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Colorado researchers spent decades trying to save disappearing rainbow trout. Finally, they’re making progress.

Genetics from Germany and a hardy cross with Gunnison River trout seem to be overcoming a nightmarish parasite that causes deadly whirling disease

Colorado Parks and Wildlife aquatic biologists Boyd Wright and Dan Brauch net fish off the front of an electrofishing boat captained by Dan Kowalski, CPW aquatic research scientist, during adult population estimates conducted in the Gunnison River in 2009. (Provided by Eric Fetherman)
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Eric Gardunio had fished this stretch of the Gunnison River throughout his youth, filling the seasons with short expeditions to the river gorge’s East Portal near Delta. There, his father handed down skills passed to him from his grandfather, and Eric took their passion even further while learning every rock and riffle.

By the summer of 2003, he’d become well acquainted with how the nature of the fishery had changed. Brown trout, the speckled species that roams the slower-moving shallows, remained plentiful. But rainbow trout, the colorful cousin that prefers deeper and faster currents, had all but disappeared — victim of a vicious parasite that triggers an affliction called whirling disease.

Yet, on several consecutive trips that year, Gardunio spotted a giant rainbow in a shallow riffle that was among his favorite spots. One blistering hot day, he fixed two flies to his line — a Turks Tarantula with a small red beadhead nymph tied about two feet below it. Wearing shorts, he waded into blessedly cool, thigh-deep water and headed toward the middle of the river. 

He cast the flies into the head of the riffle, upstream from where he expected the giant rainbow to be lurking, so the nymph could sink to an enticing depth. Almost immediately, his act of faith was rewarded with a strike, and he set the hook. Game on. 

The fish thrashed in front of him and he instantly recognized it to be The One. It caught a fast current downstream and Gardunio felt its pull rapidly deplete his reel. He soon found himself battling both fish and flow in the roiling waters.

Sensing he couldn’t give chase along the riverbed, he made his way back to the bank while downstream the giant fish arced out of the water again and again. Slowly, he closed the gap with rising anticipation until he stood ready to net the giant rainbow. 

Suddenly, the hook disengaged. The fish disappeared. Gardunio fell to his knees.

Eric Gardunio, right, a fish biologist with Colorado Parks and Wildlife, brings in a rainbow trout on the Gunnison River with the help of his wife, Dana. (Provided by Eric Gardunio)

“It was absolutely heartbreaking,” he recalls. “I had a chance, but couldn’t seal the deal.”

Seventeen years later, the intensity of the quest, the exhilaration of the battle — and the crushing disappointment — remain with him, like every detail of that day. It was the largest rainbow he ever hooked in the Gunnison. 

Gardunio didn’t realize at the time, but he was destined to remain inextricably connected to the species. Now an aquatic biologist with Colorado Parks and Wildlife serving the same region where he grew up casting for rainbow, he joined a far more consequential quest in progress  — a wide-ranging effort dating back to the 1990s to meet the threat of whirling disease and restore the rainbow to the state’s fisheries.

Through dogged research that called on experts throughout the U.S. and even Europe, the rainbow has staged a remarkable recovery that required years of genetic testing, cross breeding and painstaking reintroduction into Colorado’s waters. Only recently have those efforts shown signs of enduring success against the parasite that nearly destroyed it.

And in large part, it has been developments in the rugged Gunnison River waters, where researchers cultivated a strain of rainbow — dubbed the HXG — that’s both disease-resistant and hardy enough to survive in the wild, that have pushed the effort toward sustainability.  

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More than 1.3 million of the new fish will be introduced into Colorado’s waterways this summer.

“It’s been an ongoing sort of thing, an evolution of little successes over time,” says George Schisler, chief of aquatic research for CPW and one of the key players in the long-running drama. “Now that we’ve got a lot of these HXGs in production, that’s the tipping point. We’re starting to see more and more little rainbows surviving in the wild.”

To get here, the fish beloved by anglers for its colorful appearance, relative ease to hook and admirable fight, had to overcome a nasty parasite, hungry browns and a whole lot of trial and error.

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The disaster one man saw coming

Most researchers suspect the parasite whose activity devastated the rainbow population arrived via infected fish accidentally imported into the region by state and private fish hatcheries in the mid-1980s. It first appeared in Colorado at two hatcheries in the Arkansas River basin in late 1987.

When state fish and wildlife authorities began catching and testing, they found infected fish in more than 40 waterways across Colorado. But there seemed to be no discernible difference in their population levels, and it was assumed there would be no harmful effects.

State aquatics researcher Barry Nehring remembers finding rainbow trout spawned by a state fishery in the Colorado River in April 1992 that showed evidence of infection. 

