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Blurring the lines between Earth and life

For decades, “geo” and “bio” have been seen as separate disciplines. No longer. USC has become the center of the emerging field of geobiology, involving rock-eating bacteria and intra- and extra-terrestrials.

by Terah U. DeJong
Katrina Edwards in lab
Professor Katrina J. Edwards’ discoveries centered on life forms beneath the ocean floor. (Photo/Philip Channing)

Meet the Intraterrestrials.

They’re not little green men—as far as we know—but the minuscule microbes swarming deep in the Earth’s crust and teeming under the ocean floor, pulling invisible strings that influence some of the most important nutrient cycles on the planet.

These diminutive creatures might even be our earliest ancestors. Some scientists suggest that life may not have started at the surface with sunlight or a spark of lightning, but deep in Earth’s rocky womb.

The young field of geobiology seeks to understand these intraterrestrials (as well as ocean-dwelling microbes), and through them, to understand our place on the planet. Freed of traditional boundaries between disciplines, geobiologists go wherever their tiny prey lead them. And since a recruiting spree in 2006 that was itself tradition-busting, the country’s top geobiologists have been coming to USC.

Assembling this critical mass of scientists has not taken long to produce results. In a groundbreaking paper published in Nature last year, lead author Katrina Edwards of the USC College of Letters, Arts and Sciences reported that intraterrestrial life is among the world’s most diverse microbial environments, and that it appears to thrive by “eating” the rocks it lives in. In a Nature Geoscience paper, Edwards and USC colleague James Moffett, with co-authors from Woods Hole Oceanographic Institution and UC Berkeley, showed how this “eating” in the deep ocean floor may have a significant influence on the amount of iron available to life at the surface.

Edwards, who piloted small planes as a teenager and should have maxed out her thrill-o-meter long ago, still goes wide-eyed at the thought, once controversial but now widely accepted, that most life on Earth is intraterrestrial.

“Where is life? Where is it not?” she asked at a recent presentation. “What are all those microbes doing down there, and what, if any, consequence does this have for Earth as a whole – for us?”

This is what she hopes to find out through her most recent adventure: spending a month with 22 other scientists on a research vessel in the North Atlantic, laying the groundwork for a sub-sea observatory 15,000 feet below the ocean’s surface – and documenting the adventure through her North Pond Expedition blog, produced by USC and syndicated by Scientific American online.

Written from on board the RV Maria S. Merian, somewhere between the Caribbean and West Africa, Edwards’ dispatches offered a rare glimpse of life as a working scientist on a mission.

“We have a ship full of sleep-deprived scientists,” she announced on February 28. “This morning’s breakfast discussions revolved around strategies for staying in your bunk … [and about] bizarre dreams that tend to result from attempting to sleep while being flung here and there all night long.”

Working up to 20 hours a day, the researchers retrieved and analyzed sediment cores from the depths. Among Edwards’ goals was to choose a spot where her team of 30 scientists will soon drill nearly 2,000 feet into bedrock to study the planet’s intraterrestrials, potentially numbering between a tenth and a third of all Earth’s life. This effort is the first to study the deep biosphere, one of the planet’s final frontiers that has, until recently, been completely ignored.

“We know much more about the surfaces of other planets in our solar system than we do about the surface of planet Earth – most of which is expressed at the bottom of the ocean,” Edwards says.

Edwards’ work in the deep biosphere is just one compelling research avenue in geobiology. She was one of the first scientists to receive a doctorate in geomicrobiology (from the University of Wisconsin-Madison, in 1996) and came to USC as part of a 2006 “cluster hire,” an innovative strategy in which USC College’s Wrigley Institute for Environmental Studies invited potential faculty members to self-organize into a team, choose their own research direction and then apply as a group.

Kenneth Nealson – a geobiology pioneer and current holder of USC’s Wrigley Chair in Environmental Studies who started USC’s geobiology program in 2001 – said at the time: “The notion that you could put an ad out there and ask people to form their own research group and apply for a job – at first it struck me as just a crazy idea.”

But the “crazy idea” resulted in more than 200 responses, and eventually a “cluster” of seven top scientists, spanning disciplines from biogeochemistry to marine environmental genomics but united by an interest and ability to straddle these disciplines, came to USC. Since then, Southern California and USC in particular have been increasingly regarded as the hub of geobiology.

For example, USC College earth scientist Will Berelson’s summer course in geobiology – which he has taught since 2002 – is drawing students from around the world. He notes that the course has created a generation of geobiologists from various backgrounds in less than a decade.

Some geobiologists say the field was born before geology and biology became separate academic disciplines.

“The interdisciplinary part of geobiology is not new,” says USC geophysicist Thorsten Becker. When one looks at the work of seminal thinkers like James Hutton (1726-1797) and Charles Darwin (1809-1882), certain lines of inquiry appear remarkably geobiological.

