probably be adding CO2, but this will depend on the price of the H2 and of the biomass. converting fully-oxidized carbon (=CO2) to hydrocarbons is an extremely energy-intensive activity, which - at the moment - produces much more CO2 than it consumes.


I'd rather just bypass the whole biomass requirement and engineer cyanobacteria instead of E. coli.

That way you could take CO2, water and light and convert it directly to diesel with no middle man.


HG - Have you seen the biomass after a grain harvest?


There are 100 million tons of biomass in stalks from the 100 million acres of corn grown in the U.S. That is after leaving HALF of it in the field for the land. Combine that with the cobs and you have 20 billion gallons of biofuel per year and that is just CORN. Then take the biochar after gasification and return it to the land for even healthier soil.



"I'd rather just bypass the whole biomass requirement and engineer cyanobacteria instead of E. coli.

That way you could take CO2, water and light and convert it directly to diesel with no middle man."

I think everyone would rather that. The Devil is in the details.

Meanwhile, I believe fuel from biomass will progress faster and can reduce our energy imports.


People only use E. coli because it is an easily grown and genetically tractable organism with a long history of characterisation (many vectors and the full sequence are readily available). If we cared and we invested the time and effort, it wouldn't take too long to get to a similar state of competence with Cyanobacteria.

Tim Duncan

I am all for this. But it sounds like there will be a hodge podge of products, they only realy talk about diesel. I wonder if the separation of products from bacteria, lignin (or what ever is left) and all the products will really be cost effective and energy efficient? I hope the by products are as lucrative as the allude to.


Separating the mixture of chemicals would be semilar to the actual distilation of crude oil to its constituents.


Kelly, there isn't enough biomass even after you account for straw and stover.  The NPP just can't keep up; not even the Billion-Ton Vision paper's figures come close to what we burn.

If you want to run the USA on biofuels, you need to get rid of the 7% field-to-wheel efficiency of liquids in ICEs and think direct-carbon fuel cells charging electric vehicles.

Gr Na

These franken bacteria are great as long as they stay were they're supposed to. If they somehow survive and reproduce outside of the lab or production areas, they might wreak havoc with crops and/or "biomass" consuming farm animals - cows, for example. Wouldn't it be lovely, if our wheat crops were slowly being converted to biofuels before the wheat grain had chance to develop or was harvested !

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