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The Forest Laboratory

A coastal woodlands on the UC Santa Cruz campus could alter U.S. trade policies. Madolyn Bowman Rogers hikes in to find out how. Illustrated by Jon Wagner.

Illustration: Jon Wagner

Gregory Gilbert doesn’t look like a classic adventurer. A soft-spoken, slender man with glasses and a neatly trimmed beard, he would look more at home in a lab. But on this chilly January morning he’s striding through a sodden forest in boots and a black leather jacket, wielding a trowel and a 5-gallon pail. I struggle to keep up, jumping over rivulets and clambering over tangles of fallen branches crusted with gray-green lichens. Mud sucks at my boots, and an incautious step into a puddle sends water squelching through my toes.

Gilbert, an ecologist at UC Santa Cruz, is oblivious to the soaking ground. He’s gazing through the jumbled maze of Douglas fir, oak, and thickets in search of one particular tree. Dappled sunlight dances over a patchwork world of green and brown, gleaming on great oak trunks cloaked in emerald moss like wet velvet. The only sounds are a faint twitter of birdsong and the rush of cars from a distant road. I stare where Gilbert does, but I know we’re not seeing the same things.

To Gilbert this California forest is no maze, but a laboratory where his team knows the location of every last tree and shrub down to a few centimeters. Every woody plant for acres wears an aluminum ID tag, and a grid of yellow flags spots the forest floor. It’s part of the powerful new way modern ecologists like Gilbert are studying natural ecosytems, gathering data in exhaustive detail.

Gilbert finds his target, a Shreve oak tree. He kneels beside its trunk, scrapes leaf litter aside with his trowel, and ladles thick black muck into a labeled baggie. His fingers are dark with dirt, but he’s got his prize. The soil is a treasure trove of microorganisms, which Gilbert will take back to the lab for experiments.

Gilbert studies disease ecology, or the way natural plant diseases shape forests and other ecosystems. His discipline is only two decades old, and wide open with opportunities for an enterprising pioneer. Just last year Gilbert completed a ground-breaking and massive study in the jungles of Panama suggesting that individual plant diseases can infect a broader range of species than was thought. Now he’s repeating the study in the temperate coastal forests of California. If his results hold true here, it will mean U.S. forests are more vulnerable to an invasion by foreign diseases than was hoped. His results could alter U.S. Department of Agriculture plant quarantine rules and have far-reaching consequences on global trade and plant imports.

A new way to study forests

Scientists have studied plant disease for more than 150 years, but they paid attention mostly to its effects on agriculture. Not until the 1980s did they begin to consider the role that plant disease plays in shaping ecosystems. They found that disease in forests is not a destructive force, but a natural check and balance that prevents any one species from dominating the woods. Diseases actually may help maintain the dizzying diversity of tropical rain forests. Although plant diseases, or pathogens, come in many forms, the most numerous, diverse, and powerful ones by far are fungi.

Gilbert fell in love with the weird world of fungi as an undergraduate at the College of Environmental Science and Forestry in Syracuse, New York. Each person in his mycology lab was given a glass bowl full of horse dung and told to identify the fungus that grew from it. Dung can sprout Pilobolus fungi that look like little eyes on stalks, or the twisting white tubes of Coprinus, but Gilbert’s bowl grew a fuzz he couldn’t identify. His professor was just as stumped. It took a fungus expert to explain it: Gilbert had discovered a new species.

“I thought that was a really cool thing as an undergraduate to take a pile of horse dung and discover something nobody had ever seen before,” Gilbert says.

His fascination with fungi led him to study plant pathology as a graduate student, but his interest was in how fungi affected natural communities. When he graduated in 1991, only five or six researchers in the world studied plant diseases in natural ecosystems. Gilbert traveled to the Panama rain forest to collaborate with a leading plant ecologist, Stephen Hubbell. The event would shape the rest of Gilbert’s career.

Hubbell, then a professor at Princeton University, and his colleague Robin Foster, a scientist at the Smithsonian Tropical Research Institute, had recently set up the first large mapped research plot in the world. The plot spanned 50 hectares—about 124 acres—in the rain forest of Barro Colorado Island, a vibrant green jewel in Gatun Lake along the Panama Canal waterway. Hubbell’s team had slaved for two years to tag, identify, and map every tree and shrub in the plot—about 200,000 plants representing hundreds of species.

