Exploring U-M’s Opportunities Around the World



September 18, 2015
Written by

TAPACHULA, Mexico—John Vandermeer risks breaking a bone falling on the steep mud-slicked trails here in the mountains of southern Mexico. Despite the danger, he is relaxed and there is a great-to-be-back-home vibe about him as he hikes through the organic coffee farm he has been studying for nearly 20 years.

But the gray-bearded ecologist suddenly turns tense when he comes to a waist-high bush with clusters of green coffee cherries. A closer look reveals something odd about the leaves—all of them are numbered with a black felt-tip pen.

“Let’s try not to touch this plant,” says the professor with an edge to his voice. “Seriously, let’s sort of stay away from it. You can look at it, but don’t touch it.”

There is something else strange about the coffee bush. Some of its waxy green leaves have orangish yellow spots on them. This is what worries Vandermeer and millions of other people in this part of the world whose livelihoods depend on coffee.

The blotches are caused by coffee rust, a plant-choking fungus known as “la roya” in Spanish. Each one of the yellowish splotches contains about 100 to 200 spores. They’ll eventually burst out and infect other plants.

It's early in the season and this coffee plant is already under attack from the fungus that has devastated the crop in Latin America.

It’s early in the season and this coffee plant is already under attack from the fungus that has devastated the crop in Latin America.

Spreading across Mexico and Central America with alarming speed, the fungus has caused more than $1 billion in crop losses in recent years and has left hundreds of thousands of people jobless.

Two years ago, the coffee rust outbreak was so devastating that Mexico, Guatemala and Costa Rica declared a national crisis. Many coffee sellers just absorbed the costs of the damage, but they might not be able to do this much longer. Prices might rise for your favorite brew.

“If the epidemic this year is as bad as it was two years ago, you’ll come here in December and you’ll see this whole thing will look yellow,” Vandermeer says, sweeping his hand over a mountain slope covered in verdant coffee trees. “It reduces production by a tremendous amount. It’s a huge problem.”

Sri Lanka was once one of the world’s leading coffee producers until the fungus wiped out the crop in the 1800s, forcing the country—then known as Ceylon—to switch to tea. If Central America had to quit growing coffee, it would trigger an economic apocalypse for the region, which produces one-fifth of the world’s arabica—the smooth-flavored beans favored by the Starbucks sipping crowd.

Vandermeer and his research partner, Ivette Perfecto, both professors at the University of Michigan, are trying to better understand how the fungus spreads and what natural predators attack la roya. That’s why they are numbering the leaves on coffee trees. They’re creating a mathematical model—or network analysis—that will track how the fungus moves from leaf to leaf.

“Most experiment stations are focused on trying to find a fungicide to get rid of this disease,” says Vandermeer of the Department of Ecology and Evolutionary Biology. “That might not be the best thing to do, and it’s one of the things we are studying.”

After years of field research, Vandermeer and Perfecto have developed strong views about how coffee should be grown and why current methods that rely on chemicals are so harmful and unsustainable. They have also made fascinating discoveries about biodiversity—how complex relationships between plants, insects, reptiles, fungi and other organisms affect the coffee crop.  

“Saving the world with pesticides, that story was told 50 years ago. And we all know it didn’t work,” says Perfecto, a professor in the School of Natural Resources and Environment. “Pesticides basically generate more problems than they solve.”

Vandermeer and Perfecto are among the founders of a field called agroecology. The big questions they’re trying to answer are: Does biodiversity matter and why? How does it affect agriculture? And what kind of impact does farming have on biodiversity? They recently published a book on the subject: “Coffee agroecology: A new approach to understanding agricultural biodiversity, ecosystem services and sustainable development.”

Growing coffee like corn

Anyone who watched any U.S. television in the 1980s might remember the commercials created by the coffee growers of Colombia. The ads featured the iconic Juan Valdez—the Marlboro man of caffeine. With a bushy mustache and straw hat, the fictional farmer would go into the fields with his faithful burro to pick coffee by hand.

When the camera panned across the sun-dappled valley, it showed neat rows of coffee trees on terraced plots climbing up the mountain slopes. For many, this is what comes to mind when they picture coffee fields.

