A parasite that thrives in warm conditions adds to Yukon River salmon woes

This story was originally published by the Alaska Beacon.

When Stan Zuray began noticing white spots, a mushy texture and a weird “sour watermelon” smell in the Chinook salmon he was pulling from the Yukon River, he knew something was going wrong.

That was back in the 1980s. By about 1990, he and others just stopped fishing what he calls “the ass end of the king run” because the fish were so low in quality, he said.

Everyone stopped fishing earlier than normal, he said. “You just get tired of the bum-looking fish,” said Zuray, who lives in the village of Tanana but still has his Boston accent after spending half a century in the Alaska Bush.

It was an ominous turn for a river famous for producing some of the world’s biggest and most prized wild salmon. Chinook salmon, also known as king salmon, is so exalted among the five Pacific salmon species that it is designated Alaska’s official state fish. And the Yukon River Chinooks were traditionally considered among the best of the best.

The culprit in the mushy, weird-smelling salmon was Ichthyophonus, a parasite found in oceans around the world, but a particular menace to the health of Yukon River Chinook salmon.

Zuray is known nationally as a featured character in the reality TV show “Yukon Men” and from his own YouTube broadcasts and a biographical documentary. Within Alaska fishing circles, he is well known as a former subsistence representative on the Alaska Board of Fisheries.

In the science community, he is known for his work as one of the early Yukon River Ichthyophonus researchers. He set up a program and documented infection rates at Rampart Falls, a spot on the river near the tiny Alaska village of Rampart, collecting data that has become critical to current studies.

Zuray said he could smell the infection as fish dried on racks in the traditional way and the parasite multiplied rapidly in the warm sunlight. He dissected samples and documented how Icthyophonus attacks a salmon’s heart. “I squish it in my hand by closing my fingers, and the heart will ooze out through my fingers,” he said.

Waves of infection as salmon runs dwindle

Since Zuray began documenting Icthyophonus in the late 1980s, there have been waves of infections — periods when the parasite was so prevalent that half or more of tested fish were infected, followed by slower periods, followed by new increases.

Those waves, especially the most recent infectious wave around 2022, coincided with a devastating crash in Yukon River Chinook runs. They also coincide with a long-term warming of the Chinooks’ freshwater habitat.

Once thought of as a fungus but now classified as a protist, a category that lies somewhere between fungi and bacteria, Icthyophonus was first identified more than a century ago. It exists in oceans all around the world, as well as in some freshwater bodies. Fish typically become infected by consuming it through prey, but can also get infected through physical contact or absorption of water.

As with other parasites affecting fish, the warming climate is a factor in the spread of Ichthyophonus. It multiplies faster in warmer conditions, and fish enduring warmer conditions are more stressed and weaker, making them more vulnerable to infection.

Alaska fish known to get Ichthyophonus infections include herring, halibut and pollock, for which the parasite can be a minor nuisance.

But for Yukon River Chinook, once plentiful and the backbone of commerce, communities and culture, Ichthyophonus is adding to the long-term problems plaguing the runs. It can kill fish, and those that survive infections can be in weakened states, with meat that is not dangerous but unpalatable.

Yukon River Chinook numbers have plummeted. In 2022, the Chinook return to the Yukon River was about 80% below the previous 30-year mean, according to federal scientists.

The picture at the far end of the river’s spawning grounds is especially grim. In recent years, less than a third of the minimum number of adult Chinook salmon needed to sustain the population have made it back to Canadian spawning grounds. Chinook salmon fishing has been closed entirely for several years on the Canadian portion of the river, and closures will likely continue until 2030, under an Alaska-Canada agreement signed in 2024.

Exactly what role Ichthyophonus plays in the decline is yet to be determined, but it could be important, said Alaska Department of Fish and Game pathologist Jayde Ferguson.

“From a research priority perspective, it ranks high to figure it out,” said Ferguson, who works at the department’s fish pathology lab in Anchorage. The lab tracks numerous fish diseases, but Ichthyophonus has become a major focus.

