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Frontlines

Voyage of the Sorcerer
J. Craig Venter cracked the human genome. Now he's set his sights on a new frontier: life under the sea

Photo of J. Craig Venter
Add this term to your environmentalist's vocabulary: whole system shotgun sequencing. And add these facts: Each milliliter of seawater contains about a million bacteria and 10 million viruses. In a two-year cruise from Halifax, Nova Scotia, to Florida aboard his yacht, Sorcerer II, taking 200-liter samples of seawater every 200 miles, geneticist J. Craig Venter discovered some six million genes, more than doubling all the genes known so far to science. Consider this possibility of an alternative to fossil fuels: the creation of a living cell that produces hydrogen from photosynthesis. Take all this in and you begin to understand the environment from Craig Venter's point of view.

In 1998, when the federal government had been struggling for six years to decode the human genome, Venter said he could do it better and faster. Instead of identifying the chromosomes one tiny section at a time, he would cut the entire genome into fragments that would then be put together again, like pieces of a puzzle, by computers looking for matching edges. He called this whole genome shotgun sequencing. With Venter's former company, Celera, on its heels, the government-funded Human Genome Project completed a first draft of the genome by 2001. So did Venter. But he did it in a third of the time.

His process proven, Venter decided to explore the invisible genetic diversity of the world's oceans, imagining them as a single organism whose functional units are not single cells like those in our bodies, but single-cell microbes. Instead of sequencing a pile of genome fragments, Venter sought to sequence the genetic material in a bucketload of seawater and see how many new genes -- and new species -- appeared. It would also be a kind of prospecting mission, since he hoped to find genes that he could use to create cells with serviceable properties.

Three years and six million genes later, I met Venter in his spacious, high-ceilinged office, decorated with hand-carved wood furniture, at the nonprofit J. Craig Venter Institute in Rockville, Maryland. A tall, bald, bearded, blue-eyed man, he had just arrived on his butter-yellow Harley-Davidson. He still had on his silver-buckled black motorcycle boots.
-- Bruce Stutz


Graphic: Question & AnswerI'm someone concerned about the environment. What are your findings going to tell me?
Most life on this planet is not visible to the naked eye. Yet but for these organisms we would not be alive. They are the source of our atmosphere and the source of a large part of the biology we depend on. People can't see them and the tools of biology didn't allow them to be very well characterized. But that doesn't mean they don't exist. With the modern tools we developed for genomic sequencing, we see some of this diversity through the lens of genetics and DNA.

Like Galileo with his telescope or van Leeuwenhoek with his microscope...
We're able to see things we couldn't see before, and what we find out is that we know less than 1 percent of the biology on our planet. Most scientists thought there'd be very little diversity in the Sargasso Sea, for instance. It was described as an ocean desert. Nutrient levels, as in parts of the Pacific, are really low. Yet we found this tremendous diversity of life there.

So we know less than we thought we knew about how the planet functions.
About how life functions. We've been a very egocentric species throughout the millennia. Copernicus and Galileo were threatened with burning at the stake for saying Earth was not the center of the universe. As a species, our view of biology is an extrapolation of our own biology. When we expand the biological universe around us, it's far more extensive than we would ever imagine. We can't survive in boiling water or zero-degree Celsius temperatures, and yet we have microorganisms that can. We have organisms that live in conditions of such strong acid that if you put in your finger it would dissolve the skin immediately. We have organisms that can take three million rads of radiation. We'd be killed with just a small subfraction of that. Yet our own biology is dependent on them.

And what you're finding in the invisible environment will allow us a new understanding of visible ecosystems?
If you're measuring what happens with salmon in an ecosystem you can measure what happens with salmon, but you may not know the real cause. So now we're measuring the true fundamentals of an ecosystem -- all the life that's in it. When I look at the ocean I try to imagine the billions of microbes that are there. It's a thick soup of microbes.

Are they the same everywhere?
Quite the opposite. We're finding that something on the order of 85 percent of the sequences are unique in every 200 miles we sample. They could be unique every mile. We don't know. The ocean could be 10 million microenvironments. These are the first real measurements of their kind. We're finding as many as 40,000 new species of bacteria in a barrel of seawater. And that's not counting viruses. There may be as many as 400,000 of those.