Mexico - Feature - 2

John Vandermeer and Ivette Perfecto have been studying coffee in Mexico for nearly 20 years.

The crop is also grown like this in places where Vandermeer and Perfecto work in Mexico. It’s an approach called “sun coffee,” with farmers growing the beans like corn in fields that only have coffee plants.

The upside is that the plants grow faster and produce more. The downside is that the approach makes the plants more vulnerable to weeds, insects and fungi. So chemicals are often used to control these threats.

The fields the U-M ecologists research would be terrible for a sweeping scenic shot for a TV commercial. That’s because from a distance, they don’t look like coffee fields at all. They resemble a forest or nature preserve. It’s hard to see the coffee because it grows under a canopy of other trees and vegetation. So it’s aptly called “shade coffee.”

Such an approach brings lower yields. But the benefits include fewer weeds because the taller trees block out some of the sun and minimize the undergrowth. There’s also greater biodiversity—a more robust mix of plants and creatures that often protect the coffee from pests. Many of the other trees are legumes, which enrich the soil with nitrogen.

Finding a finca

The shade coffee farm that Vandermeer and Perfecto have been studying for 17 years is called Finca Irlanda, a 300-hectare (740-acre) farm set in the mountains above the city of Tapachula in southern Chiapas state, near the border with Guatemala. It’s believed to be the first certified organic coffee farm in the world.

The Finca Irlanda shade coffee farm in Mexico's southern Chiapas state.

Where’s Juan Valdez? It would be hard to find him in the Finca Irlanda shade coffee farm, which looks more like a jungle or nature preserve.

Getting to the farm involves a head-thumping one-and-a-half-hour drive up a narrow rutted mountain road in a 4×4 pickup truck. Much of the road has been paved over the years, but there are still long stretches made with rough-cut cobbles and stones embedded in mud. Drivers honk their horns as they go around switchbacks so they don’t collide with oncoming vehicles that often appear suddenly around the blind curves.

Boulders that have tumbled down the slopes in landslides rest on the side of the road, serving as the only guardrails preventing vehicles from plunging over the side of the road.

Like many of the coffee plantations in the area, Finca Irlanda is owned by a German family that immigrated to Mexico after World War I. The patron of the family is Walter Peters, known by everyone as “Don Walter.” He’s a slight, soft-spoken man in his 80s who dresses casually in tan slacks, an untucked button-up shirt and black sneakers designed for indoor soccer. If you saw him on the streets of Tapachula, the only giveaway that he’s a man above ordinary means would be his Swiss-made Patek Philippe watch.     

His grandfather, who bought the farm in 1928, had a pet jaguar that roamed the house at night, serving as a “guard cat.”

Don Walter’s biggest passion is nature, especially birds. He raises peacocks in cages behind his house, and in the morning you can hear their distinctive call: Waaaaah…Heeeeeh…Heeeeeh…Heeeeh!

His faded mustard-colored home with a red tin roof sits above a large coffee-processing facility. After you climb the stairs to his wrap-around porch, one of the first things you see are large posters on the side of the house showing different species of native and migratory birds.

Bird posters decorate the home of Walter Peters, whose passion for wildlife inspires his commitment to growing organic coffee at Finca Irlanda.

Bird posters decorate the home of Walter Peters, whose passion for wildlife inspires his commitment to growing organic coffee at Finca Irlanda.

The two-story home has a turret, where Don Walter has a wood-paneled office, which looks more like a workspace for a professor than a businessman. On his desk are neat stacks of scientific journals. A large poster of frogs decorates the wall.

Don Walter says he inherited his love of nature from his grandfather, who bought the farm in 1928 and had a pet jaguar that roamed the house at night, serving as a “guard cat.”

His love of nature inspired his decision to grow organic shade coffee, mostly exported to Germany and other European markets. He bemoans the way other farms in the area are leaning more toward sun coffee.

“The producers want to double the yield, but it’s not sustainable,” he said. “They aren’t thinking of the long term. They don’t care about the land.”

