To the beachcombing tourists of Seaside, Oregon, the dark, brownish foam that washed up on the peaceful resort town’s shores one day in February looked like an oil slick. Up and down the beach, swaths of coffee-colored froth bubbled in with the surf, settling in unsightly clumps on the sand. Worried visitors poured into boardwalk shops, asking if there had been a ship wreck off shore. The tourism office got so many calls that it issued a press release. No need to panic, the release soothed. It’s just diatoms. Billions and billions of diatoms.
Diatoms—microscopic, single-celled algae that grow in virtually every body of water on the planet—have been likened to the grass of the ocean because they are so plentiful and so humble a part of the ocean food chain. They bloom in huge numbers near the ocean surface, where they take in energy from the sun, along with nutrients in the water, and convert them into carbohydrates. Fish feast on them—the nutritionally valuable omega-3 fatty acids in seafood come from the diatoms they eat.
Diatoms are also unheralded players in the Earth’s carbon cycle: They remove the same amount of carbon dioxide from the atmosphere each year as all the world’s rainforests combined. Yet they do all this with very little fanfare. In fact, most people never hear of them, except on the rare occasion when winds push blooms of diatoms onto a seashore, as happened in Seaside. And even then, they appear en masse, as an oily muck that conceals their amazing beauty.
Up close, diatoms are actually quite stunning. They are encased in cell walls made of silica, a kind of glass, and each of the thousands of species of diatom features a unique pattern of intricate grooves, lines and notches. When they were first discovered shortly after the invention of the microscope, parties were convened just to marvel at their filigreed, jewel-like shapes.
But with that beauty also comes intriguing possibilities. Using the high-tech tools of biotechnology, scientists are starting to learn how diatoms do the things they do, including their remarkable ability to create their intricate cell walls using tiny lines of silica. The answers could help advance a field of human endeavor that is critical to modern life as we know it.
“Diatoms are beautiful organisms that are able to lay down nanometer-sized lines of silica,” says CALS molecular biologist Michael Sussman. “If we could genetically control that process, we would have it nailed. We would have a whole new way to make computer chips.”
These kinds of intuitive leaps are entirely in character for Sussman, whose interest in diatoms was sparked by a single, one-hour talk he attended at a genomics conference organized by the J. Craig Venter Institute. Born and raised in New York City, Sussman brings a free-associating spirit to his laboratory, which is filled with equal parts laughter and inspiration. “Things are usually pretty mirthful [around the lab],” says Matthew Robison, one of Sussman’s graduate students who worked with him researching diatom genetics. “Sometimes it can be difficult to keep him on topic, but we try our best.”
Sussman spent much of his early career studying Arabidopsis, a model plant that scientists like because it has a rapid life cycle and can be grown in Petri dishes. He joined CALS as a horticulture professor in 1982, before switching to biochemistry in 2002. But the most significant turn in his work came in 1997, when he agreed to direct UW-Madison’s Biotechnology Center, a core facility that assists scientists with high-end research tasks such as gene sequencing and DNA analysis.
I do believe quite strongly that the true strength of biology will be its odd organisms: the electric eels, the silicate sponges and diatoms.
The position allowed him to turn his creative energy toward dreaming up and perfecting new research tools, such as a DNA chip he developed with UW-Madison electrical engineer Franco Cerrina and geneticist Fred Blattner. The technology led to the 1999 launch of NimbleGen Systems, which last year was acquired by the pharmaceutical giant Roche for $272 million.
But for all his technological skill, Sussman has the heart of a naturalist. He lives on a quiet hog farm 12 miles from Madison, about which he enthuses, “We eat breakfast with Bambi and Thumper every morning.” He also shows a near-fanatical obsession with The Life Aquatic with Steve Zissou, a quirky movie that chronicles the adventures of an aging oceanographer in search of a mythical “jaguar shark.” In interviews, he references the film repeatedly, and he occasionally blasts songs from its soundtrack on his office computer.
“He’s got this fantasy that he could move his lab onto a boat and cruise around the world doing research on it,” says Robison.