A mapped plot allows ecologists to collect rigorous data. Scientists examine the spatial distributions of plants to look for patterns, and they track individual trees for years to see whether they thrive or die. Chaotic forest is transformed into laboratory. “When Hubbell and Foster did their first plot in 1981, it revolutionized thinking about tropical forests,” Gilbert says.

Revelation in the jungle

Gilbert continues to work on mapped plots in Panama, spending two to three months a year there, usually in the summer. In a side project, he’s helped a local Indian population deal with a mysterious palm disease (see sidebar). He has a house in Gamboa, a former canal town that has become an enclave of scientists. The town has no stores or gas stations, and only one restaurant. Gamboa, Gilbert says, is the end of the road. There’s nothing beyond but forest. Gilbert and his team bicycle out a mud road every morning into the hot, muggy jungle, where they decipher the arcane rules of pathogen and plant interactions.

Plant pathogens prey on specific plants. No pathogen can eat everything, Gilbert says, but some have broader host ranges than others. In 2006, Gilbert and his team decided to find out just how broad a range pathogens could have. “Everybody knows that more closely related plants are more likely to have a common plant pathogen than two plants that are not closely related,” he says. “But until we published a paper last March, nobody had ever actually measured this or done the testing to say, ‘How different do the plants have to be?’”

To answer this, Gilbert’s team gathered 53 fungal species that grow on leaves in the Panama forest. The fungi normally spread by airborne spores. The scientists clamped small cultures of each fungus on leaves of other tree species that grow in the same area. Each fungus was tested on about 15 tree or shrub species, for almost 1000 total pairings of plant and fungus. After a week, the team returned and plucked the infected leaves. Taking them back to the lab, they looked for signs that the new trees were succumbing to infection.

The results surprised them, Gilbert says. The assumption in the field has always been that a pathogen might attack plants in the same genus or family as its normal host, but nothing more distantly related. In other words, a pathogen that feeds on one species of palm would attack only other types of palms. Some quarantine policies in the U.S. are based on this assumption.

Gilbert’s work, published March 2007 in the Proceedings of the National Academy of Sciences, confirmed that closely related plant species are most likely to share pathogens. Yet it also showed that fungal pathogens could attack a much broader range of plants than anyone had guessed. Even among plants in different orders—two levels of classification beyond plants in the same family—fully one-quarter of them could share pathogens. That would be like a palm sharing a disease with a pea plant, Gilbert says—two species as distantly related as an elephant and a mouse. “That’s something we were not expecting at all.”

Gilbert’s data sparked great interest among his colleagues. Keith Clay at Indiana University, one of the founders of the field of disease ecology, calls Gilbert’s paper “a really massive effort” with important practical implications for quarantine policy. “The kind of exhaustive, detailed study they did here has never been done before. I give him a very high rating for taking on such a large project and providing definitive data supporting what traditionally has just been assumed,” Clay says.

Slideshow: Author Madolyn Rogers assembles images from the team's field research in Panama. (Click image to launch show.)

Matteo Garbelotto, a mycologist at UC Berkeley, says of Gilbert, “His biggest contribution to the field is to provide these large data sets that prove or disprove scientific theories.” The proven theory of plant-pathogen interactions will allow scientists to build better predictive models of disease susceptibility, Garbelotto says. “Invasive organisms are a big issue right now. So to have this tool so solidly laid out for us in the paper is quite important.”

Mapping the northern forest

Nonetheless, Gilbert’s Panama experiment was limited to tropical forests and tropical diseases. To find out if the results reflect a general rule in biology, Gilbert’s lab is repeating the experiment in temperate coastal forest on the UC Santa Cruz campus. In late 2006 the team laid out a six-hectare plot—about the size of 12 football fields—in the northern hills of the 2000-acre campus. Over the next year, teams of undergraduate interns, graduate students, and technicians mapped and identified every tree and shrub on the plot, creating only the world’s third mapped plot of this size in temperate forest.