The relationship between Don Walter and the U-M professors began in the late 1990s when the researchers were in Costa Rica studying biodiversity and coffee. Finding the right environment was difficult because Costa Rica was rapidly transitioning to sun coffee.

Some colleagues in Mexico told the U-M professors about Finca Irlanda, and Don Walter welcomed them. During their first two summers doing research on the farm, he let them live in his house, and they joined him for dinner each night.

Farm house to research station

One day, Don Walter told the professors that there was a little house in the back of the property that they might be able to use.

“When he showed us this place, you couldn’t see the house. It was all covered in vines,” Perfecto said.

Don Walter got some help to clear away the vegetation, and the professors, who had just received a grant, kicked in some funds to restore the property. It has now become one of the world’s most famous tropical field stations, mentioned in a long list of scientific research articles.

When asked what do you do if a coral snake bites you, Vandermeer simply says, “You die.”

The white stucco single-story house has a dormitory-style room with eight bunk beds for students. Vandermeer and Perfecto, who are married, have a room, and there’s another one for field technician Gustavo Lopez Bautista, who is based at the home all year. A screened-in porch serves as another living space for researchers who prefer sleeping in a tent to avoid the mosquitos.

The farm house was covered in vines before it was converted to a research station.

The farm house was covered in vines before it was converted to a research station.

There’s no hot water, but the cold showers are refreshing after a long day in the field. Shade trees and cool mountain breezes in the evening make air conditioning unnecessary. The house usually smells like a potpourri of tortillas, wild flowers from the forest and soggy socks taking forever to dry in the humidity.

Deadly coral snakes have been found on the home’s concrete floors at night, so it’s wise to wear shoes and headlamps for nocturnal trips to the bathroom. When asked what do you do if a coral snake bites you, Vandermeer simply says, “You die.” Fortunately, there has only been one snake-bite death in the history of the farm—a worker who mishandled one of the reptiles that had been caught.

When Perfecto and Vandermeer move into the house during the summer with a group of students, the daily routine involves an early wake-up with a simple breakfast of eggs, freshly made tortillas, beans, fruit and coffee. Then they’re off to the field by 7 a.m. to  work on research projects. At about 2 p.m., they make their way back to the house to beat the afternoon rains.

The biggest meal of the day is lunch, prepared by local cooks who serve up a delicious menu of simple local fare: chicken, beef, rice, black beans, string cheese, guacamole, lentil soup, salads with onions, tomatoes and avocado. Vandermeer announces the meal by walking around the house yelling, “Comida!” If you don’t come right away, he notices and shouts your name along with another “Comida!”

For dinner, people fend for themselves, foraging for lunch leftovers or cooking quesadillas.

The afternoons are spent reading, recording data, maintaining gear and strumming guitars. There is no Internet. The group gathers again at 7 p.m. to discuss a paper or talk about their research. Sometimes a fiesta follows, with salsa dancing in the dining room. Spanish is spoken just as much as English, and the young graduate students have achieved impressive fluency.

Rust never sleeps

Amid the beauty of the farm, there’s a palpable sense of foreboding about coffee rust. Some fear that fungus will devastate this year’s crop.

Don Walter is less concerned about another outbreak. After last year’s harvest, he applied to his crop copper sulphate mixed with calcium carbonate—also known as lime. The chemical solution—which organic farmers are allowed to use—is sprayed on the coffee trees, turning the fields white as if they’re blanketed in snow.

Perfecto and Vandermeer are less optimistic the treatment will be completely effective. They also point out that the chemical solution kills some of the natural predators of la roya.  

“Most experiment stations are focused on trying to find a fungicide to get rid of this disease. That might not be the best thing to do, and it’s one of the things we are studying.”  John Vandermeer

Coffee rust grows on the underside of the leaf where the spores enter the plant through the stomata, little openings that let in oxygen. As the spores grow inside the leaf, they put little organs into the plant’s cells that suck out the juice from the cells, eventually killing them. When it’s time to reproduce, the fungus goes back out of the stomata and forms stalks that release spores that infect other plants.

