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.

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