Project coordinator Beth Howard describes how every morning the team would assemble at the lab, grab their gear and venture into the woods. Half an hour’s hike up a steep fire road, in the green depths of the forest, they would begin their day’s work.

To turn wild woods into precision laboratory, the team first mapped out a grid, dividing the plot into 150 squares each 20 meters by 20 meters, then dividing each of these into four squares 10 meters on a side. Every line on the grid had to be straight and accurate to the centimeter. The team used a compass to measure direction, but instead of measuring distance with an old-fashioned tape measure, they used a hypsometer, a fist-sized black box that looks like a tiny video camera. It emits a laser beam that travels to a transponder unit several meters away, which chirps and sends back a signal. The signal’s transit time reveals the distance. The students marked the grid by driving small yellow flags into the forest floor.

Once the grid was in, the team went back to each small square to map every woody plant in it, starting systematically in the southwest corner of the square and circling clockwise around it. Every tree and shrub was identified, measured and located on the grid, again using the hypsometer. The 8,175 woody plants on the plot included only 31 species, less than one-tenth the diversity of the Panama rain forest.

One of the most common plants on the plot is poison oak, and the team had to wade straight into it to measure and map it. Although they wore protective suits, it wasn’t enough to prevent several nasty cases of the rash. “Probably everybody had it at a low level the whole time they worked on the project,” Howard says. The team also worked through pouring rain, cold, and sweltering heat. Yet Howard and graduate student Barbara Ayala say the camaraderie of the team more than made up for these discomforts.

“When you’re in the poison oak, you can complain together, and when it rains on you, you can huddle together under a tree and eat trail mix. You get past any barriers with each other pretty quickly,” Howard says.

Ayala and Howard also speak with passion about gaining a deeper understanding of the forest. “It’s like when I first started using glasses,” Ayala says of her new ability to see details. “In the beginning the forest is just green. It’s all blurry and you have no idea what is what. And then suddenly you can see the layers of vegetation and the different species and their distribution.”

For today’s ecologists, this old-fashioned connection to the land is now married to the most modern techniques of biology.

A new way to regulate plants?

Gilbert’s lab rooms are a clutter of machines, microscopes, and sterile plastics, like any modern microbiology lab. Here the team is seeking to repeat Gilbert’s results from Panama. They place infected leaves from the UC Santa Cruz plot into Petri dishes to cultivate the fungi inside them. Rows of tiny dishes line a cart, each one covered in a fungal fuzz of slate-blue, black, or tan. The fungi will be identified not by microscope as in the old days, but by DNA fingerprinting. The team will then take the native fungi back to the field and spread them on new tree leaves to track which species succumb to infection.

Gilbert’s team will collect the data within the next few months, and by fall 2008 will have the answer he seeks. Was the broad infectiousness of fungal diseases unique to the rain forest, or a general rule that applies to U.S. forests as well?

The U.S. tries to seal its borders to any plant that might harbor a pest capable of attacking native plants or crops. “The regulations on what can come into the country are based on data from other countries that show damage to particular species of plants,” says Larry Hawkins, California spokesman for the USDA’s Animal and Plant Health Inspection Service. The agency frequently updates its regulations as it receives new data, Hawkins says. But if the data don’t exist, mistakes can be made, with devastating consequences.

For instance, Sudden Oak Death invaded California about 12 years ago. It almost certainly escaped from a foreign plant in a nursery, ecologists believe. This aggressive disease already has infected billions of trees and threatens the survival of oaks over much of the state. It probably escaped quarantine because it can feed on more than 120 different plant species, making it even more voracious than the multipurpose fungi Gilbert documented in Panama.

If Gilbert’s work shows that distantly related temperate plants can share diseases too, the result might be both worrisome and empowering to the USDA. Although the risk of invasive diseases might be higher than was thought, Gilbert thinks ecologists will have enough data within two years to create a predictive model of which pathogens will attack which plants, providing an important tool to help prevent another crisis like Sudden Oak Death.

Gilbert envisions a web-based program that would examine the known pathogens of any plant being considered for importation and provide a short list of native plants that might be affected by the diseases. Those plants could then be tested for susceptibility. “I don’t see it as a way to stop movement of plant material. It’s more a way of making those decisions on an informed basis, which are currently made based on rough guesses,” he says.

