Coffee Rust Is Going to Ruin Your Morning

The Atlantic
Story by Maryn McKenna

In the southern corner of Guatemala, outside the tiny mountain town of San Pedro Yepocapa, Elmer Gabriel’s coffee plants ought to be leafed-out and gleaming. It is a week before Christmas, the heart of the coffee-harvesting season, and if his bushes were healthy, they would look like holiday trees hung with ornaments, studded with bright-red coffee cherries. But in a long row that stretches down the side of his steeply sloped field, the plants are twiggy and withered. Most of their leaves are gone, and the ones that remain are drab olive and curling at the edges. There are yellow spots, brown in the center, on the leaves’ upper surfaces. On the underside they are pebbly, and coated with a fine orange dust.

The dust looks like rust on a piece of steel, and that is how it got its name: The plants are infected with coffee-leaf rust, a devastating fungus. Gabriel recognized the problem as soon as he saw it. The rust, la roya in Spanish, arrived almost a decade ago, at about the time he bought the hilltop parcel he calls Finca La Felicidad, the “farm of happiness.” He knew about it from his childhood: His father had been a coffee farmer too, and in the 1970s the rust had come and parched their plants. His father sprayed the plants with fungicides, and the disease retreated. Gabriel did the same when the rust returned and flecked the bushes of La Felicidad a decade ago, and the disease retreated again.

But now the fungicides were no longer working as they had. “La roya does not respect them,” Gabriel told me through a translator. One day, with no warning, the golden dots bloomed on a few leaves on a single plant. Gabriel sprayed them, and sprayed again, but the spots widened, then turned dark and dry and cracked through the middle. The leaves crisped, curling at the edges, and fell from the plant when breezes jostled them. The dust, the fungal spores, drifted across the field and infected another bush, or fell to the ground and splashed onto the next plant when rain fell. The cycle of slow plant death began again.

Gabriel shrugged in discomfort, and the polo shirt he wore bunched under his ears. “I thought it would go away after a year or two, the way it had before,” he said. “But it’s totally infested … And in spite of using fungicides, it seems like it’s not enough.”

With no leaves, the plants did not have the energy to bloom and set their fruits, the brilliant fleshy cherries that hide coffee beans at their core. With no fruits, there was no crop, and no income to buy better fungicides or replace the dying plants with healthy ones. In the lesions freckling his coffee plants, Gabriel glimpsed the end of his livelihood, and the death of his hope that he could pass down his land and his knowledge to his son.

In that anguish, Gabriel is not alone. In tens of thousands of small farms across Central and South America, coffee plants are stumbling under the assault of rust. In some areas, more than half of the acreage devoted to coffee has ceased producing. From 2012 to 2017, rust caused more than $3 billion in damage and lost profits and forced almost 2 million farmers off their land.

In the midst of the coronavirus pandemic, talking about a plant disease might seem frivolous. But around the world, 100 million people draw dignity and income from coffee, one of the world’s most traded agricultural products. Coffee is a lifeline for tiny towns and small farmers in areas too thin-soiled or forested or steep to grow much else.

As farmers run out of cash to combat coffee-leaf rust—and climate change diminishes the likelihood of relocating plants to safer ground—scientists are trying to blunt the power of the disease. But their efforts to rebreed plants and retrain farmers are up against a long history of ruin: The first caution about the disease, and the first proof of its destructive force, dates back more than 150 years.

On november 6, 1869, a short notice appeared in a British publication, The Gardeners’ Chronicle and Agricultural Gazette, describing a plant pathogen that no one had seen before. “We have recently received … a specimen of a minute fungus which has caused some consternation amongst the coffee planters in Ceylon, in consequence of the rapid progress it seems to be making among the coffee plants,” the note read.

Ceylon, now Sri Lanka, was a colonial possession, controlled by the United Kingdom since 1815. Dutch traders had imported coffee to Ceylon, and the British had made the plant the basis of a plantation system and trade empire. The colony produced more coffee than anywhere else in the world. Just ten years after the notice in The Gardeners’ Chronicle, all of it was gone.

“A horrible, devastating epidemic—90 percent, 100 percent crop loss,” Mary Catherine Aime told me. She is a professor of botany and plant pathology at Purdue University and the director of its plant and fungal collections. “And ever since, we’ve been moving coffee around the world to keep it away from the disease.”

