COLUMN ONE : Test Tube Salmon in River Test : Man-made projects threaten the chinooks with extinction. In a bold effort to save them, 11,500 were bred in paper cups and then dumped into the Sacramento River.

It is not the way nature would have done it: more than 11,500 baby chinook salmon, bred in Dixie Cups and raised in a warehouse, unceremoniously dumped in the Sacramento River from a government truck.

Launched from a boat ramp in a busy city park last month, the four-inch salmon began their instinctive trek to the sea, bearing with them the hope of scientists that they will revive a nearly extinct species.

The fry are among the last survivors of what for centuries was a huge winter migration of chinook, or king salmon, up the Sacramento River. Hatched in captivity by the U. S. Fish and Wildlife Service, they are part of a last-ditch, multimillion-dollar effort to engineer the survival of the nation’s only population of winter-run chinook.

“What we’re doing here is an attempt just to continue the species,” said Roger Shudes, a Fish and Wildlife biologist who oversees the captive breeding program. “A lot more needs to be done to bring the winter run back.”

Once, the Sacramento River chinook migrated 480 miles each way from the icy streams near Mt. Shasta to the Pacific Ocean and, after three years, came back to spawn in the Northern California mountains. But as the state’s mightiest river became more of a conduit for the dams and aqueducts that supply Central Valley farms and Southern California cities, the winter run all but vanished--dwindling from more than 100,000 salmon in the 1960s to just 191 last year.

Faced with ruination of a historic species, federal and state agencies have embarked on an ambitious, multi-pronged campaign to save the winter-run chinook that is similar in concept to biologists’ effort to save the nearly extinct California condor.

Unlike the condor restoration program, the effort to rescue the chinook has implications for people in a wide area of Northern California. Fishing for salmon is banned in the river, San Francisco Bay and Sacramento-San Joaquin River Delta during the months when winter-run chinook are present.

Dredging of San Francisco Bay has been curtailed to avoid churning up toxic materials that could endanger the fish--a move fought by port officials in Oakland and San Francisco who said it could interfere with shipping. On a smaller scale, extra gravel has been spread in streams where the remaining mature chinook lay eggs.

Under pressure to reverse the damage its dams helped cause, the U. S. Bureau of Reclamation has released cold water from the bottom of Shasta Lake to keep the river cooler during spawning--at a cost of $20 million a year in lost power generation. The bureau has also spent $16 million to install state-of-the-art fish screens at the intake to the Tehama-Colusa Canal to prevent the loss of salmon to one of their main predators--irrigation pumps.

And this month, to help more newly released baby salmon survive their trek to the ocean, the transport of water across the delta to the pumps that feed Southern California reservoirs will be rerouted. Later in the summer, pumping of water to Sacramento Valley farms will be cut back under court order to protect the fry in the river.

But the most ambitious and painstaking step is the breeding program, the first to successfully raise winter-run chinook in captivity. The more than 11,500 salmon dumped in the river last month were raised at a federal hatchery in a desperate experiment to revive the species.

On their way downriver, the newly released fry and the small number that hatched naturally last year will face a gantlet of man-made hazards. Some 300 irrigation canals along the way pump water to farms, and also suck vast numbers of young fish out of the river and strand them in fields to die. Other threats include toxic chemicals, urban sewage and fishing hooks.

Most of those obstacles and more harass the returning mature salmon. One of the greatest hazards to the winter-run chinook is the Red Bluff Diversion Dam, which blocks the passage of many adults trying to spawn. Its turbulent waters also disorient juvenile salmon passing downriver, and they become easy prey for the squawfish that lie in wait just below the dam.

When the adults arrive in the upper Sacramento, they often encounter water so warm that many of their eggs will, in effect, be hard-boiled by the river.

Given the odds, biologists expect about 115 of the artificially bred fish to come back in spawning season, a few more than they expect of the wild salmon. To enhance the species’ chances of survival, biologists kept 1,000 hatchlings to raise in saltwater tanks as the foundation of a permanent breeding program.

While many government officials are optimistic, some scientists and environmentalists caution that the attempt to save the salmon amounts to too little, too late.

“Personally, I don’t have a whole lot of hope for the winter run,” said Steve Evans, conservation director for Friends of the River. “We’ve ignored them for so many years, it’s going to take possibly more than we can give to bring them back from the edge of extinction.”

Some wildlife advocates contend that the only answer is to take water that now goes to cities and farms and give a larger share back to nature--release it in the river in hopes of restoring something close to the salmon’s natural habitat.

“Clearly, some water has got to be reallocated,” said Rep. George Miller (D-Martinez), chairman of the House Interior Committee. “Otherwise, we are in a position of artificially maintaining this species in hatcheries--sort of nursing homes for fish.”