Hutton, regarded by many as the founder of modern geology, was famous for going out into the Scottish countryside and observing that “a vast proportion of the present rocks are composed of materials afforded by the destruction of bodies, animal, vegetable and mineral, of more ancient formation.” In his book Theory of the Earth, he conceived of the Earth as a dynamic system of build-up and erosion of mountain that offers conditions for life.

Years later, Darwin was said to be deeply influenced by Hutton’s thinking as he came up with his theory of evolution. Indeed, both shared the insight that geologic time is much longer than human comprehension, and can explain changes too slow for us to perceive.

What is striking about those early thinkers is their lack of compartmentalization of “rocks” and “life” in the way that the modern disciplines of geology and biology seem to do. Modern geobiologists feel a nostalgic pull toward this liberty to think big, which modern science can make difficult. “A couple hundred years ago you could be an expert in everything,” Becker notes.

There is a sense in which geobiology represents a return full circle to those old days without the big gap, when larger-than-life Victorian gentlemen roamed the hills and seas pondering life’s origins. But it’s coming full circle in a context where geology and biology have had centuries to evolve themselves into specific and disparate fields, each with its own adaptations, dialects and strange appendages, like those deep-sea fishes with oddly resplendent adaptations.

Which brings us to USC College earth scientist Frank Corsetti and the story of aliens.

For Corsetti, the birth of modern geobiology is inseparable from the search for extraterrestrial life. Specifically, the founding of the NASA Astrobiology Institute in 1998 was particularly important, since it brought together a diverse range of scientists to unite around a particular pursuit: the discovery of life on other planets.

The institute is “virtual” – involving researchers from different universities – and its tasks have included choosing the landing sites for the Mars Rovers based on where life is most likely to be found. More generally, astrobiology is about defining, as Nealson puts it, “the difference between a living planet and a dead planet.”

This is necessary for space missions to know what to look for. Indeed, a fair number of geobiologists – including Corsetti and Nealson – remain involved in the search for extraterrestrial life. (Corsetti is an expert on stromatolites, fossils found on Earth and other planets and believed to be formed by bacteria, although there is debate about this.)
But for many involved in the institute, the conversations among geologists, biologists and physicists were so fruitful that talk soon turned to the blurry boundaries between Earth and life closer to home.

“This is really what I would call the underpinnings of modern geobiology,” Corsetti says.

“NASA’s Astrobiology Institute got people thinking about things from an interdisciplinary perspective, and that’s where I see the major advances being made: when you get two groups that wouldn’t normally work together, each bringing something to the table that the other wouldn’t have thought of.”

He cites the example of Jake Bailey, a USC doctoral student in the earth sciences, who happened to be reading a biology journal about giant bacteria while studying 600-million-year-old fossils thought to be embryos. The journal, which earth scientists don’t usually peruse, inspired him to cold-call the biologists, arrange a collaboration, and later publish a paper in Nature that reinterpreted the fossils as giant bacteria.

“Had Jake not been thinking in a geobiological way, he wouldn’t have been reading that other journal, and that connection never would have been made,” Corsetti says.

While modern geobiology owes much to these conversations begun at NASA and continued thanks to institutions like USC, its spread as a field is due also to key technological advances. There is a quantitative aspect of modern geobiology that distinguishes it from past incarnations, one that has been made possible because of instruments that have come on board in the last decade or so.

Perhaps no other technology has done more to advance geobiology than metagenomics. Not normally prone to hyperbole, scientists refer to this field – which involves sequencing the genes of entire communities of microbes – as a revolution. This ability to sequence millions upon millions of genes owes much to machines such as the 454 Life Sciences gene sequencer acquired by USC after the cluster hire in 2006, and located on Catalina Island at the Wrigley Marine Science Center.

“It’s the machine that goes ‘ping,’ ” says marine biologist John Heidelberg, referring to the Monty Python sequence in which John Cleese uses a newfangled medical doodad renowned for its “ping” sound. About the size of an office printer, the machine hums along to the squawking background of Catalina’s seagulls. Perhaps appropriate given geobiology’s connection to space exploration, the camera lens it uses to read a genetic sequence was designed for deep-space telescopes. And the images it produces of genetic code look like a million stars. Yet the machine’s true power is its speed.

“Let me put this in perspective,” says marine microbiologist Eric Webb, who collaborates regularly with John and Karla Heidelberg and Bill Nelson, marine biologists who work most closely with the sequencer and live year-round at the Wrigley research station. “When I was in grad school, I spent six months sequencing a gene that was a thousand base-pairs long. Now, on Catalina, they’re sequencing an entire genome – which can be millions of base-pairs long – in a week.”

