Coffee as we know it is in danger. Can we breed a better cup?

The rare coffee plant sat on an isolated ridge in northern Sierra Leone, a lone shrub with thin leaves and marble-sized fruits. A team of researchers had spent over a year searching for it, only to discover the plant hadn’t begun to fruit. If they hoped to scale up this uncommon variety, they would need to find it a mate.

This wasn’t just any species of coffee plant. It’s one that could help pull the world’s beloved beverage out of the dire straits it finds itself in today. Coffee is under attack from all sides. It’s threatened by climate change, by a deadly fungal disease that has devastated crops, and by risky farming practices. And at the root of it all is a startling vulnerability: The coffee we cultivate and drink today, which sustains an industry valued at over $100 billion, comes from just two species — and research on others is woefully behind.

In the meantime, rising global temperatures are exacerbating threats to production. “Climate change is a major issue for coffee plants,” said Aaron Davis, head of coffee research at the Royal Botanic Gardens, Kew, who led the search effort in Sierra Leone. That’s because the plants need such specific conditions to grow. Around half of the suitable areas for coffee growing could be lost due to the climate crisis by 2050, according to a 2014 study published in the journal Climatic Change. In Latin America, which produces around 60 percent of the world’s coffee crop, this figure could be as high as 88 percent. Before the end of this century, the more widely produced — and better tasting — of the two species cultivated today runs the risk of disappearing in the wild completely.

It’s a familiar story in the world of food. When farmers in Ireland started growing the “lumper” variety of potato (one of an estimated 4,000 potato varieties) in the 1800s, for example, they probably didn’t imagine a blight would eventually destroy the whole crop and infamously push them into famine. And while the loss of coffee wouldn’t necessarily cause mass starvation, a whole lot relies on it: hundreds of millions of smallholder farmers and coffee-processing jobs in the tropics, as well as the gross domestic product of several countries like Nicaragua and Uganda. Not to mention, each day worldwide, coffee fills 2 billion cups with joy.

Like so much of our food system, coffee’s problems are intricate and interrelated. If the species Davis’s team found growing on a West African hilltop represents a safeguard against the biggest threats facing tomorrow’s coffee, it also illustrates how any global commodity that relies on just a few species is increasingly vulnerable to environmental shocks.

The situation is especially complex, given that the coffee industry is simultaneously fueling the climate crisis by clearing ecologically rich habitat for rows of tightly packed coffee plants. “There’s no doubt about it that coffee production has been a cause of massive deforestation,” Davis said.

But a possible model for creating a more resilient coffee system already exists. It’s an approach to growing that has been used by smallholder farmers and Indigenous peoples throughout the world for millennia. And if scaled up to meet today’s threats, it could fight climate change and conserve — and even increase — biodiversity. The challenge is convincing enough people it’s worth a shot.

The coffee crisis is fueled by climate change and a deadly fungus

The world drinks more than 500 billion cups of coffee every year, or around 22 billion pounds. But not just any of the 124 known coffee species. Most coffee (which comes from roasting and grinding the seed of the plant’s cherry-like fruit) is generally perceived as tasting too harsh. That’s why about 99 percent of all coffee consumed today comes from just two palatable African species: arabica and robusta.

The more preferred is arabica. Think fancy latte and single-origin selections from your neighborhood roaster — or a bigger chain like Starbucks that claims to serve 100 percent arabica beans. Despite accounting for over 60 percent of global coffee production, arabica is a delicate crop. The species can only be produced in the “Bean Belt,” a narrow strip of land between the Tropics of Cancer and Capricorn with optimal temperatures (65°F to 70°F) and ideal altitudes, where the plants get the right amount of rain and sunlight. Arabica is also quite susceptible to coffee leaf rust, the fungal disease that’s been plaguing crops. (This partially explains why the price of a “good” cup of joe is rising. This year alone, the cost of arabica beans is up 43 percent.)

The other species widely consumed today, robusta, entered the picture shortly after a fungus, coffee leaf rust, wiped out almost all of Sri Lanka’s arabica crop in the late 19th century. The British had deforested large swaths of land to create industrial-style arabica coffee plantations, turning it into one of the world’s leading coffee producers. But in 1869, the fungus was detected on Sri Lankan shores, and by 1885 it had ravaged nearly the entire crop and spread to other Asian countries. Around 90 percent of the land used for coffee growing in Sri Lanka was abandoned and later converted to grow tea.