The department and various partners, including the U.S, Fish and Wildlife Service, Alaska Pacific University and tribal entities, are spending a lot of time and money trying to find answers “not because we think we can reverse the infection but to better manage the runs as they are now,” Ferguson said.

Myriad factors blamed for crash

The Chinook salmon crash is a multifaceted story that extends far beyond the Yukon River, caused by stressors that scientists say are overlapping and cumulative.

Throughout their North Pacific habitat, Chinook runs have faltered, even as runs of other salmon species such as sockeye have boomed.

Some reasons are directly related to climate change, including recent heat waves, scientists say. Warming in the ocean has shifted salmon food sources from high-fat prey to low-fat and lower-quality prey, affecting not only Chinook salmon but another species important to Yukon River residents, chum salmon. Warming in the rivers where salmon return to spawn creates heat stress: In the summer of 2019, the hottest on record in Alaska, masses of dead chum salmon were found in the river system. Permafrost thaw is releasing mercury and other minerals; some formerly clear rivers are now tinted rust-red, with levels of minerals that are now occasionally toxic.

Beyond the Yukon, invasive species can degrade the habitat, a problem exacerbated by climate change. In Southcentral Alaska’s Matanuska-Susitna Borough, for example, numerous freshwater bodies are infested with invasive northern pike that are gorging on juvenile salmon, and warmer temperatures increase the predation, University of Alaska Fairbanks researchers have found.

Some reasons for the Chinook crashes, along with crashes of chum salmon, are related to fishery practices at home and abroad. Increasing loads of hatchery fish pumped into the ocean from Asian operations result in depletion of food sources. Subsistence salmon fishers like Zuray have also faulted management decisions that they say favor large-scale commercial harvesters. They are especially concerned about the interception of salmon at sea by trawlers targeting other species like pollock, a phenomenon called bycatch.

The degree to which bycatch at sea is responsible for the declines in the Yukon and other river systems is a subject of heated debate. Trawling industry defenders point out that only a tiny percentage of the Chinook netted in the ocean as bycatch in the Bering Sea is from the Yukon River. But fishers on the river say percentages mean little because every Chinook salmon that fails to return to spawning is another reproduction dead end. The river residents have a slogan: “Every salmon counts.”

The desire to preserve every possible fish affects Ichythophonus research.

Only dead fish can currently be tested for the parasite, as the heart and other tissue must be examined to confirm infections. To limit pressure on the run, the Department of Fish and Game and its partners sample only a few dozen fish a year. The researchers are currently trying to develop nonlethal ways to test, such as muscle biopsies, Ferguson said.

Parasite’s role

The Fish and Game researchers and their partners are examining not only the frequency of infection in runs but also the concentrations of parasites within individual fish. They are trying to understand how much infection salmon can withstand before succumbing, as well as what the sublethal effects are.

Recent years’ troubles pose some specific questions. How many of the missing fish — those unaccounted-for fish that entered the river’s mouth but failed to reach spawning grounds — were lost to infections? And to what extent is the parasite hampering U.S. treaty obligations to allow a sustainable amount of Chinook to reach Canadian spawning ground?

Ferguson and his research partners have some preliminary answers.

Using a model based on samples collected between 2022 and 2024, a time of high infection rates, they came up with some percentages, as detailed in a study newly published in the Journal of Applied Ecology.

For Canadian-origin Chinook salmon, between 8% and 15% of the deaths occurring as they swam through the Alaska part of the river during those summers were caused by Ichthyophonus infections, according to the model. That percentage rose to nearly 35% at the Canadian border, the mathematical model shows.

The intensity of infection is emerging as an important factor. Over all three years in that study period, the prevalence of infection was largely unchanged, ranging from 36% to 49% of fish sampled at three different sites. But the intensity of infection was lower in 2024 — and in that year, there was no evidence that Ichthyophonus was responsible for any of the Chinook that were missing and presumed dead.

Indications are that the rate of infection, which was about 35% in 2025, according to preliminary data, is on the wane, Ferguson said.

