The idea that we could grow fuel from a renewable resource is incredibly exciting. Researchers have been hard at work developing biofuels that will allow us to run our society using easily renewable resources. These efforts have gained a lot of media attention in recent years, and are being touted as a way for the US to decrease its dependence on foreign oil and to mitigate climate change. The longest standing method for creating biofuels is extracting ethanol from corn and sugar cane. More recently, researchers have begun engineering bacteria to produce biofuels, a method that may avoid many of the problems associated with making biofuels from plants, but that also presents new scientific and engineering challenges.

When food crops like corn and sugarcane are grown for fuel, they use land and resources that could otherwise be used for food production. This leads to competition between food and fuel that raise worries about food shortages [1,2]. While plants other than food crops can, in theory, be used to produce fuel, extracting and isolating the useful compounds from them is not as straightforward. “Cellulosic” plant crops such as switch grass can be grown abundantly on land unsuitable for food crops. However, the precursors for energy production in switch grass are trapped in the woody stem and body of the plant. These structures are composed of a chemical called cellulose, commonly known as the “fiber” in the vegetables we eat, which is very difficult to break down. To obtain products from these plants, the plant material must be heavily processed, and scientists are actively researching ways to use bacteria as a means to break down the cellulose in plants for fuel [3,4]. At the same time, researchers have started exploring ways to produce fuels using bacteria alone to avoid the problems associated with plants altogether [5,6].

Making biofuels in bacteria solves many of the challenges associated with making them in plants. Bacteria can be grown in large tanks, in places such as deserts, where food crops cannot grow. Bacteria are also easier to engineer than plants, creating the potential for a much larger variety of compounds. These compounds range from things like simple sugars that you put in your coffee, to complex chemicals with long names like those found on the labels of processed foods.  Scientists can also manipulate bacteria to excrete or pump the products outside their cells, making the compounds easier to extract [5,6,7].

E. coli and cyanobacteria are two of the most commonly employed bacteria for producing biofuels. E. coli, a common bacteria found everywhere including our guts, can be easily manipulated to do a wide variety of things and is fairly cheap to grow. However, E. coli need to “eat” sugar, and that has to be produced from somewhere else. Cyanobacteria, which are found nearly everywhere where there is water, combine sunlight and carbon dioxide to produce sugar in the same way that plants do. While cyanobacteria have not been studied or manipulated for as long as E. coli, they only need light, carbon dioxide, and some salts and minerals to grow. In the last 20 years or so, scientists have learned enough about cyanobacteria that engineering them is now possible [7].

One setup that scientists are working on involves the use of cyanobacteria to produce simple sugars, which the cyanobacteria “feed” the E. coli, which then use the sugars to make more complex chemicals like the precursors to jet fuel [6]. Others are planning to not use E. coli at all, and re-engineer the cyanobacteria to directly produce the desired product [5]. Being able to take carbon dioxide out of the atmosphere and produce fuel products in an almost self-sustaining and inexpensive system would be green-fuel-dream come true!

How do we manipulate bacteria to make these products for us?  Well, there are a few challenges we have to work through. Engineering the bacteria to make a product in large quantities that they don’t normally make is a huge problem in and of itself. Bacteria normally convert carbons sources like sugars into all of the different compounds that make up a bacterial cell, including things like proteins, the cell membrane, and DNA. To do this, bacteria use molecular machines in the cell called enzymes,  to convert the sugars into different chemical compounds. These processes require many enzymes in very complex pathways. In order to use bacteria to make products that we want, scientists sometimes need to insert new enzymatic pathways into the bacteria. Scientists do this by changing the genetic code, the  “program” that instructs how the bacteria grow. An example of these “instructions” would be the ones for a series of enzymes that work together to make sugar by using light energy to link multiple carbon dioxides together. These instructions could also be for enzymes that take a chain of carbons, the raw ingredients of fuels such as ethanol or gasoline, and make it into a loop or combine with other chains. We could also insert instructions to build a transporter that moves the sugar or fuel out of the cell, allowing it to be easily collected.

Just because we give the bacteria instructions to produce a product, doesn’t mean that they will follow them! In the wild, bacteria that grow most quickly will be the ones that survive and make more of themselves. Therefore, most of their biochemical pathways are set up to produce the ideal amount of each chemical they need to grow and divide into more bacteria. For the bacteria to be useful for making biofuels, we need them to stop using all their energy to grow and instead produce sugar or fuel for us. Sometimes this means shutting down some of the bacteria’s natural biochemical pathways, which could make them weaker or grow more slowly. There is a delicate balance between having bacteria that are healthy and can grow quickly enough, and ones that can produce enough of the product that we want.

Last year, researchers at Harvard Medical School successfully engineered cyanobacteria to produce sugar and used the sugar to feed E. coli [8]. They chose to produce sugar because it is non-toxic to the cell at high concentrations, unlike many fuel compounds. By choosing a non-toxic product, biologist can manipulate the bacteria to produce very high quantities of sugar without killing the cells. Sugar is a relatively high-value product by itself without any further processing, but it can also be used as a feedstock for making other products such as fuels, food additives, plastics, or chemical products [7, 8].

Like any of today’s “green technologies”, such as solar panels and wind power, biofuels from bacteria will probably not solve all our energy problems. Each technology has its own limitations and difficulties. In addition to the challenges of engineering described above, cost of the facilities to grow the bacteria needs to be taken into account. Cyanobacteria can only be grown in tanks that have good sunlight and carbon dioxide throughout. Open ponds would be the cheapest, as plastic coverings can be expensive over large surface areas. However, since these bacteria would be weaker than bacteria in the wild, it would be difficult to keep wild bacteria from invading the pond and overgrowing. In the specific case of using cyanobacteria to produce sugar, it would be especially difficult to keep E. coli, or other sugar-eating bacteria, from invading and consuming all the product. To make an enclosure cost-effective, the bacteria need to produce more product than has been achieved in labs so far [7, 8].

Continuing advances in our understanding of metabolic engineering, as well as improvements in enclosure design, will bring bacteria-made biofuels closer and closer to an economic reality. One of the best qualities of using bacteria to produce fuel is that they are living creatures that can rebuild, replenish and maintain themselves. They are literally factories that grow themselves. However, for researchers this strength is also the greatest challenge; working with “living factories” also mean they will grow, evolve and change, sometimes in unexpected ways. It will be up to scientists and engineers to figure out how to either control or use these changes.

Niall Mangan is a doctoral candidate in Harvard University’s Systems Biology Program. She does theoretical work with Prof. Michael Brenner, Harvard Applied Math, on how efficient cyanobacteria are at turning carbon dioxide into sugar.


[1] A report requested by the United Nations from the High level Panel of Experts on Food Security and Nutrition. “Price volatility and food security” 2011. < >

[2] New York Times . “Biofuels” 2011. <>

[3] David Biello. Scientific America. “Biofuel from Bacteria” 2010 <>

[4] Robert Sanders. UC Berkeley News Center “Turning Bacteria into butanol biofuel factories” 2011 <>

[5] Jill Jensen. “U researchers looking at bacteria see new biofuels” 2011.

[6] Molly Line. “Energy in America: New Liquid Fuel Faster, More Efficient – and Greener Too” 2011. <>

[7] Ducat et al. “Engineering cyanobacteria to generate high-value products” Trends in Biotechnology. 2011. 29:2 95-103.

[8] Niederholtmeyer et al. “Engineering Cyanobacteria to Synthesize and Export Hydrophilic products.” Appl Environ Microbiol. 2010.

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