Gilbert also thinks his findings may change the way disease ecologists study plant and pathogen interactions. “This is not what we thought it was five years ago or two years ago,” Gilbert says. “A lot of people are excited about being able to use this quantitative model as a way of shaping ecological research.” Yet as Gilbert and his team have shown, no matter how modern the research methods get, there’s still no substitute for getting out in the field, wading through the poison oak, and getting dirt on your hands.


Sidebar: Invisible Killer Sweeps
Panama’s Palms

In an era of global trade, nations struggle to fence out new diseases. They know epidemics come mainly when pathogens invade new territory, as dramatically demonstrated by a disease ravaging the coconut palms of Panama. It appeared without warning in 1994, sweeping through groves of swaying palms. One by one the great plants succumbed, their leaves withering, leaving behind dead trunks like headless sentinels.

The effect was alarming to the Kuna Indians, who dwell on the islands and coast of Panama and still follow the old ways. Coconuts are the basis of the Indians’ diet and economy. Their culture could not survive without them.

But there was little response to the Kuna’s plight until a young plant pathologist working at the Smithsonian Tropical Research Institute in Panama, Gregory Gilbert, volunteered to study the epidemic on his own time in 1998. Gilbert and his colleague—and future wife—Ingrid Parker met with tribal chiefs and explained the work they wanted to do. Eventually the Kuna helped them map the spread of the disease and seek clues to its origin.

The disease, called Porroca by the Kuna, had migrated from Colombia. Its cause baffled the researchers. It took four years and the help of another disease specialist to finally pinpoint the organism. Porroca was caused by a phytoplasma—a tiny, wall-less bacteria that can only live inside the body of its host. Since it can’t be grown in a dish, scientists can only identify the insidious killer by analyzing its DNA.

Even after the microbe was known, Gilbert and Parker had no easy answers. Phytoplasmas are spread by tiny insects that fly from palm to palm. Among the thousands of insects in Panama, the hunt for the culprit could be long. Efforts to contain the disease by cutting down infected palms met with only mixed success.

“We showed that the easy solutions won’t work,” Gilbert says.

Fortunately for the Kuna, the spread of Porroca seemed to peak in 2000. A few areas have since recovered, following the death of infected palms. Gilbert and Parker continue to study Porroca, seeking to prevent future outbreaks. But for now, fortune has spared the Kuna’s culture.

Story ©2008, Madolyn Bowman Rogers. For reproduction requests, contact the Science Communication Program office for author's email address.



Madolyn Bowman Rogers
B.S. (Spanish) University of Wisconsin-Madison
B.S. (biology) University of South Florida
Ph.D. (developmental biology) Stanford University
Internship: Joint Genome Institute news office (Walnut Creek, CA)

As a child I idolized Mr. Spock, the brilliant science officer who sought out endlessly fascinating new worlds. He ignited my imagination with the desire to discover. I entered graduate school with dreams of solving the brain's mysteries and finding cures for devastating diseases. But after a few years, these bold visions narrowed to a microscope field crammed with colored cells. I endured countless sunny Saturdays entombed in the dark, tallying tens of thousands of cells until my mind went numb and my fires died.

My passion rekindled only when I looked up from my microscope to be dazzled again by the vast expanse of science. I realized I loved the variety and adventure of the field, not its narrow focus. When I became a science writer, I could at last explore the infinite universe.

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Jon Wagner (’08)
B.A., Earlham College, Indiana, 2004
Internship: Sonora Desert Museum, Tucson, AZ. 

I grew up in southeastern Kentucky, where I spent much of my time drawing pictures, playing outside, and watching cartoons. I liked to draw more than I like to read or write, so I used art to tell stories about the characters I saw and imagined. There were comics about the family of bullfrogs that lived in the creek beside my house and a new series of ninja turtles that included a samurai flying squirrel and a Rambo snapping turtle. My style has changed over the years, but I continue to make art about the lives of natural characters. My goal is to accurately describe plants and animals in a way that is engaging and thought provoking for a large audience. This summer, I'm doing an internship at the Sonora Desert Museum in Tucson, Arizona. For more about my work, visit




Invisible Killer Sweeps Panama’s Palms