And, just as the institutional basis of modern geobiology might be traced to NASA’s Astrobiology Institute, its technological basis could be traced to the high-stakes race to sequence the human genome in the late 1990s. It was then when J. Craig Venter, one of the two scientists credited by former president Bill Clinton with mapping the human genome, began using a controversial but powerful method called shotgun sequencing. The method involved breaking DNA into pieces, sequencing them and then reconstructing the genome using a computer.

“It’s like assembling a two-sided jigsaw puzzle that’s thrown together and all mixed up,” explains Karla Heidelberg.

When the decoding of the human genome was announced in 2000, Venter and colleagues – including Karla Heidelberg – began going on cruises around the world’s oceans, scooping up DNA and sequencing it with this new method. Because of the speed, it was possible to construct “metagenomes,” or genetic profiles of entire communities of microbes, which offered scientists a picture of who’s there (based on key genes of certain families of organisms), what they have the potential to do (for example, a gene that allows a microbe to fix carbon dioxide) and what they are actually doing in the environment (through uncovering which genes are actually used at any given time, a related field called transcriptomics.)

So far, one paper after another has revealed a startling diversity of microbes, and has paved the way for discoveries like Edwards’ deep-sea microbes.

Karla Heidelberg is currently involved in a geobiological study of the hypersaline Lake Tyrrell in Australia where metagenomics plays the star role. With water 300 times saltier than the sea, it’s a wonder that anything can survive in this outback lake.

“You get out and it’s literally sucked all the water out of your skin – it’s pretty nasty,” she says. It’s so salty that regular life would have its proteins denatured, just as heat makes runny egg whites turn opaque and solid.

But when looking at the layers and layers of solid salt, one is struck by its vibrant colors.

“It’s bright pink because of the microbes,” Heidelberg explains. “Each different color of the layer is a different community of micro-organisms.” She and her colleagues are using metagenomic samples to build the most comprehensive genomic picture of any environment to date.

They plan to take it a step further by quantifying certain fatty substances, including the pigments, found in the lake water. This geochemical analysis will then allow them to link the communities they study metagenomically with different measurements of these fats and pigments. Then, using samples of these pigments and fats pulled from six meters of mud, the scientists will measure their levels going back over 100,000 years to reconstruct changes in the communities over time.

The study is important because ground-water the world over, including in Southern California, is becoming saltier as more and more freshwater is pulled out for human use. The combination of the modern biochemical, molecular and time perspectives of a geobiological study like this one offers a remarkably comprehensive picture that might reveal how organisms adapt to the saltier conditions likely to be faced in the coming decades. This, in turn, could eventually lead to applications like salt-resistant crops or biofuels such as glycerol developed from the microbes.

Perhaps one reason for geobiology’s explosion as a field is that it offers a philosophical challenge deeply relevant to our times.

If the boundary between the planet’s rocks and its inhabitants is as porous as the oceanic basalt at North Pond, it will force us to rethink our own sense of being separate from the Earth.

In a time of unprecedented human impact on the world, environmentalist arguments often revolve around needing to care for the planet because it’s good or moral.

Yet, Edwards has countered, geobiological thinking reminds us that we are part of the planet’s delicate systems, and we should care for them not because we’ve been taught to be good stewards, but because our fates – both past and future – are more tied to the natural world, rocks included, than we’d often care to admit.

For many geobiologists, this is a motivation to keep going after spending two hours waiting for a core sample to come up through 15,000 feet of water. But there’s also the old-fashioned love of discovery.

“It’s really going back to this exploratory frontier-like feeling,” Bill Nelson says.
“It’s like hitting the coast of Africa for the first time and seeing a giraffe.”

In a world where so much seems already figured out, being part of a scholarly field that is raising more questions than answers is motivation enough.

The intraterrestrials are just a bonus.

What’s it all about?

Geobiology is nothing if not multifaceted. Here’s a quick look at some of its people and perspectives at USC.

One way of looking at geobiology is through a “modern perspective,” an approach that examines how life interacts with geology at the elemental level. New tools developed by biogeochemists such as James Moffett and Sergio Sanudo-Wilhelmy of USC College allow one to measure, with extraordinary precision, how crucial nutrients cycle through the oceans. Iron, cobalt, copper, molybdenum, nickel, zinc and even vitamin B12 are vital to supporting life that drives the carbon and nitrogen cycles. The scientists build models to understand where the nutrients come from and how they are used by organisms.

“People are finally realizing that global warming is real,” says microbiologist Eric Webb, who works with Moffett and Sanudo-Wilhelmy. “We need to know what’s going to happen with the carbon and nitrogen cycles in the future.”

A second approach can be called the “time perspective,” familiar to traditional geologists: The geologic record reveals what life looked like in the past; this is compared to the present and then used to predict the future.