By the end of the 19th century, rust had crushed coffee cultivation in South and East Asia. The colonial plantations of Ceylon were replanted with tea, turning the British into tea drinkers; those of Indonesia and Malaysia with rubber trees from seeds smuggled out of Brazil by a British explorer. Coffee growing moved across the Atlantic. In a 1952 map made by the U.S. Department of Agriculture, a dark dotted line divides the world at the Prime Meridian. Everything to the east—sub-Saharan Africa, the Arabian Peninsula, India, Ceylon, Indonesia, and Polynesia—is labeled “Diseased” in block letters. Everything to the west—Central and South American mountain ranges whose climates mimicked those of the cool, high areas where coffee once had thrived—is assertively titled “Not Diseased.”

It was confidently assumed that coffee rust could not cross the cordon sanitaire of the Atlantic. That was wrong. No one can say how rust came to the Americas. It might have arrived in shipments of other plants, living or dried. It might have clung to the shoes or clothes of travelers. It is even possible that rust crossed the planet on high-altitude winds, the route that another plant disease, wheat-stem rust, has used to spread between continents. Coffee rust moved without detection, and then, in 1970, its telltale spots and spore-laden dust appeared on coffee plants in Brazil. It spread quickly west and then north: to Peru, Ecuador, Colombia, and then up through Central America—the first wave, which Gabriel remembered from his father’s time. The disease was fierce, but when it appeared, lavish applications of fungicide and careful management of plants kept it in check.

Then, in 2008, rust flared up in Colombia as devastatingly as it had in Asia 150 years earlier, and by 2012 it had moved into Central America. As it had in Ceylon, it wiped out entire farms.

Aime is a world-renowned expert on rust fungi, one of a small number of mycologists tackling a huge field: There are about 8,000 known species of rusts, more than all the other plant pathogens put together. She has been responsible for identifying an array of new rust species, and ever since coffee-leaf rust surged in Latin America, she has been bending her expertise to understanding why. What could have allowed a low-incidence disease kept under control by agricultural chemicals to escape that control and launch an apocalyptic onslaught?

At first, she and other researchers wondered whether coffee rust had mutated, changing its genetic makeup enough to make it a more virulent organism. But in her research, Aime has been building what is effectively a genetic atlas of coffee-leaf rust, made up of genomic analyses of thousands of fungal samples. In those data, she could identify no dramatic change in coffee rust’s composition. “What we think we’re dealing with,” she said, “is the effects of climate change.”

What happened, she concluded, is that changing weather—more heat, more intense rain, higher persistent humidity—created conditions that made coffee farms more hospitable hosts. In 2012, temperatures across Central America were higher than average; rainfall was erratic and drenching. Together, those phenomena allowed the rust to cycle more rapidly through its reproductive process: infecting the leaves of a plant, generating spores, releasing the spores, and finding a new plant on which to grow. “It’s not a simple mathematical formula,” Aime said. “It’s an exponential increase.”

In San Pedro Yepocapa, I asked Gabriel whether he had thought about why the rust had grown worse. He looked at me with the polite patience farmers reserve for city dwellers.

“The rains have been heavier,” he said. “The dry season, it’s longer, and the winds are much more strong.” He shrugged again, as though the answer ought to be obvious. “It’s due to climate change.”

The pandemic of coffee rust is like the unfolding pandemic of the coronavirus in so many ways. There were warnings. There was a belief that the Americas would not suffer. There was a confidence that existing tools could manage the threat. But the deepest similarity may be that, as with the coronavirus, the burden of each disease falls hardest on those least able to afford it. For the coronavirus, that is city dwellers with little savings and no second home to flee to, reliant on mass transit to get to work to feed their family. For coffee rust, it is the farmers.

More than 90 percent of the coffee in the world comes from small farms in poor economies: properties owned or rented by a single family, planted with a single crop. Meanwhile, the wholesale price of coffee has collapsed, forcing farmers and their families to seek jobs outside their farms at just the moment when their farms need more labor to handle the intensification of rust.

There’s a parallel control strategy to spraying rust to suppress its efflorescence. That is finding coffee varieties that possess some intrinsic resistance to the pathogen and crossbreeding them to produce new varieties that are less vulnerable to the disease. To see that approach’s potential, you only have to walk to the other side of Gabriel’s field. The plants there are thick with branches, glossy with health, studded with bright, heavy cherries. Rodrigo Chávez, a tall man in a crisp shirt, crouched and rubbed a leaf gently, looking for the telltale spots. Gabriel spoke with him excitedly in Spanish, waving his hands.