Even before he learned about diatoms, Sussman was exercising his inner Zissou by exploring the unique capacities of some of the planet’s strangest aquatic creatures. For a number of years, he’s been fascinated by electric eels, and he recently wrote an article for the Journal of Fish Biology calling on the scientific community to sequence the genome of Electrophorus electricus, which he thinks could open the door to new ways to produce and store energy.
But Sussman is quick to point out that a little eel curiosity hardly makes one a naturalist. “Actually, I think about myself as an un-naturalist,” he says. “I like to do unnatural things with biology.” In other words, his interest in eels and diatoms is driven by a desire to deconstruct nature and apply the lessons elsewhere.
This, essentially, is what led Sussman to diatoms—and by extension, to Virginia Armbrust. In 2004, the University of Washington oceanographer led a team that sequenced the 13,000 genes of a diatom species known as Thalassasora pseudonana, or Thaps for short. “Once we (had a diatom sequence), then things moved into a realm where people like Mike could imagine working on them,” says Armbrust. “It gave people tools to ask additional questions beyond the basic ecology of the organisms.”
Shortly after hearing the talk on diatoms, Sussman contacted Armbrust, and a collaboration began to coalesce. Using the Thaps genome and NimbleGen technology, Sussman’s team created DNA chips containing all of a diatom’s genetic information. Using these chips, Sussman and Robison then began searching for genes of interest. “This [technology] is like a new type of microscope,” says Sussman. “But instead of looking at things that reflect visible light—that’s what a regular microscope does—it lets us peer into the nucleus and directly tells us which genes are involved in any process.”
With diatoms, Sussman and Armbrust are interested in the genes at play when the organisms create their ornate cell walls. Before a mature diatom divides, it must build enough new cell wall material to protect its two “daughter cells.” It does so by laying down lines of silica that are only a few hundred nanometers wide, far thinner than the smallest lines drawn on computer chips using today’s best photolithographic techniques. Conveniently, a diatom’s chief building material, silica, is closely related to silicon, a material often used in the manufacture of semiconductors and other industrial materials, including window glass, cement and certain car parts. Recently, researchers at the Georgia Institute of Technology were able to chemically alter diatom shells, turning them into silicon. They then used these nanoscale structures to create sensors capable of detecting minute amounts of certain toxic gases.
But Sussman is most intrigued by the potential for semiconductors. “The semiconductor industry has been able to double the density of transistors on computer chips every few years. They’ve been doing that using photolithographic techniques for the past 30 years,” he explains. “But they are actually hitting a wall now.” The limits of photolithography to pack in smaller and smaller lines of silicon onto a single chip may soon be reached.
Enter diatoms. By observing diatoms in action, Sussman expects to discover genes that give the organisms the ability to draw silica lines in such fine detail. Those genes—and more likely, the proteins that they encode to do the work—could become the basis for a new industrial process that would allow the semiconductor industry to go smaller still, adding more density, and thus speed, to future generations of computer chips.
Already, Sussman and Armbrust have reported finding a set of 75 genes specifically involved in silica bioprocessing in Thaps. Now it’s just a matter of figuring out what these genes and their corresponding proteins do inside the diatom, no small task. Thaps was the first silica-requiring organism ever to be sequenced, and as a result, more than half of the 75 genes the researchers found are novel, meaning they bear no resemblance to the 32 million genes currently found in the national GenBank database. In many ways, they are still at square one.
At the University of Washington in Seattle, Virginia Armbrust occupies what might be Michael Sussman’s dream office. From her desk in a new research tower, she enjoys a sweeping view of downtown Seattle, punctuated prominently by the Space Needle. In the foreground, Lake Union shines in the morning sun, and if Armbrust leans over, she can check out the university’s two research vessels, the very ships that regularly carry her out to sea.
Sussman makes no bones about his admiration for Armbrust’s work. “She’s a real oceanographer,” he says. “She’s (studied life) at the bottom of thermal vents, and that’s her world.”
