A disease called coffee rust has reached epidemic proportions in Central America, threatening the livelihoods of hundreds of thousands of farmers and the morning pick-me-up of millions of coffee drinkers.

Caused by a leaf-blighting fungus, possibly exacerbated by growing practices and climate change, the disease leaves coffee plants spindly and barren, their precious fruits unripened.

"Where people have been using heirloom varietals for a century, you just have trees without leaves," said David Griswold, president of Sustainable Harvest Coffee Importers. "We're already into the flowering cycle now, then it takes nine months to incubate the beans. You can see from the flowering what the losses will be. It's just twigs. It's as though you're walking through a forest of twigs."

The effects haven't been felt yet among coffee drinkers in developed countries, but history gives a sense of the problem's potential magnitude. England, that quintessentially tea-drinking nation, only became so in the 19th century, after rust outbreaks destroyed coffee plantations in Sri Lanka and shifted production to Indonesia. That's why coffee is sometimes called java.

Coffee rust first occurred in Central America in the mid-1970s, but outbreaks didn't reach industry-threatening levels. Now they have. After the latest flowering season, rust afflicts more than 50 percent of growing areas in a belt stretching from Guatemala through Honduras, El Salvador, Nicaragua, Costa Rica and Panama.

Regional production fell by 15 percent last year, putting nearly 400,000 people out of work, and that's just a taste of what's to come. The next harvest season begins in October, and according to the International Coffee Organization, crop losses could hit 50 percent.

Coffee is grown elsewhere in the world, of course, but growers in Central America – and in Jamaica, Colombia, Peru and Mexico, where the disease has also spread – specialize in Arabica varieties, which are used in high-quality coffees. Robusta varieties – which are mixed with Arabicas in mass-market, low-cost coffees – resist the disease, but don't taste as good.

"It's the better-quality coffees that are going to get more expensive and harder to come by," said Peter Giuliano of the Specialty Coffee Association of America. "People will be reminded that coffee is special and delicate."

Nobody knows precisely why the outbreak reached such extraordinary levels this year, though several factors are implicated. The most prominent is climate: In the past, environmental conditions at high Central American altitudes were not especially conducive to the fungus, which requires warm, humid air to thrive, said coffee rust specialist Cathy Aime of Purdue University.

Since the mid-20th century, though, weather patterns in Central America and northern South America have shifted. Average temperatures are warmer across the region, with extremes of both heat and cold becoming more pronounced; so are extreme rainfall events.

Those changes are reflected in coffee rust's spread to unprecedentedly high altitudes, said Peter Baker, a climate and commodities researcher at the nonprofit Center for Agricultural Bioscience International. In Colombia, where coffee rust didn't before reach higher than 5,000 feet above sea level, it's now showing up at 6,500 feet, he said. The same trend is found across the region.

If climate change is evident across decades, though, signals are less clear in the past several years, in the immediate runup to the epidemic.

Last summer is thought to have been especially warm and wet, said Aime, an anecdotal impression extended by Giuliano to the last several summers. Yet climatologist Hugo Hidalgo of the University of Costa Rica noted that as the region on average became warmer between 2009 and 2012, local temperature trends varied widely, as did rainfall.

In short, the exact role of weather variations and climate change in the rust's epidemic severity this year is uncertain, even if they're clearly implicated in its general spread.

"There's increasing evidence that climate change is part of the problem. You find coffee rust striking much farther up the valleys than it used to. There's no other plausible explanation," Baker said. "But what happened last year, and why it was so aggressive and widespread, we're still a bit [perplexed]. And if we don't really know what caused it, it's going to be hard to predict."

Contrasting shade-grown (left) and sun-grown (right) coffee plantations. Image: Ivette Perfecto/USFWS

Growing practices may also compound the problem. Coffee evolved as a shade-dwelling plant, and while some crops are planted under canopies of shade trees, many are planted in open fields under direct sunlight, allowing for high-density crop plantations. These can be more profitable to farmers, but are also vulnerable to disease.

Direct sunlight raises crop-level temperatures even more, accelerating the germination period of rust spores, said Aime. Unusual temperature patterns also stress the plants, many of which have been custom-bred to flourish in very specific microclimates.

Open-field growing practices, including increased fungicide and pesticide use necessitated by the stressful conditions, may also upset ecological relationships that typically protect shade-grown coffee plants.

Ecologist and coffee specialist John Vandermeer of the University of Michigan, who raises coffee at field stations in Chiapas, Mexico, says that sun-grown fields lack another fungus, known as white halo fungus, that protects plants against insects and pathogens, including coffee rust.

"The integrity of this once-complicated ecosystem has been slowly breaking down, which is what happens when you try to grow coffee like corn," Vandermeer said in a February press release. "This year it seems to have hit a tipping point, where the various things that are antagonistic to the [coffee rust] in a complex ecosystem have declined to the point where the disease can escape from them and go crazy."

Aime called the confluence of changing climate and sun-grown coffee "a perfect storm for the rust to create epidemic-size infections."

Fighting coffee rust won't be easy. It can take years for afflicted plants to recover, so prevention is the best strategy, and containment a necessary but limited option. In either case, the tools available to farmers are inadequate.

Farmers can spray rust with fungicides or, if they follow organic growing practices, with copper sulfate solutions. The latter are less effective and cause more environmental damage than the fungicides, said plant pathologist Steve Savage, who recently retired from Colorado State University. Organic standards may actually backfire.

Applying the fungicides correctly isn't easy, though, and non-organic farmers have been hit hard by the disease. Rust-resistant Arabicas are the ideal solution, and several industry-led breeding programs are underway, but it generally takes between 5 and 10 years to develop new varieties.

Many coffee farmers can't afford to wait that long, and the newly resistant Arabica strains have so far gained hardiness at the expense of taste – an unfortunate tradeoff, especially for farmers who specialize in high-quality blends.

Savage said breeding would go faster if the coffee industry used transgenic techniques, which they've avoided for fear of customer backlash. Giuliano countered that many other cutting-edge methods, such as gene-pinpointing selection techniques, are being used. Resistance is simply difficult to engineer by any means.

An even greater challenge, said Giuliano, will be developing heat-resistant varieties, which are also difficult to engineer. Even before the outbreak, warming was considered a dire threat to Central American coffees, and the region is expected to become even hotter in coming decades.

Peter Baker warns of "peak coffee," a riff on the phrase "peak oil," implying that cheap, accessible Arabicas could soon run out. Alternative Arabica sources may exist, however. Many wild-growing coffees in eastern Africa, where the plants evolved, have yet to be tested for commercial possibilities.

Indeed, today's varietals are relatively homogeneous, descended from a literal handful of beans carried out of Ethiopia centuries ago. "Something less than one percent of the total genetic diversity of coffee exists outside Ethiopia," Giuliano said. "What we want to do, as an industry, is go back to Ethiopia, to the mother ship, and find better varieties."

That will take more years. In the meantime, Central America's coffee industry will struggle – and could potentially fail – to survive, jeopardizing millions of livelihoods. The toll will also be environmental, as biodiversity-rich coffee plantations are replaced by ranches and resource-intensive crops.

As for coffee consumers, they'll find Arabicas replaced by Robustas on breakfast tables and office desks around the world. Caffeine will still be there, but not so much taste.

"If things keep going in the direction they're going in, good-tasting coffee will be much harder to come by," said Giuliano. "Cheap, ubiquitous, good coffee is an artifact of the 20th century."