“He’s calling it a supermarket,” Chávez told me. “You can see here where the flowers are forming; that is next year’s crop. He’s very happy that the crop looks so good, that it’s going to give him a higher income.” Chávez dusted off his hands and stood up, looking over more rows resembling the bush we stood next to. “He’s especially happy because he didn’t have to spray these plants,” Chávez went on. “So he spent less money to manage them, and he’s going to have more coming in.”

Chávez was part of the reason healthy plants were in the same field as the rust-stricken ones. He is a project director at the Norman Borlaug Institute for International Agriculture, at Texas A&M University. The institute operates the Resilient Coffee in Central America program, funded by the U.S. Agency for International Development, to bring rust-resistant hybrids to farmers—actually to farmers, not just to test plots at research stations. For three years, the members of the team—Chávez and Roger Norton, the regional director of the project, in Texas, and Luis Alberto Cuellar Gomez, Oscar Ramos, and Daniel Dubon in El Salvador—have been trekking through Guatemala, Honduras, and El Salvador, armed with educational materials and plants. They have persuaded more than 100 small farmers to plant samples of new coffees alongside their established plants, and to observe and relay back to the team how the new plants react to the unpredictable conditions that climate change has wrought.

The plants that the team brings to the farmers are complex mixtures of coffee genetics produced by research organizations, known by acronyms such as CIRAD in France, CATIE in Costa Rica, and IHCAFE in Honduras, that collaborate across the globe. They are what remain of a powerful network of national coffee institutes sponsored by governments and international philanthropies such as the Rockefeller Foundation during the Green Revolution of the 1960s and 1970s, when Norman Borlaug, the Texas institute’s namesake, was staving off international famine by breeding rust resistance into wheat. Those research institutes and others produced many of the plants growing in Latin American fields now, varieties that were bred specifically to be resistant to rust once it crossed the Atlantic.

The decades since that first flowering of international agricultural cooperation have forced a reevaluation of Borlaug’s legacy: His high-productivity hybrids fed millions, but their need for water and external nutrition drove dam construction, groundwater mining, and huge increases in fertilizer use. The last quarter of the 20th century wasn’t kind to the coffee institutes either. Big countries such as Brazil were able to keep their national research programs going. But in smaller countries, civil unrest and crashing economies forced governments to make hard decisions about where to spend limited revenue. That shortfall in funding starved farmers of scientific support at just the moment when rust began regaining ground.

“That original generation of rust-resistant varieties that were created in the ’70s, ’80s, ’90s are starting to lose their resistance,” says Jennifer “Vern” Long, the CEO of a global R&D nonprofit called World Coffee Research. “It will take some time for all of them to fail, but the process has begun.” Farmers who depended on that inbred resistance to protect their crops must now buy and apply more chemicals, and put in more labor to monitor their fields, she adds: “The cost of managing a farm that way is much higher.”

World Coffee Research and the Texas institute, with its USAID backing, represent a kind of reconstitution of the research infrastructure that spread across the world in Borlaug’s era. They have partnered with interested corporations: The Texas group with the Swiss multinational Nestlé, which may be the world’s largest buyer of coffee, and the Norwegian fertilizer company Yara; and World Coffee Research with many of the largest coffee retailers, including Starbucks, Lavazza, Jacobs Douwe Egberts, and the corporate parent of Folgers. In contrast with the Texas group, World Coffee Research also supports lab work, including Aime’s genomic analyses.

It is research that can’t be hurried—even though global warming is changing the weather right now—because developing new coffee varieties that reproduce reliably takes decades. And the researchers’ goals and the farmers’ complex needs are in competition. The farmers want to still trust the plants they have grown for years, even though those coffees are failing. The scientists want to develop resilient plants quickly, even understanding that adoption may take time.

It can take 25 years to crossbreed coffee plants into a new type, and to test-grow the new plant through repeated generations to make sure it breeds true. The farmers in places where rust is advancing don’t have that kind of time. To accelerate replacement, World Coffee Research has been supporting development of what are called F1 hybrids, first-generation crosses from genetically distinct parents that can be ready for planting in fields within 10 years.

There’s a catch, though. While hybrids grow with great vigor, they reproduce unpredictably—so the only way to replace a plant with an identical plant is to buy one from a nursery or company, not to grow it from the original plant’s own seed. That means the hybrids being developed now will need to be replaced by fresh purchases when they reach the end of their productive life, some 20 years in the future.

