Gut Reactions
BY Lisa Margonelli / 09.2008

For more than a hundred million years, termites have lived in obscurity, noticed only by the occasional hungry anteater or, more recently, by dismayed home­owners. Other social insects, such as bees and ants, are celebrated for their industriousness and engineering feats, but popular culture has not gotten around to cheering on termites for theirs—even though they build mounds as tall as 20 feet, which may be oriented north-south as accurately as if plotted with a compass, in order to maximize heat from the sun. The extraordinary powers evolution has bestowed on termites—some protect the mound by spraying chemicals from nozzles on their heads at intruders, while others have snapping mandibles that can decapitate invading ants—have similarly failed to elevate their status. On the contrary: last year, scientists at the London Natural History Museum called termites “social cockroaches” and proposed reclassifying them, in a paper brusquely titled “Death of an Order.”

The more closely one examines the termite, the more mysteries one finds. In some species, if a termite discovers a contamination in the mound, it alerts everyone else, and a hygiene frenzy begins. As a disease passes through a mound, the survivors vaccinate the young with their antennae. When a mound’s queen is no longer capable of reproduction, the workers may gather around her distended body and lick her to death.

The greatest mystery of all is found in the worker termite’s third gut, which is delineated by an intricately structured stomach valve, as unique from species to species as individual snowflakes are and, in its way, just as lovely. The size of a sesame seed, the third gut contains a dense mush of symbiotic microbes. Many of these microbes live nowhere else on Earth; they depend on adult termites to pass them on to the young by means of a “woodshake,” a microbial slurry.

This microbial mush may be a treasure trove for the human race. Recently, sophisticated genetic sequencing produced an inventory of more than 80,000 genes, spanning some 300 microbial species, from the guts of Costa Rican termites. These findings, published last November in the journal Nature, got a lot of attention, not for the quantity of microorganisms—after all, the human mouth contains 600 species of bacteria—but for their complexity, and in particular for the fact that among them are 500 genes for enzymes able to break down the cellulose in wood and grasses.

With oil prices at historic highs, the quest is on to turn such plant materials into a replacement for gasoline—call it grass­o­line. Since 2007, U.S. energy policy has been shaped by the premise that we can brew enough biofuels to replace 35 billion gallons of gasoline by 2017, and 60 billion by 2030. Corn ethanol has been a bust, blamed for wasting water, exhausting croplands, and causing tortilla shortages in Mexico and rice shortages in Asia. For all these problems, it currently contributes the equivalent of only about 4.2 billion gallons of gas a year. And the carbon dioxide emitted in the process of growing and fermenting corn and then distilling and burning ethanol is nearly as much as that emitted by extracting, refining, and burning gasoline.

Wood and grasses seem to hold more promise. They contain chains of thousands of glucose molecules that could be made into so-called cellulosic ethanol and then burned like gasoline, while releasing just 15 percent of gasoline’s greenhouse-gas emissions. But there’s a catch. Wood has evolved to keep its sugars to itself, covering them with lignin—a substance that gives cell walls rigidity—and then locking them in a matrix of cellulose and hemicellulose protected by complex chemical bonds. Because these sugars are so hard to get at, our output of cellulosic ethanol is still, after decades of research, just 1.5 million gallons a year—less than 1 percent of one day’s gasoline consumption.

But where humans have failed, the termite succeeds—spectacularly. A worker termite tears off a piece of wood with its mandibles and lets its guts work on it like a molecular wrecking yard, stripping away sugars, CO2, hydrogen, and methane with 90 percent efficiency. The little biorefineries inside each termite allow the insects to eat up $11 billion in U.S. property every year. But some scientists and policy makers believe they may also make the termite a sort of biotech Rumpelstiltskin, able to spin straw—or grass, or wood by-products—into something much more valuable. Offer a termite this page, and its microbial helpers will break it down into two liters of hydrogen, enough to drive more than six miles in a fuel-cell car. If we could turn wood waste into fuel with even a fraction of the termite’s efficiency, we could run our economy on sawdust, lawn clippings, and old magazines.

And so the termite may be poised for its moment in the sun. Speaking last year about moving toward a biofuel economy, Energy Secretary Samuel W. Bodman pointed to the termite-to-tank concept, asserting, “We know this can be done.” Another official called it a promising “transformational discovery.” Suddenly the termite is everywhere, from Popular Science to Congressional Quarterly Today to Wired. With the audience for energy speeches and articles so small and wonky, it’s too soon to say that the little bug has exactly become a celebrity (although it did recently rate a footnote in Vanity Fair). But in some circles, it has attained a certain status as the pest that could solve our energy problems, transforming geopolitics and agriculture in the process. “Deus ex termita,” you might say.

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.

And it’s too early to tell whether the termite will ever provide genes or information that will enable biofuel production. Termite research could instead provide a cautionary tale about the difficulties of replicating nature on a political schedule. It may be faster and easier to come up with a comprehensive energy policy—investing in energy efficiency, changing personal behavior, and working with other large oil consumers to control prices—than to create a cellulose economy out of the termite gut.

Termites certainly have their critics. One is Harvey Blanch, a professor of chemical engineering at UC Berkeley and the chief science and technology officer at the Department of Energy’s Joint Bio-Energy Institute, in Emeryville, California (where Hugenholtz also conducts research). “Those microbes eat pâté!” Blanch said. By the time wood reaches the termite’s third gut, he explained, it has been chewed to a fine consistency and soaked in the highly alkaline second stomach; the gut microbes don’t have to work very hard to break it down. Pretreating wood in similar ways on an industrial scale would be ridiculously expensive, he believes. He thinks the termite has been overhyped, and sees this as a reflection of unrealistically high hopes for quick, painless replacements for gasoline.

Blanch has experienced the pitfalls of research driven by political goals. In the early 1970s, he worked on creating faux meat products from petroleum, which was then thought to be a cheap way to feed the world. For example, single-celled “chicken” proteins were produced by yeasts that fed on oil by-products, and then draped around plastic bones. But when the 1973 oil crisis hit, the cost of the raw material soared, effectively ending the petroprotein business. Blanch then shifted to cellulosic ethanol; the project was progressing until President Reagan killed it, in the mid-1980s. Now, he’s at once hopeful that we will one day be able to engineer novel organisms and make better fuels, and wary of putting too much faith in quick technological solutions. “Given the scale at which we need to operate, it’s hard to imagine any magic organism that will do the trick,” he told me.

Several years ago, government labs set a goal of producing cellulosic ethanol for $1.33 a gallon by 2012, but Blanch cautions that the retail price could be $6 or $8 a gallon if the cost of the raw materials rises, and he thinks a realistic deadline is at least 10 years away. Perhaps because of his earlier experiences, he fears that projects that fail to deliver quickly are at risk, which puts a lot of pressure on both the Bioenergy Research Centers and individual researchers.

These concerns speak to an important tension underlying the termite research: the often competing agendas of work aimed at producing quick results, and of the slower, more methodical approach known as basic science, which tries to discover the fundamental logic of natural processes. Again, Julia Child (or maybe the more commercial Wolfgang Puck) versus the librarians. Some of the scientists—and even venture capitalists—I spoke with voiced fears that the race to harness nature for fuel production may cause us to neglect basic science and thus jeopardize potential long-term gains.

Consider this: half of the 80,000 genes inventoried from the Costa Rican termites remain unidentified, and each of those 40,000, Warnecke imagines, could require a Ph.D. thesis to figure out. Hugenholtz says that metagenomics is grappling with the problem of having too much information and too few references. “Sequencing is far outstripping our ability to characterize the genes,” he explains, adding that this can lead to “genome rot”—a chain of errors created when one scientist gets a gene wrong, and then the mistake is multiplied across other genomes. The popular model of science is based on “eureka” moments, but right now, metagenomics is more like a big 3-D puzzle, where every new piece of knowledge—and every mistake—affects the whole. Trying to solve just one part of the puzzle for a quick commercial breakthrough may be as tricky as solving the entire thing.

It could also cause us to give short shrift to alternative solutions. Eric Mathur was one of the Diversa executives who helped set up the Costa Rican expedition; he now works for Synthetic Genomics, a company founded by the scientific impresario Craig Venter to search for biology-based fuels and methods to cut greenhouse-gas emissions. Mathur says the Nature paper is just the beginning of a long process of understanding how symbiotic creatures deal with wood and carbon. He thinks that searching for individual enzymes in the termite will be a dead end, but that harnessing the power of whole environments might yield results. The challenge, he says, is to learn how these environments’ overall metabolisms work, and then use the tools of synthetic biology to engineer the organisms in them to evolve—creating a “slave organism” that focuses all of its resources, down to its last electron, on processing carbon. “Metabolic engineering is a very powerful method for productivity,” he told me.

But the strongest argument for more basic research may be the termite itself. Jared Leadbetter, an associate professor of environmental microbiology at Caltech, remembers feeling “like an ecotourist in Alice in Wonderland” the first time he looked at a magnified termite gut, 18 years ago. Leadbetter has pioneered the study of the metabolism of a few of the spiro­chetes in the gut. Like Mathur, he believes scientists might put the termite’s gut to work against global warming by using it to understand and possibly alter the carbon cycle—the biogeochemical give-and-take of greenhouse gases between the Earth and its atmosphere.

Leadbetter says one of the extraordinary things about termites is not how much ethanol they might make, but how little methane they produce. Cows lose 20 percent of the energy in the grass they eat, because the microbes in their stomachs combine hydrogen and carbon dioxide from the grass to make methane, a greenhouse gas that traps 20 times as much heat in the atmosphere as CO2. In 2006, the greenhouse gases produced by U.S. farm animals exceeded the emissions of the iron, steel, and cement industries combined. Termites lose less than 2 percent of their nutrients to methane production, because the spirochetes in their guts transform hydrogen and carbon dioxide into acetate, which the termites use as fuel. If we understood this process, perhaps we could put new microorganisms into the stomachs of cows and reduce their production of methane.

We’re a long way from changing the chemistry of cows’ stomachs, but the process of adapting and commercializing the termite’s role in the carbon cycle has already yielded success on a small scale. The Virginia-based company ArcTech trained termites to eat coal, and then rummaged through their guts to find the microorganisms best at turning coal into methane. It cultured those microorganisms and now feeds them coal; the company plans to use the methane they produce to make electricity, and is already selling the by-products, including one used by farmers as a soil additive. ArcTech says this method eliminates virtually all greenhouse-gas emissions from coal-based electricity production. Other companies are trying to engineer similar organisms that could be sent into abandoned mines and oil wells to scavenge fuel that goes unused because it is so hard to get at. Such efforts could have a dramatic effect on both the environment and geopolitics: experts estimate that increasing the yield of oil wells from the current average of 35 percent of the oil in a reservoir to 40 percent would be the equivalent of discovering a new Saudi Arabia.

Who knows what other answers may lurk in the termite? Elizabeth Ottesen, a graduate student doing research in Leadbetter’s lab, dissected a termite and put it under a microscope to give me a tour of its gut. At first glance, the dark mass of the gut was immobile, the organisms apparently packed too tightly to move, but as Ottesen added water, a menagerie of blobby Trichonympha, whizzing spirochetes, and other creatures materialized, all supported by gangs of bacteria too small to see. The inhabitants here are arranged in hierarchies more elaborate than Manhattan real estate, she said: Those at the edges use oxygen, while those in the middle are anaerobes. Many are high-speed commuters, outfitted with complicated sensing and swimming apparatus that helps them find hydrogen and other gases. Among the creatures in the termite’s gut, and especially among those creatures’ genes, exist redundancies that suggest the system has been over­engineered to survive the worst (including being force-fed coal). A spirochete’s flagella, for example, are between the layers of a double skin, enabling the organism to drill through the most viscous environments.

Leadbetter expects it will take at least 25 years to unravel what he calls the “teleological questions” about the termite’s complexity. Along the way, the termite will likely provide clues to solving climate change, but Leadbetter thinks its greatest value may be as a repository of biological wisdom gathered over the course of more than 100 million years of survival on Earth. “When you look at a termite and its gut,” he says, “you’re looking at a long line of winners.”

Jim Bristow
email : jbristow [at] lbl [dot] gov

Phil Hugenholtz
email : phugenholtz [at] lbl [dot] gov

Falk Warnecke
email : fwarnecke [at] lbl [dot] gov

Jared Leadbetter
email : jleadbetter [at] caltech [dot] edu


“Researchers at Berkeley Lab’s Joint Genome Institute, California Institute of Technology, and Verenium Corporation have discovered and sequenced over 300 microbes in the hindgut of a Costa Rican termite and identified over 600 genes that encode for enzymes that may play a role in the termite’s conversion of wood mass to sugars. The enzymes could enable more efficient strategies for the production of liquid biofuels from a variety of feedstocks. Termites are extremely successful at degrading plant biomass including wood and grass, and are therefore important sources of biochemical catalysts that might be used in industrial lignocellulose degradation. Recent research has supported the idea that symbiotic microbes found in the termite hindgut play a direct role in cellulose and xylan hydrolysis – the step that has been the economic bottleneck in man-made systems that convert cellulose to biofuels. In fact, these microbes are so efficient that they are capable of producing about 2 liters of hydrogen from fermentation of a typical sheet of paper. A relatively small set of fungal enzymes is used today for the hydrolysis of cellulose to simple sugars for subsequent fermentation, but the process is energy intensive, may involve toxic chemicals for pretreatment, and no discernable pathway exists for significant improvement. An optimized cocktail of the new termite-microbe enzymes could lead to conversion that is both energy and chemically efficient.

The Berkeley Lab-ClT-Verenium research is the first system-wide gene analysis of a microbial community specialized towards plant lignocellulose degradation. It revealed that the hindgut of the “higher” Nasutitermes species contains a broad diversity of bacteria representing 12 phyla and 216 phylotypes, and is dominated by two major bacterial lineages, treponemes and fibrobacters. While treponemes have been known to exist in the termite gut, fibrobacters are an exciting new find because they have relatives in the cow rumen known to degrade cellulose and are specialists in this regard. Berkeley Lab scientists are continuing research on the enzymes in order to define the set of genes with key functional attributes for the breakdown of cellulose and to determine metabolic pathways involved in the processes.”

Bioprospecting Extremophiles

“In the quest to discover novel products, Verenium has pioneered the field of “bioprospecting”. This has enabled the company to tap into the vast genetic resources of the microbial world by venturing into varied and often hostile environments, such as volcanoes and deep sea hydrothermal vents. Because the harsh temperatures and pH conditions in which these “extremophiles” live often mimic conditions found in today’s industrial processes, extremophilic microbes represent a valuable source of potential products.”

Press Release : Coal-Eating Microbes Make Coal Green / July 8, 2009

“Arctech has announced successful production of clean methane gas by coal eating microbes in a large prototype bioreactor. The researchers say that this discovery and the proven ability to scale from a lab based environment is an enormous step in the production of true clean coal technologies. In an effort to further develop this and other products pioneered by the company, Arctech has formed Humaxx, a wholly owned subsidiary, to market clean methane gas and humic-rich products. With over 20 years of research and development into microbes that can digest coal, Arctech’s scientists have successfully engineered microbes from the digestive tract of termites to produce clean methane gas and humic substance byproducts.

Arctech’s biotechnology produces a humic-rich carbon substance and converts it into ecological solutions for organically re-nourishing the soils while increasing crop yields, replenishing water and even neutralising munitions and converting them into organic fertiliser. The team at Humaxx will focus on the development of strategic partnerships to expand sales channels for its solutions. The patented Arctech Process is a significant paradigm shift for converting coal into methane gas and humic substances. Natural microorganisms are adapted to digest coal under anaerobic conditions resulting in a mixture of methane gas and humic substances. Dr. Walia, CEO of Arctech says “While people see coal as the dirtiest source of fuel, our scientists have proven otherwise. Arctech’s microbes have been bio-engineered from the digestive systems of specially-bred termites, which are unique in their ability to digest the compressed, fossilised plant matter we know as coal. The applications for this technology are exciting, and the team at Humaxx is committed to exploring new and expanded markets for our unique products.”