Around the turn of the 20th century, as coffee leaf rust spread throughout arabica crops in Asia, robusta gained a commercial foothold. It now accounts for around 40 percent of global coffee production. The species is literally more robust than arabica, capable of growing in places where arabica can’t and with greater resistance to coffee leaf rust. Many would say robusta tastes markedly worse than arabica — think instant coffee and espresso shots. Then again, it’s also much cheaper. “The reason for that cheapness is not only because it is bad coffee,” as Wyatt Williams recently wrote in the New York Times, “but also because robusta plants are unusually hardy.”

In a world without climate change, it’s quite possible that we could survive with just these two varieties, said Davis, though warming temperatures are increasingly narrowing the range of both species.

But Hemileia vastatrix, or leaf rust, is still the most immediate threat to the coffee industry today. The fungus enters the coffee plant through miniscule openings on its leaves and then sucks up the nutrients, essentially starving the plant. Leaves become spotted with tell-tale yellow and red blotches. Growers watch unripe cherries turn from green to yellow before covering the ground in half-developed, rotting fruit.

“They all fall,” Nubia Loaiza Vargas, a coffee farmer who has seen firsthand what the fungus has done to the crop in Colombia, told Vox’s Sam Ellis last year. “There aren’t branches. There is nothing.”

Latin America was free of coffee rust until the 1970s, when it first appeared in Brazil. The disease spread and reached epidemic proportions in 2012, infecting coffee plants from Mexico to Peru. (Central American countries were especially hard hit.) By 2013, the fungus had affected up to 70 percent of some farmers’ crops, leading several coffee-exporting countries to declare a state of “phytosanitary emergency.” While the situation isn’t as dire these days, local and regional flare-ups still occur and the rust continues to spread. Last year, for the first time, Hawaii’s coffee crops got hit, threatening one of the state’s most valuable commodities.

The persistence of coffee leaf rust has been a wake-up call for the industry recently, says Hanna Neuschwander, director of communications and strategy at World Coffee Research (WCR), an organization focused on improving coffee plants for farmers.

And now a different kind of disease — a coronavirus, afflicting mammals — has become yet another shock to the coffee ecosystem. A recent PNAS study on the socioeconomic fallout of the pandemic found that over the past year, Covid-19 “has become a new threat to the coffee industry by acting as a potential trigger for renewed epidemics of coffee leaf rust.” Labor shortages on farms, closed borders, and poor investment have all been linked to past Hemileia vastatrix outbreaks, according to the study. The authors predict it’s likely a matter of time in a post-Covid world before these factors could spark another rust outbreak.

The breeding solution

Relying on just two coffee species has put the industry in a vulnerable position. What’s more, even within these species, there’s very little genetic variation to work with to breed something hardier. That’s why some scientists are so excited about finding other coffee species to breed into the mix.

And for Davis, that plant is Coffea stenophylla.

Stenophylla, by contrast, is hardier than even robusta. The species can tolerate an average annual temperature of almost 77˚F, according to Davis’s study, published earlier this year in the journal Nature Plants. That’s over 12˚F warmer than arabica and nearly 4˚F warmer than robusta. An equally important factor behind its potential to uproot the coffee industry, though, is that it goes down similar enough to arabica that judges in a blind taste test couldn’t distinguish between the two varieties.

“If you’re developing even more climate-resilient coffee,” Davis said, “stenophylla has two really good attributes — heat tolerance and great taste. Those two things don’t exist in any other species.”

That’s why stenophylla is increasingly touted as a much-needed dose of genetic diversity, capable of opening up new varieties potentially resistant to disease, pests, drought, or higher temperatures — all of which threaten the planet’s coffee supply.

When Davis and his team began their search for Coffea stenophylla in 2017, it hadn’t been seen in the wild since 1954. The team had records that stenophylla had been cultivated in the Ivory Coast and Sierra Leone until at least the 1920s, before being replaced by other species. So they made dozens of “wanted” flyers for the plant and distributed them to farmers in the area. Two leads came in, but both were duds.

They did eventually find the single stenophylla shrub. But the researchers needed at least two plants in order to produce cherries for a viable population, so they expanded their search area. After hours of hacking through the bush, ​​close to the Liberian border, they stumbled across a small patch of stenophylla 100 miles from the first site. Over the next year, a researcher periodically returned until the plants were flowering and bearing ripe fruit that he could collect for breeding. The sample they gathered was tiny, albeit enough to possibly secure the future of one of the most popular drinks — and widely traded agricultural commodities — on Earth, according to Davis.