That will be a burden on the farmers, if it comes to pass. But World Coffee Research sees hybrids as part of a long-term strategy—and Aime’s work in finding the molecular markers of productivity and resistance could lead to entirely new varieties of coffee plants. Meanwhile, though, accelerating the timeline of getting better coffee into farmers’ fields is crucial, because the economic crunch of low prices, worsening rust, and weird weather is bearing down on coffee fields.

“A lot of farmers are surviving by essentially consuming their own resources,” Norton, of Texas A&M University, told me. “They’re not putting a monetary value on their family’s labor.”

Faced with withered plants and no income to pay for replanting, families who have grown coffee for generations walk away from their fields. In many cases, they walk north. When migrants were apprehended crossing the U.S.-Mexico border from October 2018 to May 2019, Guatemala was the point of origin for most.

The Texas A&M project hopes to keep farmers from having to make that choice. But finding which new hybrids and varieties fit different fields demands granular study—by the farmers and the researchers working with them—of the intricacies of tiny ecosystems. At the same time, the researchers are teaching farmers how best to maintain the new plants, and helping them identify additional crops, such as lemongrass, that could be grown among the coffee plants for extra income. Already, Norton said, they were hearing from producers who had visited the demonstration plots, seeing for themselves how their neighbors had benefited from the new hybrids, the free fertilizer, and the experts’ advice. They were clamoring to plant the new versions themselves.

How long the plants will help may be an open question, though. An hour’s drive from La Felicidad, Luis Pedro Zelaya Zamora, the fourth generation of his family to lead the coffee producer Bella Vista, described to me the relentless advance of both climate change and rust.

“Of course, la roya has been here since the 1980s,” he said, “but it never went higher up the mountains than 1,000 meters. And then, maybe eight years ago, you started seeing it at 1,200 meters, and then 1,500, 1,600, 1,800. And every year it came up higher, until it got everywhere. And since then, it has been very aggressive.”

Bella Vista means “beautiful view,” and that is an accurate description: A symmetrical volcanic cone rises above the family’s fields. From the veranda outside the farm’s offices, you can see the elegant curve of the caldera at its summit. The view is a reminder: At some point, mountains end. If the only way to escape climate change is to move crops to higher altitudes, at some point altitude runs out.

Zelaya also has given some of his property over to testing hybrids that the Texas project has distributed. The squeeze between disease and temperature has made clear to him the urgency of identifying the most rust-resistant, resilient, high-yielding plants they can grow. Handling rust costs the equivalent of one-fifth of his production per hectare, Zelaya estimated. “The only way you can pay the cost is with high productivity,” he said. “If you have low productivity, it will wipe you out.”

The hybrids’ genetic diversity is intended to slow the advance of a disease fueled by climate change, but climate change is threatening the source of that diversity.

One reason coffee is so vulnerable to the danger of rust, and to the challenges of unpredictable weather that make rust’s attack more likely, is that its genetics are narrow. It isn’t quite a monocrop—not like bananas, for instance, which worldwide are clones of one another, and could be wiped out by a single disease. (In fact, the bananas we eat today, called Cavendish, were developed because a sweeter variety, the Gros Michel, was wiped out by a fungal disease in the 1960s.) Still, coffee varieties are related closely enough—a possibly apocryphal story traces all coffee in the Americas to seedlings stolen from the Paris botanical gardens—that they lack the genetic diversity that could give them resilience to heat, drenching, or drought.

Those genes exist in coffee’s wild relatives, the grandparents and cousins of the cultivated varieties that farmers now grow. Almost all coffee producers grow just two species: arabica, highly vulnerable to rust, and robusta, less vulnerable but less tasty too. But more than 120 other species are surviving in the wild, in Africa, the Indian Ocean, and Asia. Not all of them have been studied, but the ones that have been harbor traits that cultivated coffee could make use of: tolerance to temperature swings, the ability to survive through drought, and reduced vulnerability to plant pests and diseases.

Except that, thanks to climate change, these wild relatives are under threat too.

Aaron Davis is a slight man with close-trimmed hair and a beard, and is the head of the coffee-research unit at the Royal Botanic Gardens, Kew. A scientist from Kew first confirmed what was killing the coffee plantations of Ceylon in the late 1800s. Davis, his successor across scientific generations, has spent more than 20 years doing research wherever wild coffees grow, identifying coffee species and, in his later career, determining what qualities they might offer to the international coffee trade.

“There are coffees out there that will withstand significantly increased temperatures and reduced rainfalls,” he told me. I had tracked him down at a plant-diseases symposium at the University of Georgia, and we found a seat between posters explaining research on corn genomics and the variability of tomato shapes. “But we better hurry up and preserve those wild genetic resources, because they are disappearing really quickly.”