“No one thought anything of it,” he says.

State aquatics researcher Barry Nehring, now retired, prepares for field work. Nehring was first to sound the alarm in the 1990s that Colorado’s rainbow trout were in danger of being wiped out by a microscopic parasite that causes whirling disease. (Provided by Kevin Rogers)

But the first clues pointing to a problem emerged a year later.

The department’s electrofishing along a 2-mile stretch of the Colorado near Kremmling in 1993 shocked well over 1,000 fish to the surface. Nehring recalls counting a huge population of wild rainbows from 16 to 24 inches long — but only five under 12 inches. 

It was a mystery what happened to the little ones. The results of the count were nothing like they’d seen on that same stretch of river in the early ‘80s, when there were plenty of big rainbows, but most fell in the 9-inch range — evidence that the young ones were thriving. 

At the same time, the brown trout population was virtually unchanged over that period. Nehring looked everywhere for possible culprits: water temperature, flow fluctuations during rainbow spawning and egg incubation, pollution, floods. But he could find no factors that seemed to make sense. That stretch of the Colorado seemed to be missing two years’ worth of wild rainbow trout fry — recently hatched fish — with no similar impact on the browns.

When Nehring called in to report the conundrum, his boss wondered if the answer might be something called whirling disease that plagued tiny rainbows but not browns.

“At that time I didn’t even know what whirling disease was,” Nehring says.

Although the life cycle of the parasite — Myxobolus cerebralis — has been understood only since 1984, whirling disease dates its discovery to the late 19th century at a trout farm in Germany. Scientific literature was sparse. In Colorado, a state fish pathologist determined after testing some infected rainbows that there was less than a 5% chance that whirling disease was responsible for the disappearance of the young rainbow population.

But Nehring felt sure the parasite was to blame. Adult rainbows were too large to succumb, but the very young rainbows, under 2 inches long, were vulnerable. And that did not bode well for the long-range survival of a species.

A fingerling rainbow trout with spinal deformities is shown in a swimming flume, used to determine the effects of whirling disease and deformities on a fish’s swimming ability, during a strain development experiment conducted in 2006 by then-CSU student Eric Fetherman. (Provided by Eric Fetherman)

Although Nehring sounded the alarm, most fish and wildlife experts didn’t pick up on the damage that whirling disease was doing to the state’s rainbow trout population until years after they’d studied bottom-feeding tubifex worms. The worms, which live in the mud and sediment of river and lake beds, had proved unwitting distributors of the spores that infected young fish and fed on the cartilage that later would mature into bone.

The result is a misshapen skeletal structure, with deformities that include a telltale lateral curvature of the spine. Eventually, inflammation causes nerve malfunction. The result is a rainbow that whirls in endless circles, and either dies of the infection or becomes prey — often to the large population of brown trout. Cutthroat and some other species are vulnerable to the disease, too, but rainbows are particularly susceptible. 

Although information was scarce back in the ‘90s, Nehring notes that now there’s enough research on the parasite “that you can read until you have nightmares.”

A parasite out of science fiction

The biology of whirling disease really is the stuff of bad dreams. It brings to life visceral science fiction images, though in microscopic scale, and a parasitic predator that painfully overwhelms its young prey.

A larger fish infected with these parasites may not show ill effects. But eventually it dies and releases thousands of the parasite’s hard spores or sinks to the riverbed to decompose. The tubifex worms ingest the spores.

Nehring, who became an authority on these organisms during his time with the DOW, describes the hard spores as about the size of a red blood cell, only with the appearance of an alien with black, angled eyes — “almost something out of Roswell, New Mexico.”

Inside the worm, the hard spore changes form and is either discharged naturally or bursts through the worm’s digestive system — the memorable image from early in the movie “Alien” would be the sci-fi equivalent — releasing tens of thousands of free-floating spores that drift through the water, much like dandelion seeds blowing across a field.

“The worm is an unwitting victim in the whole thing, too,” CPW’s Schisler notes. “They’re just doing their thing, eating organic matter and processing it, and they pick up these spores, which develop in its gut lining. Then they burst out.”

In this scanning electron microscopy (SEM) photo, two triactinomyxon (TAM) spores have pierced a fish’s flesh and send sporoplasm into its body. The sporoplasm divide, settle in the fish’s cartilage and feed on it, causing skeletal deformities. (Provided by George Schisler)

These spores — called TAM for triactinomyxon — have a different appearance: Picture a microscopic grappling hook attached to a rope. The three-pronged hook attaches to the outside of a fish. Then, using the bottom of that “rope,” the TAM pierces the fish with an explosive-style charge — like the sting of a jellyfish, to whom it’s distantly related.

