For the smallholder farmers who grow most of the world’s coffee, an outbreak of coffee leaf rust can wreak havoc on family finances. Diseased trees have to be pulled up and replaced with healthy seedlings. New soil and water management practices may be necessary to prevent a repeat outbreak of the fungus. Income grinds to a halt until the young trees start producing beans—and that can take years.

“The right farming practices can bring coffee back [after an outbreak], but that requires...

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