“He calls me Captain Zissou all the time,” says Armbrust of Sussman. “It’s hard for people that don’t go out to sea to know what it’s really like out there. It becomes very romantic. So Mike would ask me, ‘Is it really like it was in The Life Aquatic?’ Of course I would tell him, ‘Yes, it’s exactly like that.’ We were just joking around.”
From the start of their collaboration, Armbrust and Sussman set out to create a casual atmosphere that encouraged free-wheeling brainstorming.
The two arranged a joint meeting of their lab teams at an eco-resort in the U.S. Virgin Islands, where they took in PowerPoint presentations in an open-air cabana and went snorkeling amidst the ocean life they had come to discuss.
While Sussman is the biotechnologist, Armbrust fits the mold of a classical ecologist. She got hooked on oceanography while working a summer job on a research boat, and then started studying diatoms in graduate school. Her interests now lie in how changes in the oceans, such as increasing temperatures and acidity, are affecting diatom pop-ulations—and what implications will follow for the planet’s carbon cycle.
“For the longest time, we’ve tended to study organisms where you could see the direct impact on humans,” she says. “It’s a bigger leap for many to understand the importance of the microorganisms in the ocean, and the role they play in global biogeochemical cycles that make our planet function, that make it a place we can inhabit.”
However, put the right way, their importance is astonishingly direct: Diatoms make 20 percent of the oxygen we breathe. “As one of my colleagues always says,” says Armbrust, “every fifth breath, thank a diatom.”
While you’re at it, you may want to thank diatoms for the fact that global warming is not worse than it is. When diatoms die—which they do after a six-day lifespan—their heavy shells drag them to the bottom of the ocean, effectively trapping the carbon inside of them underwater. It can take a geological epoch for these sunken diatoms to resurface and release that carbon. (Ancient ocean beds are often caked with fossilized diatom shells, which are sometimes harvested and sold as diatomaceous earth, a natural insecticide favored by organic gardeners.)
Seeing this potential to trap and store carbon in diatoms, some scientists and government officials have suggested that they might offer a quick fix to offset the release of greenhouse gases from fossil fuels. Entrepreneurs even launched a company, called Planktos, which planned to seed swaths of the ocean with iron, which induces diatom blooms, to increase the amount of carbon dioxide absorbed from the air. That plan never got off the ground, however, in part because environmentalists objected to the idea of fertilizing the ocean with iron. Earlier this year, Planktos declared bankruptcy and folded.
Armbrust’s and Sussman’s research shows one reason why environmental groups may be right to worry. “Our study adds another concern about the efficiency of iron fertilization,” says Thomas Mock, a postdoctoral researcher in Armbrust’s lab. When grown at low iron concentrations, diatoms tend to produce thicker cell walls. This means that iron-fertilized diatoms have thinner cell walls, making them lighter and less likely to sink to the ocean floor.
To Sussman, iron fertilization sounds like a “dangerous experiment, because we’d be messing with the flask in which we live.” And that represents the wrong kind of biotechnology—the large-scale toying with biological systems that could lead to unforeseen, irreversible circumstances.
On the other hand, Sussman believes firmly in a different kind of biotechnology, one in which we observe, study and mimic natural systems to help overcome specific engineering problems. This model of innovation has already led to some stunningly creative developments. In 2007, for example, an international team of researchers reported the creation of a “bio-inspired” adhesive tape that mimics the way that flies and other insects hang on walls and ceilings. Another group is studying octopuses to improve designs for flexible robotic arms.
“I’ve always had this notion that during those 3 billion years of evolution that have been cranking away, nature has come up with some solutions to physical constraints that maybe the engineers haven’t found yet, and should use,” says Sussman. And that’s where the un-naturalist meets the naturalist: In some of the planet’s most peculiar critters—the ones that have thrived under challenging conditions or invented ingenious strategies to flourish—Sussman sees the potential for enormous scientific innovation.
“I do believe quite strongly that the true strength of biology will be its odd organisms,” he says. “The electric eels, the silicate sponges and the diatoms.”This article was posted in Environment, Features, Summer 2008, Uncategorized and tagged Biochemistry, Biology, Biotechnology, Microbes.