BIOPROSPECTING TERMITES
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Sep 25, 2009, 12:33:50 PM9/25/09
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http://www.jbei.org/
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AND THE BUGS INSIDE THEM
http://www.jgi.doe.gov/News/news_11_21_07.html
http://www.theatlantic.com/doc/200809/termites
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.”
CONTACT
Jim Bristow
http://www.jgi.doe.gov/whoweare/bristow.html
email : jbristow [at] lbl [dot] gov
Phil Hugenholtz
http://www.jgi.doe.gov/research/hugenholtz.html
email : phugenholtz [at] lbl [dot] gov
Falk Warnecke
http://www.jgi.doe.gov/research/microbialecology.html
email : fwarnecke [at] lbl [dot] gov
Jared Leadbetter
http://www.its.caltech.edu/~jaredl/index.html
http://www.its.caltech.edu/~jaredl/group.html
email : jleadbetter [at] caltech [dot] edu
DOE BIOENERGY RESEARCH CENTERS
http://genomicsgtl.energy.gov/centers/
http://genomicsgtl.energy.gov/research/index.shtml
http://genomicsgtl.energy.gov/links/tools.shtml
http://genomicsgtl.energy.gov/links/software.shtml
ABSTRACT
http://www.lbl.gov/Tech-Transfer/publications/2343pub1.pdf
http://www.lbl.gov/Tech-Transfer/techs/lbnl2343.html
"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."
VERENIUM
http://www.verenium.com/
http://www.verenium.com/research.asp
http://www.verenium.com/specialty-enzymes.asp
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."
'THE FOSSILISED PLANT MATTER WE KNOW AS COAL'
http://www.arctech.com/
http://www.humaxx.com/pdf/Coal-Eating_Microbes_PR_070809.pdf
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.”
METAGENOMICS
http://dels.nas.edu/metagenomics/
http://dels.nas.edu/metagenomics/materials.shtml
http://dels.nas.edu/dels/rpt_briefs/metagenomics_final.pdf'
http://genomesonline.org/links.htm
http://www.loe.org/shows/segments.htm?programID=07-P13-00013&segmentID=5
http://www.technologyreview.com/Biotech/18073/
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."
http://img.jgi.doe.gov
AND THE BUGS INSIDE THEM
http://www.jgi.doe.gov/News/news_11_21_07.html
http://www.theatlantic.com/doc/200809/termites
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.”
CONTACT
Jim Bristow
http://www.jgi.doe.gov/whoweare/bristow.html
email : jbristow [at] lbl [dot] gov
Phil Hugenholtz
http://www.jgi.doe.gov/research/hugenholtz.html
email : phugenholtz [at] lbl [dot] gov
Falk Warnecke
http://www.jgi.doe.gov/research/microbialecology.html
email : fwarnecke [at] lbl [dot] gov
Jared Leadbetter
http://www.its.caltech.edu/~jaredl/index.html
http://www.its.caltech.edu/~jaredl/group.html
email : jleadbetter [at] caltech [dot] edu
DOE BIOENERGY RESEARCH CENTERS
http://genomicsgtl.energy.gov/centers/
http://genomicsgtl.energy.gov/research/index.shtml
http://genomicsgtl.energy.gov/links/tools.shtml
http://genomicsgtl.energy.gov/links/software.shtml
ABSTRACT
http://www.lbl.gov/Tech-Transfer/publications/2343pub1.pdf
http://www.lbl.gov/Tech-Transfer/techs/lbnl2343.html
"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."
VERENIUM
http://www.verenium.com/
http://www.verenium.com/research.asp
http://www.verenium.com/specialty-enzymes.asp
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."
'THE FOSSILISED PLANT MATTER WE KNOW AS COAL'
http://www.arctech.com/
http://www.humaxx.com/pdf/Coal-Eating_Microbes_PR_070809.pdf
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.”
METAGENOMICS
http://dels.nas.edu/metagenomics/
http://dels.nas.edu/metagenomics/materials.shtml
http://dels.nas.edu/dels/rpt_briefs/metagenomics_final.pdf'
http://genomesonline.org/links.htm
http://www.loe.org/shows/segments.htm?programID=07-P13-00013&segmentID=5
http://www.technologyreview.com/Biotech/18073/
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."
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