he blue tanks housing rainbow trout were all but empty by Colorado Parks and Wildlife standards, with a little more than 4,000 fluttering fish where there were once 250,000.

It was mid-July, and a sign that stocking season was coming to a close at the Pueblo hatchery, one of 17 facilities across the state that had reared and released rainbows over the previous five months. Its final crop of fingerlings would tread water for two more weeks before shipping off to Chalk Cliffs, a dispensary in Nathrop where they would be raised to 10 inches.

All that was left to do was hurl fish food into the vats seven times a day and think about what a good, rainy summer it's been.

"Sustainability has definitely been better this year because of all the water," hatchery manager Dave Harris said. "We've seen rising numbers."

CPW is experiencing its best time for rainbow trout since whirling disease devastated the population in the 1990s, and continued, government-funded breeding is to thank.

Each year, fish biologists begin the process around October, securing eggs for the impending months by either having them fertilized in-house or shelling out funds to experienced distributors who mass-produce strains resistant to illness.

Carefully, the team unloads the eggs onto shelves in a cooler with water dripping from the top to keep them moist. In groups of about 25,000, they then are moved into Montana jars that hang on the edge of tubs. A funnel is attached so newly hatched trout can slither out when ready.

The process culminates with a trip to a central Colorado lake or river. CPW's bulky white trucks are a common sight for anglers, backing up toward the water with two 500-gallon tanks of squirming fish.

Unknowingly stocking bodies of water with infected rainbows might have been what triggered the whirling disease catastrophe 29 years ago, but repeating the process with a better strain - such as Pueblo's jumpers - was also what reversed it.

Slowly, with years of breeding, releasing and repeating, Colorado's most popular non-native fish was brought back from the edge of extinction.

"We're not seeing nearly as many issues as we used to," Harris said. "Rainbow trout is finally stable."

Fish, made by man

States have been feeding their appetite for non-native rainbow trout since the turn of the 20th century, when government officials discovered a colony in Northern California and artificially propagated them throughout the country. As its popularity boomed, the species was dubbed the "synthetic fish."

In Colorado, rainbows have become a favorite because of their unmistakable look - decorated in shades of green and yellow, flushed with a light pink streak across the side and peppered with black dots. Plus, they're easy to catch.

"There's really a culture with the rainbow trout," said Barry Nehring, a retired CPW biologist who was a leading researcher on the fish in Colorado waters for nearly 40 years. "That's one of the reasons they've spread all over the world."

In the fall of 1993, Nehring and his team received alarming news when they deployed to Parshall in north central Colorado to check fish populations in a small stretch of the Colorado River.

The rainbow's distinctive glimmer was nowhere to be seen, so they electro-shocked the water to get a sense of how many were left. In the past, thousands had swarmed to the surface, but on that ominous day, there were five.

The small pack was off in a corner displaying mutations such as bulging eyes, a sloped skeletal structure and blackened skin near the tail.

Nehring called his boss at the time, Tom Powell, an expert on trout illnesses, who said it was almost certainly whirling disease.

The highly contagious parasite deforms the spine of young trout, Powell told Nehring, until they whirl around in circles for a moment and then die.

"I started looking into the literature, and sure enough baby rainbows are susceptible," Nehring said. "We went back and electro-fished the same sections of streams that we had in the first week of September when 65 percent of the fry population was rainbow trout. But we couldn't find a rainbow to save our souls."

The outbreak later would be traced to a private hatchery that unknowingly imported infected trout from Idaho in 1986. Since no one knew anything was amiss, they released the fish into 40 Colorado waters, infecting thousands of rainbows as well as brooks and cutthroats.

It was a dark time for CPW employees, Nehring said. Phones rang off the hook, researchers scrambled for answers and a sense of gloom set in.

"I don't really like to talk about that time," he said. "I call it the whirling disease nightmare."

Failure and redemption

The rest of the 1990s were marred by unsuccessful attempts to boost rainbow numbers.

"We saw an absolute collapse of the rainbow reproduction," Nehring said. "It was the same all over the state."

A long-awaited glimmer of hope arrived in 2002 when a leading expert on whirling disease, Mansour el-Matvouli, spoke at a conference on the topic in Denver. The German researcher had studied the effects of the parasite across Europe and developed a strain he claimed to be resistant. He named it Hofer after his family's hatchery.

Nehring was one of many CPW employees who attended the presentation. And while state wildlife departments from Montana and Idaho said no to his pitch, it felt like a step forward to those representing Colorado.

"Nobody believed the Hofer was the answer," Nehring said, "except for the people in Colorado."

George Schisler, who worked as a postdoctoral fellow with CPW at the time, hung on every word of the speech. He even felt compelled to drive to University of California-Davis - where el-Matvouli performed extensive research on the fish - a year later to pick up fingerlings that had been reared to 3 inches from a batch of eggs that had been imported from Germany.

"We thought this was something we really needed to investigate and find out if it could work over here," he said.

Long before they could begin stocking waters, though, Schisler and his aquatic research team had to develop their "broodstock" by raising the fish for three years until they became sexually mature.

Once grown, they crossbred the Hofers with an array of native fish until they landed on something that would retain the wild behavior of the rainbow trout anglers have come to love. The subsequent years would be filled with lab experiments, concentrated stocking, population estimates, more stocking and - finally - waiting.

A June news release from CPW said one of the breakthroughs came in 2010 when researchers discovered a thriving ecosystem at the Colorado River, but Schisler can't recall any particular moment of eureka. Rainbows returned gradually, he said.

"You can never expect it all to happen overnight," he said. "You have to be patient."

Colorado responds

David Leinweber hears all the fishing stories that come through Anglers Covey. Bragging about what you catch is customary for regulars.

The owner of the 34-year-old shop in Colorado Springs is hearing far more anecdotes these days than he did during the height of the whirling disease outbreak in 1995, a time when business was slow and the outlook was bleak. Excitement has returned to his customers along with rainbow trout.

"We have more people fishing than we've ever had," Leinweber said. "We just can't keep up."

There are some anglers who are less excited, though, claiming the increase in rainbow trout populations has led to a decrease in numbers for trout native to Colorado.

Trout Unlimited, a cold-water conservation group, released a grim "State of the Trout Report" in early June that laid blame on the state for stocking hatchery trout that have "swamped the genes of the native trout through hybridization and competition."

Yellowfin cutthroat have long been extinct, the report said, and genetically pure greenback cutthroat are listed as threatened under the federal Endangered Species Act. The other native species of cutthroat trout - Colorado River cutthroats and Rio Grande cutthroats - occupy only about 10 percent of their respective habitats.

"Neither the status of native trout nor their habitat is secure," the report reads.

At the Pueblo hatchery where breeding is being done, the claims don't startle. They're well aware of the problem.

When Harris, the hatchery manager, hears about the Trout Unlimited report on the loss of native trout, he shrugs and says, "It's true." Cutthroats native to the state, which at one time had the waters to themselves, now are surrounded by brooks and rainbows and browns.

CPW has sunk money into fixing this problem, devoting time and resources to re-establish cutthroat trout, and Harris said they never would stock rainbows where they would threaten indigenous populations.

But as the fish ecosystems in Colorado evolve, the reality is that what is caught likely was raised in an air-conditioned hatchery instead of a shimmering river.

That shouldn't worry anglers, though, Harris said. The idea of the "synthetic fish," an accurate moniker in his opinion, shouldn't be seen in a negative light.

"For me, fishing is all about recreation," he said. "If you have fun catching fish, you'll have fun catching rainbows."

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