Biochem Blogs

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Move over big oil: Microorganisms strike it big with new “black” gold

Graduate Student Andrew Argo

Graduate Student Andrew ArgoI'm on ScienceSeeker-Microscope

I cannot say that I’m unfamiliar giving presentations in front of groups as I was a TA for years for Dr. Jim Knopp teaching 50+ students for 1.5 hours once a week. I will say that giving my first protein journal club (PJC) presentation was much more nerve wrecking even with a group weighing in less than half of what I am used to. Eyes staring holes into me, waiting to see if I could possibly keep their attention while presenting information on such a controversial topic as biofuels. In the end I would say it was a relatively good success and hopefully this first blog post will produce that same success.

fatty acid production

Scheme for increasing medium chain fatty acid production

When it comes down to it, most approaches to biofuel production using a microorganism involve extreme genetic engineering to obtain the metabolic products desired. Lu et al (1) demonstrate this by severally re-engineering the E. coli strain X100 to boost its production of medium-chain fatty acids which are of biggest interest in the biofuels/biodiesel community. They do this by knocking out an endogenous acyl-CoA synthetase gene (fadD), inserting a plant thioesterase gene, overexpressing an endogenous acyl-CoA carboxylase and overproduction of an endogenous thioesterase to overcome degradation caused by long chain fatty-acids. This allows for a substantial increase in MCFA, but with an efficiency of only 4.8% (0.048 g fatty acid/g carbon source), there is definitely more optimization to be done.

microorganism biofuels

Approach to biofuel production that combines microorganisms in a conducive environment

The Minty et al group (2) took a different approach when it comes to production of biodiesel. Instead of completely re-engineering one microorganism with all the possible pathways needed for production they took advantage of a “natural” consortia. Using the fungi species T. reesei and a strain of E. coli slightly engineered to create isobutanol using by-products from an already existing pathway, they were able to combine the two in an environment conducive for biofuel production. The competition for soluble saccharides created by the fungi allowed for the production of isobutanol at a steady state with neither organism dominating the other. The production of the biofuel is one magnitude below that of ethanol which is the current industrial standard. Even with a low production rate, the complexity of the system/organisms has been reduced, and with more optimization this method could overtake the single organism system.

All of this may sound great to your basic “tree huggers” and alternative fuel junkies but there are dangers that come with handling/synthesizing these metabolic by-products. The Madsen paper (3) takes a look at health risks taken by employees of biodiesel facilities in Denmark. With no current health standards in place for exposure to microbes for the employees, many may develop lung and other problems with prolonged exposure to these microorganisms. It was shown that upwards of 83% of employees were exposed to fungal spores, endotoxins and bacteria over the limit set by the study. Just as it was done for the workers who developed black lung in coal mines there should be strict health standards set in place to reduce the chance of health issues developing in any persons involved with these projects.

So it would seem that maybe we are on a good path towards development and implementation of biofuels in the everyday lives of the general public. There are issues on the metabolic and processing engineering side of things along with the health of the employees for these new jobs that need to be consider before pushing to large production. But in the end, everyone needs to wonder if this is a solution to our global problem of energy or just a bandaid on an axe wound we have inflicted.


1. Lu X., Vora H. & Khosla C. (2008). Overproduction of free fatty acids in E. coli: Implications for biodiesel production, Metabolic Engineering, 10 (6) 333-339. DOI:

2. Minty J.J., Singer M.E., Scholz S.A., Bae C.H., Ahn J.H., Foster C.E., Liao J.C. & Lin X.N. (2013). Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass, Proceedings of the National Academy of Sciences, 110 (36) 14592-14597. DOI:

3. Madsen A.M. (2006). Exposure to Airborne Microbial Components in Autumn and Spring During Work at Danish Biofuel Plants, Annals of Occupational Hygiene, 50 (8) 821-831. DOI: