Gut Reactions /2

http://www.theatlantic.com/doc/200809/termites

Perhaps—but it won’t be easy. Last year, in an initiative that has been compared to the Manhattan Project, the Department of Energy founded three Bioenergy Research Centers, which collectively house scientists from seven government labs, 18 universities, and several private companies, and are aimed at making cellulosic ethanol competitive with gasoline within five years. The effort, which has $375million in funding, is focused on plumbing the structures of woods and grasses and learning how various creatures break them down; genetic modifications, scientists hope, could then enable us to make cheaper fuels. The centers are expected to come up with ideas that can be commercialized—actually making them more like Bell Labs, say, than like the Manhattan Project.
Started two years earlier, the termite proj­ect described in Nature is based on the same model of public and private collaboration, and is now an important part of the bioenergy initiative. Indeed, termites might be seen as an “indicator species” for the larger effort—and, as scientists are learning, they are full of devilish details and vexing complications.
In 2005, the microbial ecologist Falk Warnecke, of the Department of Energy’s Joint Genome Institute, traveled with researchers from Caltech and the San Diego biotech company Diversa to Costa Rica, where they opened up a termite nest in a tree. The group dissected 165 worker termites, freezing the contents of their third guts in liquid nitrogen and shipping them to Diversa’s lab. After extracting the DNA from the microbial cells, Diversa sent a sample to the institute to be sequenced.
Housed in a low brick building in Walnut Creek, California, the Joint Genome Institute is sequencing the genes of hundreds of plants and microbes that might be useful for energy production and environmental cleanup; it is a key part of the Bioenergy Research Centers. Originally formed as part of the Human Genome Project in the late 1990s, the institute has its roots in the Department of Energy’s decades-long interest in tracking genetic mutations in atomic-bomb survivors and nuclear workers. The scale of its current mission becomes evident as soon as you enter the lobby, where a TV screen displays a ticker that tallies sequences by the minute, day, month, and year. When I arrived at about 10 o’clock one morning last spring, the day’s total stood at 25,555,288 DNA base pairs, the twinned nucleotides that are the building blocks of genes. Every second, another thousand base pairs joined the tally. Employees call this incessant data stream the “fire hose.” The institute now sequences as much DNA in an hour as it did in all of 1998, and the pace is planned to double by the end of the year.
Even for people accustomed to avalanches of data, the effort to map the contents of the termite’s third gut is extraordinary. “A disgusting mess of a data set,” says Phil Hugenholtz, the head of the institute’s Microbial Ecology Program. An angular Australian in his 40s, he speaks in rapid bursts, like a human fire hose. Traditional genomic analysis sequences one organism at a time, but Hugenholtz is a leading practitioner of metagenomics—the new science of sequencing genes from whole environments of microbes at once, and sorting out the resulting jumble of loose DNA code with the aid of computer science, statistics, and biochemistry. Metagenomics is not only breathtakingly fast; it allows us to catalog genes that were previously unknowable because so few types of microorganisms—fewer than 1 percent of all species of bacteria—can be cultured in a lab. Many biologists regard metagenomics as a scientific revolution akin to the invention of the microscope. In practice, though, it’s a sloppy art.
When the sequencers finished, they had 71 million letters of DNA code in tiny fragments. They sorted the fragments, assembled them into longer chains of genes, and scanned the genes to determine their likely functions and which of the 300 microbes they might have come from. Scientists then looked for combinations of chemicals that might be enzymes, comparing the results to enzymes known to work on cellulose. The metagenomic picture of the termite’s third gut that has so far emerged is a portrait of codes and probabilities—more sophisticated than a photograph from an electron microscope, but less satisfying, because so much remains indefinite.
Next, the scientists set about the long process of figuring out how all the parts work. “It’s like trying to learn about a house when someone’s given you nothing but the blueprints—and they’re all ripped up,” Hugenholtz says. Still, the blueprints were stunning. The termite gut contained much more than enzymes involved in breaking down wood into sugars: for example, there were a hundred species of spirochetes closely related to syphilis but here devoted to, among other things, producing hydrogen. There were also 482 appearances of a mysterious giant protein that Warnecke says looks like the international space station. He drew me a picture of a long, Lego-like scaffold with different enzymes plugged into it, hypothesizing that the protein might help strip sugars out of wood. But that was only a guess: “One of the disadvantages of finding so much is that you don’t know what it all means,” he told me.
Hugenholtz and Warnecke began sifting through the questions raised by the metagenome. Why do termites have 300 microbes and 500 different genes to degrade cellulose? How do you go about deciding which microbe is the most important? Do some termite species have stronger guts than others? And what on Earth was the space station doing? To tackle these questions, they needed more termites. They took some from cow patties on a Texas farm, surprising the elderly landowners by asking for a signed waiver on whatever intellectual property might develop.
One afternoon I watched Warnecke dissect 50 of the new termites. He worked at a rapid clip, pulling the insects’ heads and anuses in opposite directions with a microscopically violent yank; each termite’s gut unwound into a short, lumpy string. He showed me an electron-micrograph image of the inside of the gut. It looked like an undulating carpet. On it were rod-shaped bacteria; Warnecke pointed out pimple-like structures on the sides of a few, which he thought might be the space-station-like giant proteins. He speculated that the proteins work something like a Swiss Army knife, holding an array of tool-like enzymes and catalysts outside the cell to grab pieces of wood and whittle away, allowing the cell to slurp up the sugars thus released. If this hypothesis is correct, the proteins could be a great fit for biofuel production, because those loose sugars could be fermented into ethanol.
But the magnified images were far from conclusive. Hugenholtz slumped in front of the screen and complained that he saw no wood in the gut—were the termites starving? He impatiently made a list of tests he wanted done. Hugenholtz is confident that the team will eventually figure out what the proteins do. “You really see the science flailing around blindly here—but then things crystallize out of the darkness,” he told me.
One morning when I met Hugenholtz and Warnecke at a coffee shop, they began to riff on how the gut might work. “You get the feeling the microorganisms are more dominant than the termite. They must have a way to control the insect,” Warnecke said. Hugenholtz interrupted, quoting a colleague: “Maybe the termite is just a fancy delivery system for the creatures in the gut.” We tend to assume that the larger organism in a symbiotic relationship is in charge, but relationships like the one between the termite and the microbes involve constant two-way chemical communications. Even human beings, Hugenholtz said, are subconsciously eavesdropping on chemical conversations between the inhabitants of our guts; this leads us to crave, say, potato chips when our microbes want salt. His eyes fell warily on his coffee. “Do you think our stomach bacteria have trained us?”
History suggests that science follows its own timetable, often producing results long after the politicians who approved the funding have left office. Yet curiosity without the prospect of imminent practical application is something biotech investors are increasingly loath to pay for. When the Nature study began, Diversa was on the cutting edge of “ethical bioprospecting”—searching the world for novel environments and enzymes. After merging with a biofuels company, it became Verenium last year, and shifted to the more prosaic task of making commercial enzymes involved in the development of products including animal feed, paper, and fuels.
David Weiner, the assistant director of enzyme technology at Verenium, gave me a tour of the labs, showing me what he calls the “giant funnel”—the process the company uses to sift through nature’s intellectual property for enzymes that can be converted to profits. “We’re not really interested in DNA,” he said, meaning that the focus is on an enzyme’s performance, not its origins.
Whereas the Joint Genome Institute began by sequencing the termite-gut DNA—learning about its underlying structure—and only then tried to identify what might be useful, Weiner’s colleagues threw all the material from the Costa Rican expedition directly into testing, using the funnel approach to separate the most-useful enzymes from the millions of useless ones. Researchers inserted gene fragments into lab bacteria that had been genetically “tamed” to produce whatever enzyme the fragments were programmed to make. They then tested those enzymes on cellulose, to see if they would attack it. Only the winners made it to sequencing. You might think of the Joint Genome Institute as a group of diligent librarians, studying every step along the way. In contrast, a Verenium senior researcher told me, the company takes a “Julia Child approach”—once it has thrown together the ingredients (like termite guts and cellulose), it turns its attention to the final product, with far less focus on the stages in between.
Much of the action takes place in a machine—a type of robot, really—called the GigaMatrix. Clad in steel, the Giga­Matrix looks like a copier from the late 1980s, with two flat TV monitors on top and a door on the side. It can screen up to a million enzymes at a go, easily exceeding in a single day the lifetime performance of a human lab tech. The Giga­Matrix and other machines took the 500 or so most interesting enzymes from the termite gut and narrowed them down to fewer than 100 with potentially practical applications. Those were then tested for their effects on cellulose, modified, and inserted into “factory” bacteria trained to produce large quantities of enzymes while dining on cheap food, such as corn syrup. As the enzymes made their way through the process, every parameter of their growth and efficacy was measured. Only a small percentage proved powerful enough to merit continued investigation; these were stirred into multiple-enzyme “cocktails” to evaluate their speed and efficiency in combination. By the end, Weiner said, just a few enzymes remained in the running for further testing.
Geoff Hazlewood, a former senior vice president and now a consultant to Verenium, told me that the company has currently put aside studying termites for biofuels and has moved on to other potentially lucrative efforts. “You could screen ad nauseam,” he said, “but you can’t commit an infinite amount of resources.” Whatever the termites are doing may be too complicated and fragile to be useful in a large industrial process. There may be genius in the termite gut—Weiner calls it, admiringly, “a whole town”—but the wonders of symbiosis, in themselves, mean little to companies focused on the bottom line. “We want faster, cheaper, more efficient,” Weiner told me.