Biofuels may hold the key to reducing our dependence on foreign oil and cutting down on our greenhouse gas emissions. Ethanol is currently the biofuel of choice, with almost all gasoline bought at the pump in the United States containing 10 percent ethanol. Right now, though, most ethanol comes from corn and sugarcane, and there are concerns that growing our fuel from these crops could drive up food prices (“food versus fuel”).

Biofuels made from macroalgae, aka seaweed, avoid this problem. Seaweeds do not require arable land, fertilizer, or fresh water, and they are already cultivated as food (though not a staple crop like corn), animal feed, fertilizers, and sources of polymers. Traditionally, scientists ignored seaweed as a biofuel source because its main sugar component was too difficult to process. A recent paper published by Science describes how researchers genetically-engineered a microbe that is capable of producing ethanol from seaweed.

The so-called second generation of bioethanol is derived from inedible crops like wood and switchgrass, or the inedible portions of food crops like corn (the leaves and stalks). However, this cellulosic material is difficult to process due to the presence of lignin in the cell walls—although we reported on some attempts to genetically modify switchgrass to make this easier. Seaweed doesn’t contain lignin, making processing a lot easier and enabling higher yields: a Department of Energy study showed that, under ideal conditions, seaweed could produce twice the ethanol that we get from sugarcane and five times the amount from corn.

You may be asking “This sounds great, why aren’t we making ethanol from seaweed?” Well, there is a catch. Seaweeds contain three primary sugars: alginate, mannitol, and glucose. Right now, existing industrial microbes can’t metabolize alginate, so ethanol yields are severely limited.

At this point, most people would stop and say “Well, maybe seaweeds aren’t the best way to produce biofuels.”

On the other hand, if you were Adam Wargacki and a team of 13 others from the Bio Architecture Lab, you wouldn't stop. Instead, you’d look to the well-known bacterium Escherichia coli (E. coli), which has a natural ability to metabolize mannitol and glucose. Since we know of enzymes that can process alginate (alginate lyase and oligoalginate lyase), Wargacki et al apparently thought “We can make this work.”

There are several bacteria species with known alginate metabolic systems, but only one where we've identified an alginate transport system to get it inside of cells: Sphingomonas sp. A1. Unfortunately, this system is too large and complex to be incorporated into E. coli.

Instead, the team searched the National Center for Biotechnology Information genome database and found a 30,000 base-pair (30 kbp) section of DNA from the bacterium Vibrio splendidus 12B01 that looked like it might hold all the genes needed for alginate degradation, transport, and metabolism. (I pity the researcher that had to search the database for this.)

Now, a 30-kbp DNA fragment is too long to directly clone into E. coli, and the function of the genes in that DNA hasn’t been described yet. To get E. coli with the right DNA, the authors created a library of random DNA fragments from the V. splendidus genome. Each fragment is carried by DNA called a fosmid, which will stably integrate a 40-kbp piece of DNA into a target’s genome. After inserting the fosmid library into E. coli, they placed the bacterial colonies into a medium where alginate was the only food source. Only colonies with a particular fosmid (designated pALG1) grew, suggesting that this section of DNA contained the 30-kbp piece they identified earlier.

After this, they checked the individual protein coding sections of pALG1 to determine the function of each. By deleting them one at a time and testing for the ability to grow on alginate, they were able to identify an alginate transport system that hadn’t previously been described.

After inserting these genes into a strain of E. coli, they took genetic pathways for ethanol production from Zymomonas mobilis—through enzymes called pyruvate decarboxylase and alcohol dehydrogenase B, for those interested—but deleted some pathways that produced undesired byproducts. Finally, they tested their engineered E. coli strain (which they named BAL1611), in a five percent sugar mixture containing alginate, mannitol, and glucose at a ratio of 5:8:1, which represents the typical ratio in brown macroalgae (seaweeds). They found that it produced ethanol at a yield of about 20 grams per liter.

For a final demonstration, they used Saccharina japonica, otherwise known as kombu, a common edible kelp. Their microbe produced ethanol at a ratio of 0.281 grams of ethanol for each gram of algae—which is over 80 percent of the theoretical yield. In addition, 83 percent of the yield was obtained within 48 hours.

This study may have opened the door to using seaweed as a source of ethanol—there is certainly a lot of potential here. Even more fascinating is the approach to engineering a microbe to give it the characteristics we desire.

Hopefully, microbes can eventually be engineered to make more than just ethanol. It is much less energy dense than gasoline, so current vehicles can’t burn a fuel mix that contains more than about 15 percent ethanol. Butanol, on the other hand, is much more similar to gasoline, so perhaps a future microbe may produce that.

Science, 2012. DOI: 10.1126/science.1214547 (About DOIs)