While money for the three-year project evaluating returns from 2022 to 2024 has ended, there is new federal funding for additional research, thanks to a 2024 budget measure that, through efforts by Sen. Lisa Murkowski, R-Alaska, included money for Pacific salmon health research.

Yukon Chinook: Special, and especially vulnerable

Scientific studies and causal observation have made one thing clear: In Alaska, Ichthyophonus is most troublesome for Yukon River Chinook. What makes those fish special also appears to make them vulnerable.

They spend more time in the ocean than any other of Alaska’s salmon species, and they also make the longest trip to spawning grounds, up a river that extends 2,000 miles. Once they enter freshwater, all their energy goes into the reproduction mission.

The ultra-long migration is also what accounts for their extra-high oil content, something that made Yukon River Chinook the priciest of all Alaska salmon in past decades, when there was enough to support a commercial harvest.

Losses from shut-down salmon harvests go well beyond dollars, river residents say.

Christina Changsak, from the Yup’ik village of Russian Mission on the Lower Yukon River, articulated those sentiments at a February fishery management meeting.

She fishes during the summer and tries to teach her grandchildren about traditions, she said. “I teach them how to put away the meat, how to take care of their berries and tend to their fish when they’re drying and how to take care of them, to put them away, so we’ll have all that food security during winter,” she said in testimony to the North Pacific Fishery Management Council, the panel that regulates seafood harvests in federal waters off Alaska. “With the Yukon being shut down, I have no way of teaching my grandkids until we’re reopened again.”

Even if they can harvest other fish, there is no adequate substitute for the missing salmon, she said. “The king salmon have that oil that our body needs,” she said.

Shrinking fish

Yukon Chinook are not just fewer in number but also smaller. On average, they are about 11% shorter in length than they were prior to 1980, according to a research collaboration that includes scientists from the University of Alaska Fairbanks and the Alaska Department of Fish and Game. By weight, they are close to 20% smaller on average, agency and university scientists say.

The change is noticeable, Zuray said. “I’m sure I forget when the last time I caught a 50-pounder was,” he said.

Scientists say the shrinking size, documented in all Pacific salmon species but most dramatically in Chinook, is linked to warmer conditions in the ocean. Salmon are maturing faster there, thus returning to freshwater earlier and more petite.

That is part of a negative feedback loop, according to UAF-led research: Smaller Chinook salmon carry fewer eggs and are less robust as they make their journey upstream, leading to less reproduction and to yet-smaller runs of returning fish.

Wilson Justin, an Ahtna Athabascan elder from the upper Copper River region, said smaller fish create problems. “They deteriorate faster. And it’s very difficult to take the time to dry the fish right,” he said.

It used to take four to five days to dry them on a rack in the traditional fashion, he said. Now that schedule does not work, he said. It used to take “just a little bit of smoke” to process them properly; now smoking fish in the traditional way no longer works well, so people simply stick them in freezers, he said.

Infections are also part of the shrinking-fish-size negative feedback loop, Justin said. Fish that are infected do not grow as well, but it’s unclear whether infections are the cause or the result of smaller sizes, he said.

“The smaller you get, the more you’re going to be susceptible to parasitic infection,” he said.

To Ferguson, the link between smaller sizes and infections is yet to be understood: “It’s the chicken and the egg. Are they smaller because they’re wormy? Or are they wormy because they’re smaller?”

Beyond the Yukon River, and beyond Icthyophonus

A yet-unsolved mystery is why Ichthyophonus problems are concentrated in Bering Sea-swimming salmon.

Potentially, long-term climate change is a factor, Ferguson said. Reduced ice coverage, shifting of fish stocks north and other changes might have occurred too quickly for Bering Sea salmon to adapt to Ichthyophonus, compared to those runs that use the Gulf of Alaska, where fish might have been exposed to the parasite for centuries.

“But that’s speculation,” he said.

Even though the Gulf of Alaska runs have been resistant to Ichthyophonus, fishing-dependent communities outside of the Yukon River are on the lookout for that and other parasites that multiply faster in warmer waters.