California’s growing population and the competing demands for water make a radical realignment of priorities in favor of salmon politically difficult. Still, the plight of the winter run is taken by some as a disturbing sign about other Sacramento River species. After five years of drought, the winter-run chinook is one of 21 threatened or endangered species in the river environment. Three other Sacramento River salmon species are not yet endangered but are declining.

The winter-run chinook, so named because of the time of year they enter San Francisco Bay, swim under the Golden Gate Bridge as early as December and spawn in the Sacramento River the following spring and summer. The young remain in fresh water until the winter, when they begin their journey to the ocean--a year after their parents began their inland migration.

Long ago, the salmon runs extended to the upper reaches of the McCloud and Pitt rivers, northern tributaries of the Sacramento. But the species’ demise began with construction of the Shasta and Keswick dams in the 1940s. The dams blocked the fish from the upper 150 miles of their range, making it impossible to reach the spot where nature’s signals tell them to spawn.

Unable to spawn in the cold streams further north, the salmon while away for months below Keswick Dam each year before they lay their eggs in the warmer water of the river.

The characteristic that makes life difficult in the wild for the winter-run salmon--a longer spawning season than other salmon--also made it hard for biologists to raise the fish in captivity.

Attempts to breed the fish failed in 1989 and 1990 when a fungus wiped out most of the fish. This time, Fish and Wildlife scientists trapped 23 winter-run salmon last year in the river just below Keswick Dam. Twenty survived and were taken to a tank at the federal Coleman Fish Hatchery on Battle Creek about 20 miles southeast of Redding.

To overcome the deadly fungus, biologists treated the water with chemicals and installed a new filtering system. To speed up the biological clocks of the salmon, they kept lights on 18 hours a day and gave the fish hormone injections.

When the salmon were ripe, hatchery workers sliced open the females and removed the eggs, milked sperm from the males and carefully mixed the two in paper cups.

Shudes, the federal biologist and assistant manager of the hatchery, estimates that Coleman’s 20 captive adults produced more fry than the 123 winter-run salmon that spawned naturally in the river last year. This year’s hatchery fish, he predicted, will make up more than half the total that return in three years as adults.

“From my point of view, we ought to collect every one and put them in the tanks,” Shudes said. “We still have the school of thought that wild fish are better. We should be worried about saving the species. They’re going extinct in the river.”

Biologists trucked the salmon to Redding and released them in the Sacramento in the hope the fish will forget the scent of the Battle Creek water from their tanks and imprint instead on their native river. If so, the salmon will maintain the species’ migration pattern and return in three years to the area where they were set free.

Under the U. S. Fish and Wildlife Service plan, the 1,000 fingerlings kept behind would be put on display at a UC Davis facility at Bodega Bay and the Steinhart Aquarium in San Francisco. After three years in captivity, they would be bred artificially. National Marine Fisheries Service officials, who must approve the plan, like the idea of an ongoing breeding program but have yet to agree to specifics.

All this tinkering with nature, however, creates problems of its own: While the salmon bred in captivity may help prolong the species, they may also alter the balance of the species’ gene pool.

Most of the hatchery’s winter-run fry came from just three females mated with a variety of males. One set of parents was responsible for nearly a third of all offspring. Altogether, biologists ended up with just four different family groups.

The high proportion of young from so few fish exacerbates the problem of a shrinking gene pool in the wild. Scientists say a species that reaches a population of fewer than 500 animals may not have the genetic diversity to survive in the long run because it loses the ability to adapt to changing conditions.

“Two hundred individuals is dangerously low, and that is if all 200 animals breed,” said Oliver Ryder, geneticist for the San Diego Zoo, which specializes in breeding endangered species, including the California condor. “This farming operation seems appropriate, but 10% of the population is not going to save 100% of the gene pool.”

To avoid compounding the inbreeding problem, all 12,500 baby fish have been tagged with tiny pieces of metal implanted in their heads. When the salmon return to spawn and are trapped by biologists, the tags can be read to minimize breeding fish with the same parentage.

The tags cannot be read without killing the fish and boiling or dissecting their heads, but scientists say the information on the tags will help them gauge the success of the breeding program.

This year’s advance in the breeding program is the brightest spot so far in the effort to save the winter run. But federal officials acknowledge that raising the fish in a hatchery is a small part of what needs to be done if the salmon are to survive.

“The best hope is to restore and maintain their habitat in the river,” said Jim Lecky, a biologist with the National Marine Fisheries Service, which has overall responsibility for the salmon.

One longstanding obstacle for the winter run has been the sluggish pace of government action. Officials concede that during the salmon’s decade-long slide toward extinction, their agencies have moved slowly in coming to the rescue.

The National Marine Fisheries Service has refused to declare the species endangered--a move that would invoke federal law to force tougher protections for the fish and could lead to major changes in the state’s water distribution system.

Instead, the agency waited until 1990 to give the species the milder designation of “threatened.” And even now, the agency has not convened a recovery team or drafted a recovery plan--steps to save the species required by federal law.

