New Fungi on NY Apples

by Cheyenne MacDonald

Hudson Valley apple orchards have a growing new worry on their hands. Scientists have identified a pair of fungal pathogens not previously known in the region that cause the disease dubbed “bitter rot” — which, as the name suggests, causes warm-weather fruits to decay and die. The new species were found infecting fruits both in the field and in storage. And it’s only likely to get worse. 

Apple Bitter Rot (Photo by Srdjan Goran Acimovic)

The team behind the discovery, led by plant pathologists at Cornell University, says bitter rot in New York has been known to wipe out upwards of 20 percent of a given orchard’s crop on average, and local incidence has been steadily rising in recent years. For organic farms, the losses could be as grave as 100 percent. 

A Known Fungus Makes Its Debut in New York

It’s a new development for a familiar foe; bitter rot, brought on by fungi from the genus Colletotrichum, has long wrought devastation on fruiting plants all over the world, from apples and peaches to papaya and citrus. Of the newly identified species, the researchers say one (C. chrysophilum) shouldn’t even be in apples at all, as it’s typically known to infect tropical and subtropical fruits like bananas and cashews. 

“Not anywhere in the world has this species been described as a pathogen of apples,” Srdjan Acimovic, of Cornell AgriTech’s Hudson Valley Research Laboratory and senior author on the paper, told Scenic Hudson. 

But that’s not the most baffling part of the discovery. The second species the researchers identified is entirely new to science, meaning it has never been described before in any capacity. “It was shocking to us,” Acimovic said. “We were confused.”

Finding one species in an extremely abnormal host seemed peculiar enough, though the unprecedented weather conditions of the past few years — particularly in 2016, 2017, and 2018 — could provide some explanation, but finding a new species altogether seemed almost inconceivable.

“People didn’t believe us,” Acimovic says. “We had longstanding indications” that what they’d found was indeed a new species, he explained, “but we had to prove it.” And they did. 

An Unknown Fungus Is Identified and Named After New York

The team, collaborating with researchers from Pennsylvania State University, the Canadian Food Inspection Agency, and Louisiana State University, sampled apples from roughly 20 farms, including a handful out of state, and was able to isolate the disease-causing fungi in 400 separate cultures. Then, the researchers sequenced the entire genome of the new species to map out what is, essentially, its “DNA fingerprint.”

“Our collaborators all over were like, ‘You were right, this is not a known species,’” Acimovic said. 

The new species of fungus is called C. noveboracense, after the Latin name for New York.

By characterizing the species as they did, the researchers now have a better shot at understanding its ability to infect and how best to fight it. “We can learn so much from that blueprint,” Acimovic said.

Whether or not these new pathogens stick around remains to be seen. There are many factors that will play into their persistence (or lack thereof), including management and weather conditions, and there’s no telling just yet what climate change will mean for it all. Conditions in the Hudson Valley are already somewhat favorable for a disease like bitter rot; the area along the Hudson River Basin represents the largest “pocket” of a hot, humid summer continental climate in this region, the researcher explained, alongside smaller swaths along Lake Ontario and the Finger Lakes. 

These are “warm weather pathogens,” Acimovic notes, and the rising trend of higher temperatures and heavier rainfall in recent years certainly is “fitting the pattern.”

Cornell runs an outreach program to connect local growers with resources and technical assistance. Farmers in the Hudson Valley who think they might be affected by bitter rot can contact Cornell Cooperative Extension specialist Dan Donahue for support.