In Justin’s home region, there are concerns for Copper River salmon. Those fish, which also pack on extra fat to support a long migration to spawning grounds, are now among the most-prized commercially caught salmon in the world.

Copper River red salmon, also known as sockeyes, are relatively healthy, but Copper River Chinook runs, like other Chinook runs, have diminished. And some locals have complained about “mushy” fish.

The Ahtna Intertribal Resource Commission, an organization created by the eight tribal governments in the region, operates wide-ranging science programs that include studies of fish health. That program turned up one confirmed case of Ichthyophonus in 2024, but in a sockeye salmon. Other suspected cases were either ruled out or unconfirmed.

Close to Anchorage, in the Dena’ina community of Chickaloon, there was another unusual discovery.

An infected fish turned up at Moose Creek, a waterway traditionally known as Tsidek’etna’. The Dena’ina name translates to “Grandmother Creek,” and the site was so named because it used to be so packed with salmon that even grandmothers could easily catch fish there.

Ben Americus, a scientist working for the Chickaloon Village Traditional Council, found the suspicious fish in 2025: a sockeye salmon, which was one of 107 fish examined as part of a program investigating salmon declines there and how to reverse them. When Americus examined the heart, he found lesions that he’d never seen before in a Moose Creek salmon, and they appeared to be classic symptoms of Ichthyophonus infection.

Investigation by the Fish and Game lab identified the infection as something else: Lactococcus petauri, a type of bacteria seen as an emerging threat in the Lower 48 and elsewhere. It has killed fish, including salmonids like rainbow trout, but has not previously been documented in an Alaska fish. The discovery in Chickaloon was the first documented in an Alaska fish, Ferguson said. But Lactococcus petauri may well exist in other Alaska fish, as this type of bacteria is already endemic farther south in the Pacific Northwest, he said. Additionally, it is unclear whether the infection happened before or after the fish died; there were no overt signs that the bacteria killed that fish, he said.

With climate change, there are reasons to watch for Alaska fish infections beyond Ichthyophonus.

A 2022 Canadian study found numerous pathogens in four species of salmon in the Gulf of Alaska, all of which increased in quantity and infection load as temperatures increased.

A study published in January that Ferguson co-authored also detailed several parasites that affect Pacific salmon and salmonids like rainbow trout, and it contained a warning.

In the future, “with climate changes leading to warmer water and reduced water flow, it is likely that virulence of certain recognized pathogens in adult salmon will increase,” said the study, published in the journal Pathogens.

The concern about increasing disease risks to fish extends to parts of the north beyond Alaska, including Canada’s Nunavut territory and Greenland, where scientists are studying parasites in fish like Arctic char.

‘Doggiest village’ no more

Back on the Yukon River, Zuray has settled into a different lifestyle than that which made him a reality TV and YouTube star. The dog team that was so important to his identity is no more. Instead of traversing the wilderness by dogsled, he works with his son operating maintenance equipment for the tribal government and the state. He has a single dog, a pet who also occasionally serves as a “bear dog,” giving some protection in the outdoors.

At the start of the salmon crash, he gave away half of his dogs because there was not enough fish to feed them. He tried to keep a team together by feeding them commercial dog food, but that proved too expensive; dog food sold on Amazon currently costs about $1.50 to $3 a pound, not including shipping. His son held on to a team for a while, but he also gave it up. The last of his son’s sled dogs were adopted out of the Fairbanks animal shelter, Zuray said.

It is a common story along the Yukon River.

The loss is keenly felt in Tanana, where residents used to have around 500 dogs altogether, numerous dog teams and a very active mushing community, Zuray said. Now the last dog team has been disbanded, he said.

“This was probably the doggiest village on the Yukon River, without a doubt,” he said. It was possibly even “the doggiest village in the state,” he said.

“And all the teams are gone.”

This article was produced as a project for USC Annenberg’s Center for Health Journalism and Center for Climate Journalism and Communication 2025 Health and Climate Change Reporting Fellowship.