“I guess we were of the opinion that things would turn around and that enough was being done to improve the status of the winter run,” Lecky said.

The agency is considering a petition by the American Fisheries Society, a private conservation group, urging the federal government to declare the winter-run salmon endangered. Lecky said a decision is due early this year.

Some officials who have worked to save the winter run attribute the slow action to the political clout of the agriculture industry. “The bottom line is, there’s a lot of money in California agricultural production and that’s one reason it’s not listed as an endangered species yet,” charged one biologist. “What’s being accomplished is very minute.”

After a slow start, the National Marine Fisheries Service and the Bureau of Reclamation have begun taking steps to compensate for the damage done to the salmon’s environment by the dams that have blocked the Sacramento River.

“Any time you pump water from an area like the state and federal governments do, there are going to be downsides, and those downsides have been for fish and wildlife,” said bureau spokesman Jeff McCracken. “Now we have reassessed what we’re doing. We’re looking at how we can make these programs fit, given the changing times.”

Taking on the agriculture industry for the first time, the National Marine Fisheries Service is seeking a fine of $700,000 against the Anderson-Cottonwood Irrigation District for killing winter-run salmon last fall. The district, whose annual budget is only $600,000, could have averted the fish kill by installing screens but chose not to.

In a separate action, the agency won a court order sharply limiting the amount of water diverted by the huge Glenn-Colusa Irrigation District, whose poorly operating fish screens kill a portion of the winter run each year.

The Glenn-Colusa district could win back its water supply if it installs screens that protect the salmon. But Bob Clark, manager of the 140,000-acre district, argues that farmers should not have to pay the price for the decline of the winter run.

“It basically would devastate the economy of the area,” he said. “It’s a shame that it comes down to farmers being denied their livelihood. The farmers are as anxious as anyone to protect the winter run.”

From the standpoint of those who hope to save the winter-run salmon, the hardships faced by the farmers of the Sacramento Valley are just the beginning of the changes that must be made.

“It’s probably going to require some sacrifices from the agricultural industry,” Lecky said. “They have benefited greatly from the water project in the Sacramento basin and, for a number of years, those benefits occurred without regard to the wildlife resources of the river.”

Species in Trouble

The winter-run chinook salmon, once plentiful in the Sacramento River, is on the verge of extinction. Diversion of water from the Sacramento River system to slake the thirst of California’s farms and cities has created a host of problems. Government agencies are mounting a number of efforts to save the species, but some scientists and environmentalists caution it may be too late.

TROUBLE SPOTS Shasta and Keswick dams: - block overall migration of salmon. - hold back water for agriculture and power generation, increasing water temperature of Sacramento River, which often kills salmon eggs. Iron Mountain: - site of an abandoned mine that leaches toxic metals into the Sacramento River. Red Bluff Diversion Dam: - blocks adult salmon swimming upriver to spawn. - impedes progress of baby salmon heading downstream, making them easy prey for other fish. Glenn-Colusa Irrigation District: - pumps, which divert water to farmers, also pull in large quantity of small salmon. Preventive screens have been ineffective. 300 unscreened irrigation channels: - suck in salmon and deposit them in fields. State Water Project pumps: - suck in more salmon in Sacramento River Delta. Dredging for shipping: - spreads contaminants in San Francisco Bay that may harm the salmon.

SOLUTION ATTEMPTS -TEMPERATURE: Release of colder water at crucial times to reduce temperature of Sacramento River. -BREEDING: 11,500 baby salmon raised at Coleman Hatchery and released in river. -IRRIGATION: Glenn-Colusa Irrigation District has been ordered to reduce its water intake. -DREDGING: Restricted in San Francisco Bay. -FISHING: Limited in the river, delta system, bay and ocean when adult salmon are present. WINTER-RUN CHINOOK SALMON

The winter-run chinook salmon is one of four salmon species that inhabit the Sacramento River. The species gets its name because the salmon leave the Pacific Ocean in the winter, swimming into San Francisco Bay and up the Sacramento River to spawn. The fish spawn in the spring and summer; the juveniles head out to sea the following winter, passing the next group of adult salmon that are on their way upriver. THE NUMBERS

Here are the annual estimated counts of winter-run salmon passing Red Bluff. Fry that spawn in one year return three years later.

YEAR NUMBER 1968 84,414 1969 117,808 1970 40,409 1971 53,089 1972 37,133 1973 24,079 1974 24,079 1975 23,430 1976 35,096 1977 17,214 1978 24,862 1979 2,364 1980 1,156 1981 20,041 1982 1,242 1983 1,831 1984 2,663 1985 3,962 1986 2,422 1987 1,997 1988 2,094 1989 550 1990 441 1991 191

Source: Fish and Game Commission, National Marine Fisheries Service