One of the U-M professors’ newest research projects involves tracking the spread of coffee rust. This is the experiment that involves numbering the leaves on selected coffee bushes across a 45-hectare (111-acre) plot on the farm. By observing how the rust spreads on a plant, they hope to have a better understanding how it moves across a region.

“We spent about three hours working on this plant,” Perfecto says, pointing to a waist-high bush with all of its 372 leaves numbered with a black Sharpie pen.


Leaves are numbered on a coffee plant.

Leaves are numbered on a coffee plant – part of a project to track the spread of coffee rust.

Watching them work inspires a greater appreciation of how grueling and tedious scientific fieldwork can be. While they tend to the plants, mosquitoes relentlessly flit around their faces and beads of sweat form on their brows, eventually streaming down their cheeks in the sticky late morning heat.

First, the researchers number the leaves, starting from the bottom of the plant to the top. Then each branch is numbered, and the distance from the ground to each branch is calculated. The distance from the branches to the leaves is also calculated along with the angles. This enables them to create a three-dimensional model of the plant on the computer. They monitor the spread of the fungus from leaf to leaf and record the movements on the computer model.

Rust predators

Perfecto and Vandermeer are also studying the white halo fungus, small fuzzy blobs that attack coffee rust on leaves.

“How this fungus affects the coffee rust isn’t completely understood,” Perfecto says. “When the white halo fungus comes to one of the coffee rust spores, in no time at all, the coffee rust spores shrink and shrivel.”

She adds, “If this white halo fungus is important in terms of controlling the rust, which we think it is, then when you spray fungicides, you’re not only killing the rust but also one of the things that naturally kills the rust.”

“Our philosophy is mostly one of prevention, keeping the farm strong and healthy with a lot of natural enemies that can combat the pests, rather than trying to solve a problem once it has emerged.” Ivette Perfecto

Another apparent enemy of coffee rust that the U-M professors are researching is Mycodiplosis—a species of fly whose larvae appear to feast on coffee rust spores. An article published in the 1970s suggested the fly larvae were eating coffee rust but no follow-up research was done on it.

Last December, graduate student Zachary Hajian-Forooshani found the fly larvae at Finca Irlanda. Perfecto and Vandermeer also spotted it in greater quantities in the coffee fields of Puerto Rico, which has not had a devastating outbreak of coffee rust. The researchers have a running hypothesis that Mycodiplosis plays a key role in controlling the rust.


So is a possible solution raising a massive batch of white halo fungus and Mycodiplosis, unleashing them on fields like a form of natural fungicide to wage war with the rust?  

Perfecto says that approach has been tried already with the white halo fungus, and it didn’t work because of reasons that aren’t entirely clear. Besides, she is skeptical of such “magic-bullet” solutions and believes in taking a more holistic approach.

“Our philosophy is mostly one of prevention, keeping the farm strong and healthy with a lot of natural enemies that can combat the pests, rather than trying to solve a problem once it has emerged, which has been the approach of agronomists and pest-control management people,” she said. “They are presented with a problem. Let’s look for a solution to the problem. Our approach is: Let’s understand the systems that are working well.”

Vandermeer added, “Finding a poison is pretty easy. Every year, about 10,000 new poisons are introduced into the market. But trying to figure out how these ecosystems work in detail is pretty tough.”

Two years ago, Vandermeer and Perfecto used a hole puncher to take 20 samples of coffee rust lesions on plants in Mexico and Puerto Rico along with samples from plants with no rust. The samples were sent back to U-M to Timothy James’ mycology lab in the Department of Ecology and Evolutionary Biology, which discovered 100 different types of fungi in the 20 hole punches.

This raises the possibility that there are a bunch of other fungi attacking the rust. Although Vandermeer and Perfecto have been researching the Mexican coffee fields for 17 years, it seems their work has barely just begun. 

Read more:

Department of Ecology and Evolutionary Biology’s blog and Facebook page

School of Natural Resources and Environment’s Facebook page

Watching Wasmannia: Ants on a Mexican coffee farm

Coffee-defending lizards in Mexico

The rat catchers: animal migration in Mexico

Audio clips of John Vandermeer and Ivette Perfecto on Michigan News’ SoundCloud