How do you go about distinguishing all of these species?
The term we use is whole system shotgun sequencing, in contrast to what we did with humans, which was whole genome shotgun sequencing. It's important not to think of things so much as single species. Even though these are all single-cell organisms, these ecosystems are equivalent to complex multicellular organisms. Instead of every cell capturing sunlight and using that for creating energy or fixing carbon, there's specialization. Some cells do that, others specialize in fixing nitrogen. We're looking at a loosely associated megaspecies.

What's the environmental payoff?
You can start to track the health of an ecosystem by having tens of thousands, if not millions, of indicators instead of just measuring a few chemicals. And as we do repeat studies in environments over time we'll be able to see what's healthy, what's changing. During this interview we've breathed in probably several million bacterial viruses. When you swim in water you're swimming in a sea of bacteria and microorganisms. We're part of this continuum of life and we now have the ability to measure that. I think that's going to have an impact on everything from monitoring sick buildings to airplane environments. We'll see what shrimp or fish farming is doing to the ecology just by seeing how different toxins or waste products drive certain microbial populations to become overabundant. We might actually begin to predict weather based on early changes in the populations of microorganisms, because El Niños and La Niñas are largely driven by plankton and microplankton.

I understand that you've also been looking for microbes that might be put to work producing energy.

One of the key things we found in the Sargasso Sea was cells with photoreceptors almost identical to the photo pigments in our own eyes. The cells capture light with these photoreceptors and convert that into chemical energy. So that gave us the idea of trying to alter photosynthesis for hydrogen production. Photosynthesis can produce hydrogen, but only in very low levels -- and only when there's not much oxygen around. Oxygen shuts off the enzyme system that produces hydrogen. So we've been looking for what are called hydroxigenators that are oxygen-insensitive, and we found a couple in the environment. We're trying to put those in a cell that has a photosynthetic apparatus to see if we can go from sunlight to hydrogen and create a clean energy source straight from sunlight.

Have those kinds of ideas been lacking in our energy policy?
That's a little unfair to say, since people have tried for 50 years to get sources of biological energy, primarily from algae. But there's no reason that a system would evolve naturally to produce large amounts of hydrogen. The modern tools of genomics and genetics, however, allow things to be changed by as much as a millionfold. You could potentially have a solid enclosed system that, exposed to sunlight, produces a lot of hydrogen. Many environmentalists get very nervous talking about putting new organisms into the environment. But these things can be done in closed systems.

That would open you up to some criticism, and people have already charged you with everything from eugenics to biopiracy.
The biopiracy one is my favorite. We're sailing across the open ocean in international waters and there's this current moving across the Pacific at 1 knot. So there are microbes in that current that move from open ocean into the 200-mile limit of French Polynesia, and suddenly the French call that French genetic heritage. Right? And they want to own it and capitalize on it. It takes months of paperwork to take 200 liters of seawater now from the open ocean. Before we published our paper nobody cared, because nobody assumed anything was there. So I think it's quite comical that we're called pirates for describing the data and making it available for the world.


Frontlines
Home on the (Artillery) Range
News from the Department of Hot Air
Voyage of the Sorcerer
Cue the Whale Sounds
Surfer Dude to the Rescue
Avian Flu: The Silver Lining
The Planet Kicks Back


Cue the Whale Sounds -- and the Visuals
Photo
There are any number of paths to an environmental epiphany: For many people it was the first time they heard the recorded song of the humpback whale.

After a three-year "walkabout" in Baja California, an artist and software designer named Mark Fischer became fascinated by cetacean acoustics. As a trained computer engineer, he soon realized that the visual representations of whale song had not advanced much beyond crude graphs and spectrograms. There was nothing that adequately captured the sheer beauty of sounds that can be louder than a jet engine and as melodic as the human voice.

Fischer found his solution in the mathematical theory of wavelets, which he applied to sounds from different frequencies, translating them into color-coded visual forms. "It's a kind of photography to me," Fischer says, "with mathematics as the lens and the computer as the camera." He calls the result "the shape of the sound." His 2006 print Megaptera naranja, shown here, was created from the song of a Hawaiian humpback. More of Mark Fischer's work, including MP-4 videos, can be seen at www.aguasonic.com.





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Photo (top left): for OnEarth by Randall Scott
Photo (top right): for OnEarth by Steve Fitzpatrick - www.stevefitzpatrick.com



OnEarth. Summer 2006
Copyright 2006 by the Natural Resources Defense Council