Sequencing the genomes of microbial ecosystems could lead to better biological machines
BY Emily Singer / January 17, 2007

Scientists are sequencing the genomes of entire microbial communities in the hope of uncovering new genes and organisms that can create fuel, mine metals, or clean up superfund sites. Known as metagenomics, the field relies on studying bits of DNA from a variety of organisms that live in the same place. Thanks to ever-improving sequencing methods, the number of metagenome projects is growing, giving scientists myriad new genes to explore. “This opens up a new way of looking at these organisms,” says Jim Bristow, director of the community sequencing program at the Department of Energy’s Joint Genome Institute, in Walnut Creek, CA. “We’ll probably discover lots of fundamental processes that we previously knew nothing about.”

Microorganisms make up an immensely important and often overlooked part of the environment. “They constitute the bulk of our biosphere and underpin all the nutrient cycles on our planet,” says Philip Hugenholtz, leader of the microbial ecology program at the Joint Genome Institute. “But our understanding of these systems is still rudimentary.” Microbiologists would like to better understand these communities, so they can co-opt useful genes or organisms, such as those that remove pollutants from soil, or better control microbial communities, such as those that live in our mouths or gut.

The standard way to identify and study the microorganisms living in a particular community is to grow them in a lab, but this is only possible with about 1 percent of microbes. However, in the past two years, faster and cheaper gene-sequencing methods have offered microbiologists a new tool with which to study the other 99 percent. Scientists can extract the DNA from, say, a drop of seawater or a sample of sludge from a sewage-treatment plant and then sequence that DNA, deriving genomic clues to all the organisms living in that environment.

Assembling the random fragments of DNA generated during sequencing can be a challenge–even impossible in some cases. Hugenholtz likens the process to trying to put together one thousand jigsaw puzzles from a single box that holds only a few pieces from each puzzle. So rather than fully assembling these genomic puzzles, scientists try to understand the individual pieces, or genes. Identifying the genes that allow the microbes in the termite gut to digest wood, for example, could lead to better biofuels. Converting cellulose in trees and grasses into the simple sugars that can be fermented into ethanol is a very energy-intensive process. “If we had better enzymatic machinery to do that, we might be better able to make sugars into ethanol,” Bristow says. “Termites are the world’s best bioconverters.”

Researchers at the Joint Genome Institute, which sequenced some of the human genome and is now largely devoted to metagenomics, have just finished sequencing the microbial community living in the termite gut. They have already identified a number of novel cellulases–the enzymes that break down cellulose into sugar–and are now looking at the guts of other insects that digest wood, such as an anaerobic population that eats poplar chips. The end result will be “basically a giant parts list that synthetic biologists can put together to make an ideal energy-producing organism,” says Hugenholtz.

Several other projects–from whale carcasses to wastewater sludge–are under way or already complete, promising a huge volume of novel genetic data. A recent project at the University of California, Berkeley, for example, identified three new organisms living in the highly acidic environment of abandoned mines. (Bacteria covering the floors of these mines convert iron into acid, which can then pollute nearby streams.) “They are close to the size of viruses and may be the smallest organisms ever discovered,” says Brett Baker, a research scientist at UC Berkeley, who worked on the project with Jill Banfield, also at UC Berkeley. These organisms may give clues to other life forms adapted to extreme environments, such as Mars.

The next hurdle in metagenomics will be trying to find the function of many of the newly identified genes: unlike cellulases in termites, most genes have little structural similarity to genes of well-studied organisms, making it difficult to infer their function. In a sample of water from the Sargasso Sea collected by genomics pioneer Craig Venter, the two most common and likely most important gene families are totally unique: scientists have no idea what they do. “In some ways, it’s crude to focus on enormous mountains in the genomic landscape,” says Hugenholtz. “But it does immediately draw attention to interesting avenues to pursue.” Structural studies are now under way to try to figure out these proteins’ function.

Metagenomics projects may eventually be able to shed light on these unknown genes. “We can look at representations of genes of unknown function in similar environments, compare them to environments that lack a particular function, and then triangulate,” says Bristow. And metagenomic signatures could one day be used as a fingerprint to identify certain environments, he adds. They “could be used as a way of identifying places you might want to drill for oil or look for minerals or contamination of some kind,” he says. “Just seeing the genes might tell you what’s happening there.”