Once it has torn into the tissue, infectious organisms called sporoplasm migrate down that biological rope and through the tiny hole in the fish. A single spore can infect a fish with 32 sporoplasm, which divide and head for the fish’s nerve bundles and eventually the head. Hosted now by the fish, they once again become hard spores, completing the parasite’s life cycle, and begin devouring the cartilage of a young fish’s undeveloped skeleton.

“Each sporoplasm is like Pac-Man,” Nehring says, noting that they turn the fish’s skeleton into “Swiss cheese.” 

CPW aquatic research leader George Schisler, left, and Colorado State University Ph.D. candidate Brian Avila net fish off the front of an electrofishing raft captained by Dana Winkelman, Colorado Cooperative Fish and Wildlife Research Unit Leader in 2010 during the brown trout removal experiment conducted by then-student Eric Fetherman in the Cache la Poudre River. (Provided by Eric Fetherman)

By the fall of 1994, aquatic biologists knew that whirling disease was present in some of the state’s major waterways — the Cache la Poudre, the South Platte, the Gunnison, Rio Grande and Colorado rivers. It also was discovered in Montana’s Madison River, where 95% of the wild rainbow trout population had vanished over the preceding five years.

Nehring recalls walking to the bank of the Colorado River one day in 1994, when “one of these little rainbows started to whirl like a runaway boomerang and whipped itself right up into the mud. At my feet.” 

He sat down on the bank and cried, realizing what a huge problem the state’s fisheries faced. Meanwhile, the world of fish biologists remained in denial.

“That was pretty traumatic for me,” Nehring recalls, “since I had taught my two sons to fly fish down there — they had caught big rainbows. But I could see the handwriting on the wall, even though at that time we were not even a full year into the research studies.”

Fortunately, the theory that whirling disease was behind the rainbow’s decline gained traction, thanks in part to the data collection of Nehring and Montana fisheries biologist Dick Vincent. In 1995, the Whirling Disease Foundation formed to raise consciousness — and money — in an effort to curb the impacts of the parasite. 

Symposiums were convened, a Nobel laureate and members of the National Academy of Science were enlisted and discussion ensued. Funded by the WDF (which later merged with Trout Unlimited) and with millions from the federal government, research took off.

How the research evolved

As a graduate student at Colorado State University, George Schisler dedicated his doctoral dissertation to looking at other environmental factors that might contribute to the loss of rainbows. He, too, concluded that whirling disease remained the single biggest factor.

As the aquatic research chief for Colorado Parks and Wildlife, Schisler has been at the forefront of the decades-long effort to create a strain of rainbow trout that would be more resistant to whirling disease, while also resilient enough to survive from tiny fry to a size that would ensure safety from predators.

But the quest for a solution stretched across the Atlantic Ocean. Because rainbows are easy to raise in hatcheries and make fine eating, they had been exported to Europe, where they’d been exposed to the whirling disease parasite for more than a century. A German researcher, Mansour El-Matbouli, used eggs from rainbow hatcheries there to experiment.

George Schisler, chief of aquatic research for Colorado Parks and Wildlife, in his laboratory located at the Parvin Lake Research Station near Fort Collins. (Provided by George Schisler)

He exposed the fish to the parasite under controlled conditions and tracked the results. He found that fish from the Hofer trout farm in Bavaria had developed a resistance to whirling disease. That would prove a turning point.

Researcher Ron Hedrick, who collaborated with Schisler, imported some of the so-called Hofer trout to his lab at the University of California, Davis and replicated El-Matbouli’s findings. In the spring of 2003, Schisler went to UC Davis and picked up a truckload of 4,000 of the disease-resistant trout, obtained permission to bring them to Colorado and started his own brood stock.

During the course of his experiments, he noted that the German fish were highly domesticated — countless generations of being reared as a farm fish had bred the flight response from danger right out of them. That characteristic didn’t bode well for survival in the wild.

“We thought, if we’re going to make these successful, we have to cross them with the Colorado River rainbow trout,” Schisler says, referring to an iteration they dubbed HXC — shorthand for Hofer crossed with Colorado. “So we did that for a few generations, built up a brood stock, and then put them out (into natural waterways) for a while. They were doing OK, but not gaining as much ground as we’d like.”

But one stretch of water they’d stocked the HXC where it seemed to take hold and shed some of its domestic characteristics was the East Portal section of the Gunnison River Gorge. Those fish were renamed Gunnison River Rainbows and tabbed with the shorthand HXG.

