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Until this year, John Vandermeer, an ecologist and coffee researcher at the University of Michigan in Ann Arbor, had never lost a tree to fungus.

The smattering of orange dust that marks the seasonal arrival of the coffee rust fungus, Hemileia vastatrix, has long been commonplace. But this year, one of the worst outbreaks of the rust in memory is under way in Mexico and Central America, and Dr. Vandermeer has witnessed the die-off of 9 percent of the trees in a sample plot at his Mexican research plantation.

What is normally a lush green field now consists of “little sticks sticking out of the ground,” he said.

The outbreak threatens to almost halve the 2013-14 coffee harvests in Guatemala, Colombia, Honduras and Costa Rica; Guatemela’s coffee industry association has already declared a state of emergency. Meanwhile, debate persists about the cause of the spread and how to arrest it.

Coffee rust appears to have originated in Sri Lanka in the 1860s before traveling to other parts of the globe. Normally, it occurs seasonally in Central America as a luminous orange powder that filigrees the edges of foliage. When the fungus enters pores on the base of leaves, it consumes tissue until the leaves die, and occasionally fall off, Dr. Vandermeer said.

The more leaves that fall and compromise a plant’s ability to photosynthesize, the fewer coffee berries the plant can produce.

Some farmers and researchers suggest that climate change may be the root cause of the sudden advance of coffee rust this season. But Dr. Vandermeer attributes it mainly to changes in farming methods.

Over time, he said, the shift from small plantations to vast fields has led landowners to turn to pesticides and fungicides to keep pests in check. But these sprays have wiped out another organism known as white halo fungus that actually attacks the coffee rust, Dr. Vandermeer said.

“What we feel we’ve seen in our system is that this white halo fungus provides partial control over the coffee rust,” he said. The systematic spraying has not only eradicated the defensive fungus, but also the insects that the white halo spores latch onto to germinate, he suggests.

“My hypothesis is that because of the gradual simplification of the coffee ecosystem, the disease has effectively escaped its controls,” he said. He has not ruled out the possibility that climate change could be playing a role as well, Dr. Vandermeer said, although “I haven’t seen the patterns you would expect if global warming was the culprit.”

Yet Peter Baker, a senior scientist with the Center for Agricultural Bioscience International in Britain, believes that a changing climate has indeed brought on the explosion in coffee rust. The fungus enjoys a “nice long period of humid conditions,” he said, “and that’s what increasingly we see with these long cycles of wet weather.”

Colombia, for instance, has seen a surge in rust outbreaks in the last four years. Multiple years of very wet weather coupled with frequent spraying allow the rust spores to proliferate, Dr. Baker’s thinking goes, enabling the fungus to cross a threshold and take hold.

Others say the devil is in the details of rainfall patterns. The prolonged light rains that the region has seen may abet the creep of the orange rust, whereas heavy rainfall acts as a sluice that frees the trees and the the air of spores.

At least that’s the opinion of Phil Arneson, a retired plant pathologist who tends a small coffee plot in a remote part of Honduras. “A good hard rain will cleanse the air of the wind-borne rust spores and even wash them off the leaves before they can germinate and infect,” he said in an e-mail. “But a light drizzle will maintain the moisture on the leaves and provide the microenvironment that the spores need to germinate.”

Based on his observations in Colombia, however, Dr. Baker counters that the rust would capitalize on any kind of wetness, not only light rain. “The experience of Columbia has been huge rainfalls there,” he said, and the spread has only worsened.

No matter what microclimate is the focus, nearly all of the hypotheses seem to circle back to climate change. Dr. Arneson recounts the stories of farmers he knows in Honduras: “They tell me that they used to be able to plant by the calendar, but they can’t anymore — the climate has gone crazy,” he said.

Dr. Vandermeer said that longer-term solutions should include scaling back the size of today’s vast, uninterrupted plantations and reducing the application of pesticides as much as possible so that natural controls can reassert themselves.

To address the scourge in the short term, Central American farmers are meanwhile turning to new variants of coffee plants crossbred with strains that are more rust-resistant. Coffee specialists say that the cup quality is not as good, but brews from the new crossbreeds are starting to improve, Dr. Baker said. He said the industry should be investing more in research into this genetic variants.

In Honduras, Dr. Arneson sees a “bright spot on the horizon” in a new strain of resistant plants known as Lempira that farmers are experimenting with in place of the regular criollo variety.

“Right next to the criollo plants that are nearly completely bare, with just a tuft of rust-spotted leaves at the top, the Lempira plants are spotless, with dense, dark green foliage,” he said. “I have already placed my order for the planting season at the end of May.”