Scientists try to explain dismal salmon run

Jan Kay, Chronicle Environment Writer

March 24, 2008

Amid growing concern over an imminent shutdown of the commercial and sport chinook salmon season, scientists are struggling to figure out why the largest run on the West Coast hit rock bottom and what Californians can do to bring it back.

The chinook salmon - born in the rivers, growing in the bay and ocean, and returning to home rivers to spawn - need two essential conditions early in life to prosper: safe passage through the rivers to the bay and lots of seafood to eat once they reach the ocean.

Yet, the Sacramento River run of salmon that was expected to fill fish markets in May didn't find those life-sustaining conditions. And some scientists say that's the likeliest explanation for why the number of returning spawners plummeted last fall to roughly 90,000, about 10 percent of the peak reached just a few years ago.

The devastating one-two punch happened as the water projects in the Sacramento-San Joaquin River Delta pumped record amounts of snowmelt and rainwater to farms and cities in Southern California , degrading the salmon's habitat. And once the chinook reached the ocean, they couldn't find the food they needed to survive where and when they needed it.

"You need good conditions in the rivers and ocean to get survival and good returns for spawning," said Stephen Ralston, supervisory research fisheries biologist with the National Oceanic and Atmospheric Administration, or NOAA, and a science adviser to the Pacific Coast Fishery Management Council.

Without those favorable conditions, the salmon run crashed. Five years ago, the peak was 872,700 returning spawners. Roughly 90,000 were counted in 2007, and only 63,900 are expected to return to spawn in fall 2008.

Helped by cool-water winter

The fishery council, a regulatory body charged with setting fishing limits, has recommended a full closure or a strict curtailment of the commercial and sport season. A final decision will come in April.

NOAA researchers say a cool-water winter will help the beleaguered run in the future. An influx of cold Alaska waters, along with a shot of nutrients from vigorous upwelling of deep waters, have been fueling the food chain that feeds salmon, birds and marine mammals.

But the scientists warn that chinook, which have swum through the San Francisco Bay for thousands of years, have suffered human harm over the past half-century and now also need human help.

They've proposed a number of solutions, including sending more water over the dams and reservoirs and down the tributaries where salmon spawn; removing barriers to migration such as old dams; screening the fish away from the pumps and diversion pipes that suck them up, misdirect or kill them; controlling pesticide and sewage pollution - and catching fewer fish while the populations try to rebuild.

Over the millennia, salmon have been born in the Central Valley rivers. At about six months, they head through the delta. At 10 months and only 4-inches long, they reach the ocean and start feeding voraciously in the Gulf of the Farallones on small shrimp, krill and young rockfish.

From there they move to the open waters from Monterey to Vancouver Island in British Columbia until 3 or 4 years of age or older. Then they return home to their birth river to reproduce and die. The young come down the rivers, and the cycle begins again.

The problems for the troubled fall run began in 2004 and 2005, the years the chinook were born and traveled to the ocean. In those two years, the federal Central Valley Project and the State Water Project exported record amounts of delta water to urban and agricultural customers in Southern California .

2005 a bad year for chinook

In 2005, a crucial year for the young salmon, 55 percent of natural river flows never made it out to the bay, according to records of the state Department of Water Resources. The water was either exported by the water agencies, diverted upstream of the delta or held back by dams.

"The flows were less than what the salmon needed, and the populations are collapsing," said Tina Swanson, senior scientist with the Bay Institute. Even if water agencies are meeting minimum standards, they are inadequate to protect the fish, she said.

A network of nonprofits, including the California Sportfishing Protection Alliance, filed a notice Tuesday with the State Water Resources Control Board, saying it would sue if it doesn't curb pumping.

But when looking for an answer to the fall run collapse, Jerry Johns, deputy director of the state Department of Water Resources, said there are many causes for the salmon's decline.

"You can't just simply blame it on the pumps," he said. Ocean conditions, a reduction of phytoplankton in the bay, the amount of salmon fishing, natural die-off and other factors are part of the broader picture, he said.

There may have been increases in exports to water customers in recent years, but the crucial point is whether there was also an increase in rainfall and snowmelt, he said. That would mean there was more water to divert.

State and federal water project representatives say they follow requirements put forth in their permits, which, among other things, ensure a big enough water supply to protect endangered species and provide certain minimum temperatures. They've aided the salmon by removing dams, screening off diversion pipes and improving habitat.

Biologists caution that salmon need generous flows of cold water at almost every life stage. The fish also need the fresh river water from the reservoirs at the right times, particularly in the fall and summer.

"The adults come upstream in the fall to spawn partly because they're responding to cooler water temperatures," said Peter Moyle, professor of fish biology at UC Davis. "If the females have to swim through water that's too warm, their eggs don't mature as well. Some don't hatch at all."

Some females, Moyle said, just stop migrating and wait for cool water. "They know from evolutionary perspective that if they don't wait until the water gets cold, the young won't survive," he said. In the end, they spawn or die before spawning.

'Squirrelly' ocean conditions

According to Moyle, good ocean conditions can somewhat make up for drought in the river systems and vice versa. But ocean conditions have been "squirrelly" in the last several years with a number of anomalies that produced abnormally warm conditions not good for salmon, he said.

"Usually, salmon populations are at their worst when conditions are bad in both fresh water and salt water," Moyle said. Some scientists think that is what happened to the 2007 fall run.

Once in the ocean, salmon must gorge on small sea creatures to survive.

In 2005 and 2006, the years that the 2007 fall run needed food near the shore in the Gulf of the Farallones, the upwelling of nutrients apparently came too late to produce the small fish that feed the salmon.

Most of the scientists studying the ocean link the unexpected bouts of rising temperatures to global warming. As the atmosphere and oceans have warmed, researchers have had to discard the theory of decades of warmer, then cooler, ocean temperatures. Now they expect an unpredictability, which is projected in climate models.

"What's happening is that the rockfish, the squid, the krill, the anchovies and the community of critters that salmon feed on changed dramatically in 2004 to the prey that is not as favorable to salmon," NOAA's Ralston said.

The distribution of the sea life also changed. Young rockfish moved well to the north or to the south of Central California , he said.

Ralston's hypothesis is that animals are adapted to finding food at certain times and in certain locations. "When salmon arrive in the ocean, they'll go to certain areas to find their food as they have for millennia," he said. "If we have a major change, their fitness, their ocean survival is compromised."

Bill Peterson, a NOAA researcher in Newport , Ore. , offered some hope for a cooler offshore current, although he cautioned that there would be a few years of hard times for chinook.

"It's looking kind of good this year" with five months of cold ocean currents, he said. But the scientists are "very guarded" because in the past two years the ocean was cold in the winter, and then the winds that brought upwelling quit in May and June, reducing the zooplankton that feed the prey of the salmon.

Peterson would like to see measures that would aid the salmon.

"These fish are so resilient and tough," Peterson said. "We should be a little nicer to them."  

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Source:  http://www.sfgate.com/cgi-bin/article.cgi?file=/c/a/2008/03/24/MN1BVMR10.DTL