After more than a decade of hunting coffee species from Ethiopia to Madagascar, Davis turned to studying the plants’ climatic backdrop, looking at the weather and temperature in the areas where cultivated and wild plants grow, and asking how the plants would be affected if those metrics changed.

The Kew team combined the field research with computer modeling. The results were unnerving, indicating that the areas where coffee grows in the wild in Ethiopia—the plant’s historic home, and the place where it ought to grow best—will become inhospitable as temperatures rise and rain patterns change. Before the end of this century, according to the Kew study, 85 percent of the areas where wild arabica grows will no longer support it. Similar models applied to Ethiopian farms cultivating coffee predict that 60 percent of that land will no longer support the crop.

Last year, Davis and his collaborators estimated that under current climate-change scenarios, at least 60 percent of all species of coffee—the two on which production now depends, and many of their relatives as well—are at risk of going extinct..

There would be no remedying that loss. The genetic diversity contained in wild plants has the potential to boost cultivated coffee’s resilience to weather and climate change. That opportunity will vanish when they do, because only about half of the world’s known coffee species are represented in germplasm collections—archives of preserved tissue from which new plants can be propagated. If species die out before their germplasm can be preserved, their promise will be lost for good.

To test its findings, the Kew team trekked through the mountains of southwest Ethiopia, measuring conditions and talking with farmers in the areas where the models had predicted that coffee production would diminish and wild plants would be lost.

“The correspondence between what the farmers were saying and our modeling put goosebumps on our arms,” Davis told me. “They told us: Their father’s father had a good crop every year. Their father had a good crop every other year. Now they were getting a good crop every five years.”

What was true for the cultivated plants was even more true for the wild ones, he added. On one of his team’s trips, the researchers went to Sierra Leone, hunting for a wild coffee species recorded in the 20th century. The botanists who recorded it had noted qualities that might make it climate-resilient, and had noted that the coffee it produced was tasty too. The team hiked to the recorded locations, looking for forested areas that would cast the right amount of shade for the coffee to grow and not scorch in the sun. They struggled to find the coffee—or the trees that would have encouraged it to grow. “There was almost no forest left,” Davis said. “In 10 years’ time, there may not be any there.”

Listening to davis and aime, examining the diseased plants in farmers’ fields, I found it hard not to be pessimistic. Rust’s rampage across the globe had been relentless. With climate change reinforcing its power, its domination seemed inevitable—meaning small farmers like Gabriel would be crushed.

But Gabriel was not crushed. On the hill at the top of his farm, he seemed buoyantly hopeful. Standing in his field, between the withered old plants on one side and the verdant new growth on the other, I asked him what he thought the future might bring his farm. He thought for a minute, and then asked Chávez to translate.

“It is a blessing to have these,” Chávez said, translating. Gabriel gestured to the healthy plants rolling down the slope below us, glossy leaves shining, brilliant red coffee berries peeking between them. His neighbors had distrusted the new plants, he said. They assumed that the bushes had done so well because they were artificial, transgenic, GMO in some imaginary way. But Gabriel invited his neighbors over again and again, trying to show them that the bushes were thriving in the strong wind and uncertain rainfall, and were not succumbing to the disease that had threatened to destroy his farm. Eventually, he said, some of them started to believe.

Because the new bushes resisted la roya, he said, he could spend less money on fungicides. Because he needed to spray less often, he could spend less time mopping up the damage, and more time managing the plants so they would do well. For the first time in a while, he said, he felt as though his farm’s future might be stable. He felt so positive that he had given part of the farm to his son, Brian. They were about to start working together, to pull up all the vulnerable plants. They were going to plant all of La Felicidad with the resilient new hybrids instead.

Perhaps that was short-term thinking, the intense relief of a respite from an onslaught that threatened to ruin his family. Perhaps it was an expression of trust that science could keep improving the plants, outpacing the disease’s advance. I wanted to ask more questions, but Gabriel had to leave the farm. He was due at his job as a bus driver, a job that he might be able to relinquish if his new plants continue to do well. He smoothed his polo shirt and turned to go, and then turned back to deliver a final thought.

“He said, ‘The world changes, and we need to change with it,’” Chávez relayed.

Gabriel nodded, hard. For the first time since we met, he spoke in English, carefully. “No … fear … changes,” he said. He put the sentence together in his head, and spoke again. “Don’t fear change.”

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