Coffee is considered an “under-innovated” crop in the breeding world, says Neuschwander. That’s in part because cultivated coffee is extremely homogeneous; nearly all coffee in production today derives from a few wild plants originally taken out of the Horn of Africa. The genetic diversity found in arabica and robusta represents only around 1 percent of the total genetic diversity of wild varieties found just in Ethiopia (one of coffee’s birthplaces and a huge natural genetic reservoir).

“Genetic diversity is basically the raw material of breeding,” said Jorge Berny Mier y Teran, WCR’s breeding and technical manager. “If you don’t have variation, there’s nothing to select.”

Adding variation into existing coffee strains requires breeding in traits from wild species. But even those plants are at risk. Close to two-thirds of wild coffee species are threatened with extinction, including stenophylla, which is currently listed as “vulnerable” on the International Union for Conservation of Nature’s global Red List.

Some breeding has been done with wild coffee, to be sure, like crossing a wild species with arabica or with robusta, Neuschwander explained. (Most coffee breeding has focused largely on the threat of leaf rust.)

But because coffee doesn’t provide calories, it occupies a somewhat different space from crops of the same economic value that do. That explains why coffee breeding is nowhere near the scale of what’s been done for other globally important crops. As of 2015, a few dozen plant breeders were working to improve coffee, in comparison with thousands working on corn, rice, or wheat, WRC founder Timothy Schilling told the BBC.

The coffee industry is resting on “a perilously narrow genetic base,” according to a study published in 2018 by the WCR and Crop Trust, an international organization working to safeguard crop diversity. That’s because of the lack of genetic material and funding for breeding programs — and perhaps also because the crop is largely grown in poor countries in the global South.

All of this underscores just how susceptible the entire coffee chain is to the kind of environmental jolts that have stimulated some investment into breeding projects. (Many of those projects are led by the WCR, which recently announced plans to launch a global breeding network in 2022.)

“You want to be prepared for the future,” Berny Mier y Teran said. “If you know that the temperature is going to go higher, you will start doing selection now under conditions that would be kind of normal in 20 and 30 years.”

What’s more, unlike annual crops such as corn that produce a new generation every year, a coffee plant is a tree that takes three to four years to mature enough to produce seeds. That means breeding takes a lot longer. In other words, developing a new, commercially viable coffee variety with stenophylla could take upward of a quarter century.

“It is an iterative slog, rust and breeding and drought and breeding,” said Neuschwander. Stenophylla, she added, “is not a silver bullet.”

That’s why most experts agree that the pathway to commercially viable stenophylla would be a costly project requiring years, if not decades, to carry out, by which point it could be too late.

Growing practices may be a major problem as well as a solution

While most coffee researchers agree that crop production is facing a crisis, some argue that the focus on climate change and leaf rust is overshadowing the real dilemmas — and potential solutions — of coffee growing.

“The industry’s response has been to fund and promote new varieties designed to contend with the challenges, involving a plant breeding scheme that will undoubtedly take years to put into effect and be fully realized,” Robert Rice, director of the Bird Friendly Coffee program at the Smithsonian Migratory Bird Center, wrote in 2018.

At the same time, there is an alternative path. It involves growing coffee alongside an array of species in a way that mimics the web of life within natural forests.

This model of production, called agroforestry, has been around for thousands of years. It creates a more ecologically diverse system that provides an abundance of crops and environmental benefits for farmers. Some smallholder growers in India, for example, utilize over 100 different types of trees on their coffee farms, forming canopy cover that provides shade for coffee plants and habitat for birds, along with food and medicinal plants for the farmers themselves.

A study published last year in the journal Agriculture, Ecosystems and Environment found that agroforestry could actually mitigate many of the effects of climate change, too, by cooling the surrounding air. This kind of system could help maintain three-quarters of the Earth’s area that’s suitable for producing even picky species like arabica.

Ivette Perfecto, a University of Michigan researcher who has been studying coffee for three decades, says it’s the move away from agroforestry, not climate change alone, that has heralded a true crisis for coffee and the livelihoods of those who produce it. “The kind of system that is intensive coffee plantations, or very large-scale coffee monocultures, I see that as the crisis,” she told Vox.

Historically, small-scale farmers cultivated coffee as an understory species, growing coffee shrubs on the ground among a mix of larger shade trees. Beginning in the 1980s, governments globally started to back the widespread conversion into dense, unshaded monocultures, as technological advances in coffee processing, population growth, and globalization opened up new markets. Coffee was then planted in high densities and, lacking shade, the plants soaked up more sun and grew bigger and faster — a hyper-focused production cycle that also saw an increase in fertilizer and pesticide use, Perfecto says. Thousands of hectares of agroforestry systems were razed as a result.

