Image: Cow with hole cut into it to allow placing switchgrass inside to incubate
Jonas Lovaas Gjerstad  /  Jonas Lovaas Gjerstad
Researchers studying the enzymes inside cows cut a hole through the top of two so as to get direct access into their foreguts. They then incubated switchgrass inside the gut for 72 hours to see what enzymes worked to break it down. Cutting such holes, known as cannula, is common in the bovine research field.
By Miguel Llanos Reporter
msnbc.com
updated 1/27/2011 3:21:10 PM ET 2011-01-27T20:21:10

It may not be glamorous, but the holy grail for efficient biofuels — the kind that don't compete with our food supply — could end up being found inside the guts of cows.

In a study published Thursday in the peer-reviewed journal Science, researchers described how they incubated bags of switchgrass inside cow rumens and from that found 27,755 "candidate genes" with the potential for efficiently breaking down plant cellulose into usable sugar that can then become ethanol.

Ethanol from corn is already widely in use in vehicles as an additive, but that has also driven up the cost of all corn-based foods.

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"Cellulosic ethanol" would use non-food plants such as switchgrass, which is one of the most promising bioenergy crops. But, while advances have been made, it's still not economically viable.

The researchers didn't come up with the magic mix of enzymes that will most efficiently break down switchgrass and other non-food plants. But they — and the two cows that served as their labs — did do what hundreds of scientists had earlier failed at: narrowing the seemingly endless number of enzyme combinations.

"Cows or rather the microbes in their rumen have had millions of years to optimize their capabilities of digesting grass," Eddy Rubin, lead author and director of the federal Joint Genome Institute, told msnbc.com. "We in the lab are just trying to copy what they have developed over millions of years of trial and error."

'Major step forward,' observer says
Jim Lane, editor of biofuelsdigest.com, called it "a major step forward." But he added it's not the holy grail in itself. Rather, he said, it's a step "in a long journey that will gain biofuels significance as soon as one of the novel microbes — or cocktail thereof — is identified as having superior properties."

Image: Microscopic view of switchgrass being decomposed
Damon Tighe
A fragment of switchgrass is seen under a microscope being decomposed after contact with cow rumen microbes.

Rubin's team used gigabytes of DNA data taken from the rumen to make their breakthrough.

"People have studied the microbes in cow rumen for years," Rubin said, "but this is the first time that the genes and genomes of the microbes in the cow rumen where intensively studied using recently developed DNA sequencing technologies and high performance computing to analyze the massive amount of data."

Because of this "ultra-deep DNA sequencing," he added, "we identified a thousand fold more genes involved in the breakdown of plant material than all the previous studies of rumen."

"I sure like the technique," said Lane, referring to the use of the rumen lab instead of other approaches like seeking enzymes in termites as they eat up wood. "Hard to duplicate on the termite side with wood biomass studies," he joked.

The U.S. Department of Energy, which sponsors the genome institute, noted that the rumen lab was unique. "Only about one percent of the planet's microbial species can be readily grown in the laboratory," it noted in a statement released with the study. "The vast majority — in the soil, water and residing in the other larger life forms such as in cows — cannot be cultured in a lab."

Rubin expects industry to quickly use the DNA data to speed up commercialization of cellulosic ethanol.

"With the paper being published all the data will be publicly available," he said. "Discussion with people in the industry makes it clear that a major challenge in the commercialization of next-generation biofuels — cellulosic biofuels — has been the lack of efficient enzymes needed to break down plant material. They are anxious to have access to the massive number of new enzymes involved in plant/cellulose deconstruction that we are going to provide them with."

"Companies that are in this business have been limited in the availability of enzymes," he added. "They will be testing the enormous diversity of enzymes that we have discovered in this one study for ones that have the properties they are seeking for their industrial processes."

270 billion letters of DNA code
Study co-authors Matthias Hess and Alex Sczyrba carried out the switchgrass testing, using the guts of two cows as fermentation chambers. Holes were surgically cut into each cow to allow access. Cutting such holes, known as cannula, are common in the bovine research field.

Switchgrass in nylon bags was inserted into the cow rumen for 72 hours, during which they were digested. "Switchgrass degradation was substantial," the experts wrote in their study.

The team then isolated and sequenced the DNAs from the microbes involved in digesting the switchgrass.

"The amount of data generated for this study of rumen microbes, 270 billion letters of the DNA code, was enormous," the Department of Energy stated, "about 100-fold greater than the number of letters in the entire human genome."

Hess said an even tougher task was to "identify and produce full-size functional enzymes based solely on information obtained from billions and billions of short snippets of DNA sequences."

Using massive computing power, the team eventually zeroed in on a subset of 90 gens chosen as representative of the 27,755 candidate genes. More than half of those were able to degrade cellulose, and nearly 20 percent were able to break down switchgrass.

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"This made it clear to the team that a significant faction of the 30,000 genes identified are indeed active against plant material and would be a treasure trove of novel enzymes for biofuel researchers," the Department of Energy stated.

Sczyrba compared the challenge to "someone mixing hundreds of jigsaw puzzles with millions of pieces each into a big pile."

"We tried to put as many of these back together, making as few mistakes as possible," he said in the Department of Energy statement. "It is not an easy problem. You need a good strategy and a lot of computational resources to solve this problem."

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