Gardunio, who started with CPW’s Montrose office in 2013, has been monitoring efforts to establish the cross-bred rainbows in the waters he grew up fishing and notes that over the past several years, the population of adult rainbows has increased markedly — from about 170 per mile of river to more than 600 per mile in 2019. 

“That’s a big jump that seems related to our stocking,” he says, noting that he’s also seen more wild rainbow fry since 2014 — which would suggest that the disease-resistant fish are also learning survival techniques. “Now, as those adult fish start to successfully reproduce, the number of rainbows should continue to increase in the Gunnison. It’s the ultimate trial for these fish, put in the wild with brown trout to compete with, and it looks like they are starting to turn things around.”

Eric Fetherman, a CSU classmate of Gardunio, has focused on creating new strains of rainbow and strategies for reintroducing the various iterations to different waterways across Colorado. He arrived at CSU shortly after the Hofers were brought to the U.S. and started working with Schisler on whirling disease as an undergraduate in the early 2000s — and eventually took Schisler’s position when he moved up to manage CPW’s aquatic research.

Fetherman picked up where Schisler left off with genetic experimentation that produced the Colorado River rainbow, HXC, and afterward tinkered with the strain by “back crossing” — taking a 50-50 mix of Hofer and Colorado River rainbow and spawning that fish with a pure Colorado River female, reducing the Hofer influence to 25%. In all, he figures, there were five variations of that combination.

Aquatic research scientist Eric Fetherman did much of the genetic testing and cross breeding that helped produce the strains of rainbow trout resistant to whirling disease and hardy enough to withstand the challenges of Colorado Rivers. (Provided by Eric Fetherman)

Hofers also have been tested with Harrison Lake rainbows from Montana, a strain raised in several state hatcheries and considered well-suited to regional lakes and reservoirs.

Most of the early experiments were performed in the lab, where Fetherman would expose the varieties to whirling disease parasites and determine their level of resistance. He also evaluated their swimming ability on a “running track” for fish, and used that as a proxy for their ability to survive in the wild.

When CPW lost a lot of its brood stock to bacterial kidney disease in 2015, researchers harvested rainbow eggs from the upper Gunnison to replace them. Schisler describes those as version 2.0 of disease-resistant Gunnison River rainbows. 

TODAY’S UNDERWRITER

Fetherman says the rainbows that came out of the East Portal of the Gunnison River were definitely resistant to whirling disease, based on experiments done in 2014. But nobody knew why. Did they develop resistance over time because the population had a low level of exposure and were able to reproduce despite the disease? Or had past stocking efforts incorporated that resistance gene?

What further research showed was that the Hofer genetics had been quickly incorporated into the fish stocked in that section of the river. 

“Genetically, they looked like wild fish, but using techniques we were using at that time, we couldn’t detect the Hofer gene in that fish,” Fetherman says. “So we changed techniques to look at a known resistance gene that originates from Hofer fish.”

They discovered that gene, and up to nine others that work together to convey resistance, had been incorporated into the population. But natural selection had worked rapidly toward producing a wild fish, while maintaining Hofer genetics.

“Now we have a really good wild-type fish coming out of the Gunnison River that has those Hofer resistance characteristics but should be able to be used all over the state,” Fetherman said.

The Gunnison River Rainbow strain has provided a viable option for many Colorado waterways, and CPW’s Glenwood Spring hatchery is producing those and other variations on that successful experiment. From there, the more than 1.3 million fingerling (2- to 3-inch) rainbows resistant to whirling disease will be dispersed this summer in rivers and streams. 

But there’s still more to be done. The Gunnison River variety may not be the best fit for every aquatic environment.

“If only there was just one,” Fetherman says. “That’s part of the reason we’ve gone through all these iterations. Gunnison River Rainbow do better where they act like river fish. The Harrison Lake Rainbow strain has a lake life history, and may work better in a reservoir setting.” 

Schisler, Fetherman and Nehring also have been consulting with fish experts in Alberta, Canada, to address problems they’ve been having with whirling disease.

For Gardunio, the success in Colorado comes with the personal satisfaction of knowing that, while the big one might have gotten away years ago, so many others along his favorite stretch of the Gunnison River have been restored.

“It’s fun for me every year,” he says. “We do the survey work in Gunnison Gorge, then I look at the data and sure enough. My wife and I go down there and fish, and you just catch so many more rainbows than you used to.”

Eric Gardunio, who grew up fishing the Gunnison River when rainbow trout were becoming scarce, shows off a healthy rainbow — part of a project in which he has played a prominent role. (Provided by Eric Gardunio)

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