Sarah Feakins, an earth scientist in USC College, has been able to detect wet-dry cycles in Africa by examining waxes from leaves preserved in marine sediments going back millions of years. She is currently establishing similar techniques across a swath of land in California stretching from Malibu to the Mojave to examine the climate history recorded in lake sediments. Such information is of tremendous use, since human-measured climate records only go back about a century.

“We know of the Dust Bowl in recent history,” she says.

“But we suspect that there were bigger and longer droughts in the past.”

A third approach to geobiology is from a “molecular perspective,” using new genetic tools to understand at a molecular level how the animate and inanimate worlds interact. Eric Webb, for example, uses genetic tools to detect when crucial marine microbes like Trichodesmium are dying off because of iron shortages. He can do this because the bacteria express a gene when they are “stressed” that he is able to detect.

A related development is the rise of metagenomics, in which scientists look at the genes of all organisms in a community, rather than a single one. This has allowed marine biologists such as John Heidelberg, Karla Heidelberg and Bill Nelson to probe huge questions such as how organisms are related genetically, and whether a certain organism has the genetic capacity to live with or without a substance like iron, for example.

On the sea

Excerpts from Katrina Edwards’ North Pond Expedition Blog


FEB. 12, 2009
It is kind of hard to wrap my head around this concept, but we are planning essentially a 10-year-plus program at North Pond. Ten years! Let’s see, in 10 years my oldest daughter should be in college, my younger two finishing high school.

FEB. 15, 2009
We are here in Martinique at last – and have had a really busy day unpacking and setting up. We essentially bring portable laboratories and set them up in empty shells of rooms inside the ship. Oceanographers have to plan very carefully and be organized to make sure they bring everything they need for the entire expedition. Simple mistakes, like forgetting one type of tube or one set of pipettes, can sink your experimental plans.

FEB. 18, 2009
We’ve known about biogeography in the plant and animal worlds for a long time, but it is a frontier in microbiology, owing in part to the fact that we have only recently had tools available to give microbial species meaningful “name tags” and also, because microbes are so small and easy to transport, some skeptics have wondered whether we will see any differences in biogeography at this scale.

Biogeographers in the macroscopic world go to islands or continents on land. We do the same analogy in the ocean – go to a very isolated little pond of sediments in
the middle of the Atlantic.

FEB. 21, 2009
We are over a major hurdle – our first drill core up and in the cold room! The biogeochemists are making measurements in the cold room: oxygen profiles, and drawing off fluid samples – like taking blood samples except there is no vein. It is done in bulk for different “horizons” (depth intervals). This will continue all night.

FEB. 24, 2009
We know fractionally little about microbiology in the oceans, and almost nothing about microbiology in the ocean below the ocean – the sub-seafloor intraterrestrials. We have to work and plan extra hard to do work in the oceans – but the rewards, oh the rewards.

MARCH 2, 2009
Remember that great sampling I was talking about yesterday? As the data rolled in, things went from great to greater. We have evidence to support the hypothesis that water is flowing OUT the other end of North Pond.

It is simply amazing to see data that confirm a hypothesis. As a scientist, you get used to being right and wrong a lot in your hypotheses. Hypotheses are really just educated guesses, in practice. A good scientist is always trying to prove her/himself wrong, or back up a correct hypothesis with lots and lots and lots of really compelling data.

MARCH 5, 2009
One of the things I really love about going to sea is getting to work with my hands and getting back in the lab. As a professor, I don’t get to do that nearly as much as I did earlier in my career.

But when I go to sea, I am there to work. You do what needs to be done, when it needs doing – seagoing science parties require a lot of teamwork in general. I have to say that I have never worked with a group as talented, hardworking and amicable as this one.

MARCH 6, 2009
I don’t think I’ve mentioned one bittersweet fact about this project and my own personal research agenda for North Pond. I’m heavily involved in all aspects of the broader project, but my own interests really lie with rocks – the aquifer system that is flowing underneath North Pond, and what kind of intraterrestrial microbes might colonize rock, inhabiting the nooks and crannies of volcanic basalt and catalyzing reactions that result in “weathering” – like what you can see on old buildings, roads and rock outcrops on the continents.

I bring that up only to point out that this has not been a rock cruise: No rocks – well, big rocks, anyhow – were collected. We’ve spent a month at sea collecting mud.

MARCH 13, 2009
Decorated in bruises from head to toe, stuck with a vaccination to yellow fever in my arm, a few pounds lighter, overwhelmed with the collective experiences of the past month, I wonder how in the world I’m going to get recalibrated to non-sea life.

Thank you for your interest in this research cruise. Stay tuned to news about North Pond, a deep, dark place that will set a new standard for research on the intraterrestrial inhabitants of the Earth’s crust.

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