This led to a drastic reduction in plant, insect, and animal diversity on coffee farms, and it diminished other vital functions this kind of ecosystem performs, like pollination, erosion control, watershed management, and storing carbon.

Large-scale, high-intensity coffee monocultures are also breeding grounds for coffee leaf rust, a throwback to the late 19th century crop collapse in Sri Lanka. “When you have these very dense coffee plants that are touching each other, that is a great way for the rust to pass from one plant to another in a very fast period of time,” said Perfecto. Studies have shown rust outbreaks are more severe in deforested areas where coffee plants are close together — essentially, unshaded monocultures.

Shade trees, by contrast, are a feature of coffee’s natural environment. Planting more of them helps bolster a refuge for critters that eat the pests that eat coffee, rather than having to rely as much on chemical sprays. The fungus Lecanicillium lecanii, for instance, lives in forests and feeds on coffee rust, while certain species of snail and even a type of mite also eat coffee rust spores. This biodiversity buffer is traditionally what has kept this sort of threat in check. “A variety of natural enemies are found in these very diverse systems that also contribute to the reduction in the levels of rust,” said Perfecto, who has studied how the shift to monoculture coffee plantations reduced insect diversity in Costa Rica.

The economic argument for more diverse farming systems

Shade-grown coffee from biodiverse agroforestry systems is the more ethical and sustainable production model, but it still has a trade-off: lower yields. And when coffee prices drop and farmers want to quickly increase production, they will often cut down the shade trees.

Although over time coffee prices have gone up, historically there has often been an oversupply of coffee. (Enough to keep up with increased global demand that is expected to reach $134 billion in 2024.) “I think the main problem with coffee production right now is overproduction,” Perfecto said.

Coffee has been in a boom-and-bust cycle for the past four decades, driven by the financial market and speculation about crop prices.

In 2019, coffee reached its lowest price in over a decade, forcing farmers to sell their product at prices under the cost of production. The World Coffee Producers Forum warned it could trigger a widespread humanitarian crisis as farmers switched to growing illicit crops like coca and cannabis, were forced into poverty, or migrated in search of better opportunities.

Then, a historic bumper crop in Brazil (the world’s biggest coffee producer), coupled with weakened Brazilian currency, helped push down the global price of coffee.

But these days, consumers are likely paying more for a cup due to a recent spike in global bean prices stemming from pandemic-related supply chain delays and a historic drought and cold snap in Brazil.

In such a volatile market, most coffee farmers have little to invest in taking proper care of their plants, let alone adopting eco-friendly agroforestry practices. For all of coffee’s global appeal, creating financial incentives for those with their hands in the dirt — and the most to lose — remains a significant challenge for governments and environmental organizations. “Now, they are desperate for us to plant [trees] and have shade again,” another Colombian coffee grower, Fabio Enrique Hoyos Salazar, told Vox’s Sam Ellis last year. “But at today’s cost, it is very difficult for a farmer to plant things like this.”

Still, research indicates that farmers who had diversified coffee systems were better suited to weather the price crisis and maintain their crops compared with those who had not. When prices dropped, they still had income from other crops grown on their farms, like bananas and papayas. That’s why experts like Perfecto recognize how the economy impacts farmers’ ability to conserve species diversity, and how important that is to making coffee farms the biodiversity hotspots and carbon sinks they once were.

“I think we can have a more rational system where the farmers have a stronger say into how much coffee is produced,” she explained. If farmers are able to set a fair price for coffee, Perfecto says, they will also have more money to invest in diversified systems that will benefit them and help mitigate the interlinked threats of coffee leaf rust and climate change.

Davis, for his part, sees that connection for consumers, too. “Coffee is a very good example where your purchasing choice might be beneficial for biodiversity,” he said. Not only that — buying coffee grown in shaded agroforestry systems, rather than on shadeless monocultures, also helps farmers and locks up carbon. (Here’s a coffee buying guide from Audubon.)

After Davis and his team announced they had located a wild population of stenophylla, he says he received hundreds of inquiries from farmers. Many were eager for a replacement for their arabica plants, which they told him aren’t viable anymore in a warming climate. The irony isn’t lost on him that the same forces causing climate change are also threatening the very diversity that might help us adapt to a warming world. “We think if we had waited another 10 years, stenophylla wouldn’t be there any more due to deforestation,” he said.

The reverse, he believes, is also true. There’s a lot of buzz around the drive to zero emissions and carbon neutrality, but “not about stopping biodiversity loss,” he said. The two — climate and biodiversity — he says, are essentially one and the same.