Not long after Mark Boyer planted the apple orchard he co-owns in Schellsburg, Pennsylvania, the trees started to die. First, their leaves turned yellow. Then, their trunks shed bark. In two short weeks, they were completely dead. And once the physical signs started to appear, there was nothing Boyer could do to stop the progression. Whatever was killing his trees was already too far along.

Whatever it was, it had no particular season. It happened during the spring, as the trees blossomed, or later in the fall, when they were laden with fruit. Some trees even died after the final harvest, just before winter set in. 

Awais Khan

In the years since the term was coined, scientists haven’t figured out what causes Rapid Apple Decline.

To make matters worse, there was no discernible pattern. Five healthy trees could surround a single dead one, suggesting that the problem wasn’t spreading through leaves or soil. Boyer first spotted trouble in 2011. By 2013, it was much worse. 

Boyer investigated every possible cause. He tested his soil for heavy metals and nematodes.  He checked his records to make sure he hadn’t misapplied weed killers. Nothing looked obviously wrong, but the trees continued to die. 

He asked other growers if they were having similar problems. Many said they had lost trees, but they attributed the deaths to the stress of cold winters and other identifiable hazards like the contagious bacterial disease fire blight. 

“I kept saying, ‘no, this is different. You know, this is really something different,’” Boyers says. 

Around the same time, Kari Peter, a plant pathologist specializing in tree fruit, joined the faculty at Penn State University. She had noticed a few trees dying at random in her own orchard, but didn’t think too much of it—apple trees die all the time. It wasn’t until 2014 that a grower approached Peter with concerns about a mystery illness that was affecting young trees. By the latter half of the year, more and more growers had gotten in touch. “And then I heard from New York that they were seeing something similar, and also from North Carolina,” she says. 

Kari Peter

At Penn State University, Kari Peter and her team are focusing on one newly-discovered virus they call apple luteovirus

Peter called the phenomenon Rapid Apple Decline, a name that describes the short timeframe between the appearance of symptoms and the collapse of the tree. (It’s also known as Sudden Apple Decline.) In the years since the term was coined, scientists still haven’t figured out exactly what’s going on. But the phenomenon persists. Last month, the Allegheny Front, a public radio program covering environmental issues in Western Pennsylvania, reported that up to 80 percent of the orchards in North Carolina have been affected by the decline. The problem is impacting growers as far north as Canada. And there are no signs it will disappear on its own. 

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Peter joined forces with the Pennsylvania Department of Agriculture to rule out all the usual suspects. The deaths don’t appear to be caused by insects or common fruit tree diseases. And she didn’t quite buy the prevailing theory that tough winters had weakened the orchards because she’d first noticed the problem in a year when the winter had been mild. So-called “winter injury” might have been a contributing factor, but it didn’t seem to tell the whole story.  

The phenomenon got weirder and weirder. Bruce Hollabaugh, co-owner and production manager for Hollabaugh Bros. in Biglerville, Pennsylvania, tested his trees when the deaths started plaguing his farm, and ruled out most familiar pathogens. “We’d have a row of trees, and there would be two [dead trees] here, and then five perfectly healthy trees, and then a strip of 18 trees that were all dying or dead,” he says, adding that the most common diseases tend to spread from tree to tree or to adjacent trees through soil. But, oddly, Hollabaugh says, he noticed the whole tree wasn’t dying. “The final thing that was really puzzling was that in almost all cases, the tree was only dead on top, but the root system wasn’t dead,” he says. 

Apple trees are grown from biological components joined together. The top part, which eventually bears the fruit, is called the scion, and it’s joined to the rootstock by grafting, a process that involves fusing the two together until they grow as one tree. With Rapid Apple Decline, the rootstock remains healthy—it’s only the scion that dies off. Awais Khan, a plant pathologist at Cornell University, says stressors like cold weather can start to weaken the union between the rootstock and the scion. “And then the nutrient flow from the soil to the root to the above part doesn’t happen as efficiently as it should,” he says. 

Most of the trees impacted by Rapid Apple Decline seem to be planted in high-density orchards, which have come into vogue in recent decades because they bear fruit quickly and can produce higher quality apples. Khan says the density might be stressing trees out. Densely planted roots are competing for nutrients and water, which can in turn weaken the whole plant.

Khan’s working theory is that Rapid Apple Decline may be caused by a variety of factors, kind of like bee colony collapse. “I think maybe, in a way, we can rule out that there’s no one common mechanism, and not one common factor across every Rapid Apple Decline. It might be multiple causes that that could be a combination of biotic and abiotic stresses,” he says. A cold winter may weaken a tree, then a virus that may otherwise be non-fatal can finish it off.

Awais Khan

Khan says stressors like cold weather can start to weaken the union between the rootstock and the scion

Peter is focusing on one newly-discovered virus in Pennsylvania that her team calls apple luteovirus 1. “I don’t believe it’s the smoking gun,” she says. “However, I don’t believe it’s helping the situation either. We’re trying to understand: Is this a latent virus that’s just guilty by association, or is this something we have to worry about?” Her team is working with a nursery to study trees that have been infected with the virus, but it may take years to determine whether or not it is fatal. Still, she agrees with Khan that there are multiple factors involved. “It’s a handful of things probably contributing to this.” 

Elsewhere, researchers are looking into black stem borers, also known as ambrosia beetles. They have a tendency to appear on trees affected by Rapid Apple Decline, but it’s not clear whether they’re part of the cause or part of the clean-up crew. They feed on ethanol, which is emitted by stressed-out trees. It’s possible they’re the vultures of the apple tree world, showing up to feast on the corpses. 

As for Boyer, he thinks nurseries might be partially to blame for the spread of any virus. He explains that they’ve been under pressure to produce huge numbers of trees over the last few years, and high demand for rootstock may have led to quality control issues and allowed for the spread of viruses like the one Peter is studying. He suspects that the trees he’s buying may be infected before they even go into the ground. “When you buy a tree, really the only guarantee that you have is that that tree will bud out and that will grow,” he says, meaning growers have no recourse if a tree dies from a virus it contracted before reaching the orchard. 

Boyer is even starting his own nursery so he can control sourcing. “I don’t feel as if the nurseries are holding their part on what they’re doing,” he says, adding that he visited nurseries in Italy and was blown away by the level of government oversight. “We’re the Wild West, we’ve always been that way,” he says, referring to regulations in this country. 

Awais Khan

Awais Khan examines the roots of a honeycrisp apple tree

For now, Khan and Peter are urging growers to minimize tree stress wherever possible. The stronger the tree, the simple logic goes, the less likely it’ll keel over and die. 

Peter adds that the phenomenon is not so severe that apples will start disappearing from supermarket shelves. “We’re not going to lose our apples. This is more impactful on the local scale at the grower level.”