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http://www.nytimes.com/2008/03/17/sc.../17salmon.html

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Chinook Salmon Vanish Without a Trace

By FELICITY BARRINGER
Published: March 17, 2008

The New York Times

The Chinook salmon that swim upstream to spawn in the fall, the most
robust run in the Sacramento River, have disappeared. The almost
complete collapse of the richest and most dependable source of Chinook
salmon south of Alaska left gloomy fisheries experts struggling for
reliable explanations — and coming up dry.

Whatever the cause, there was widespread agreement among those
attending a five-day meeting of the Pacific Fisheries Management
Council here last week that the regional $150 million fishery, which
usually opens for the four-month season on May 1, is almost certain to
remain closed this year from northern Oregon to the Mexican border. A
final decision on salmon fishing in the area is expected next month.

As a result, Chinook, or king salmon, the most prized species of
Pacific wild salmon, will be hard to come by until the Alaskan season
opens in July. Even then, wild Chinook are likely to be very expensive
in markets and restaurants nationwide.

“It’s unprecedented that this fishery is in this kind of shape,” said
Donald McIsaac, executive director of the council, which is organized
under the auspices of the Commerce Department.

Fishermen think the Sacramento River was mismanaged in 2005, when this
year’s fish first migrated downriver. Perhaps, they say, federal and
state water managers drained too much water or drained at the wrong
time to serve the state’s powerful agricultural interests and cities
in arid Southern California. The fishermen think the fish were left
susceptible to disease, or to predators, or to being sucked into
diversion pumps and left to die in irrigation canals.

But federal and state fishery managers and biologists point to the
highly unusual ocean conditions in 2005, which may have left the
fingerling salmon with little or none of the rich nourishment provided
by the normal upwelling currents near the shore.

The life cycle of these fall run Chinook salmon takes them from their
birth and early weeks in cold river waters through a downstream
migration that deposits them in the San Francisco Bay when they are a
few inches long, and then as their bodies adapt to sal****er through a
migration out into the ocean, where they live until they return to
spawn, usually three years later.

One species of Sacramento salmon, the winter run Chinook, is protected
under the Endangered Species Act. But their meager numbers have held
steady and appear to be unaffected by whatever ails the fall Chinook.

So what happened? As Dave Bitts, a fisherman based in Eureka in
Northern California, sees it, the variables are simple. “To survive,
there are two things a salmon needs,” he said. “To eat. And not to be
eaten.”

Fragmentary evidence about salmon mortality in the Sacramento River in
recent years, as well as more robust but still inconclusive data about
ocean conditions in 2005, indicates that the fall Chinook smolts, or
baby fish, of 2005 may have lost out on both counts. But biologists,
fishermen and fishery managers all emphasize that no one yet knows
anything for sure.

Bill Petersen, an oceanographer with the National Oceanic and
Atmospheric Administration’s research center in Newport, Ore., said
other stocks of anadromous Pacific fish — those that migrate from
freshwater to sal****er and back — had been anemic this year, leading
him to suspect ocean changes.

After studying changes in the once-predictable pattern of the Northern
Pacific climate, Mr. Petersen found that in 2005 the currents that
rise from the deeper ocean, bringing with them nutrients like
phytoplankton and krill, were out of sync. “Upwelling usually starts
in April and goes until September,” he said. “In 2005, it didn’t start
until July.”

Mr. Petersen’s hypothesis about the salmon is that “the fish that went
to sea in 2005 died a few weeks after getting to the ocean” because
there was nothing to eat. A couple of years earlier, when the oceans
were in a cold-weather cycle, the opposite happened — the upwelling
was very rich. The smolts of that year were later part of the largest
run of fall Chinook ever recorded.

But, Mr. Petersen added, many factors may have contributed to the loss
of this season’s fish.

Bruce MacFarlane, another NOAA researcher who is based in Santa Cruz,
has started a three-year experiment tagging young salmon — though not
from the fall Chinook run — to determine how many of those released
from the large Coleman hatchery, 335 miles from the Sacramento River’s
mouth, make it to the Golden Gate Bridge. According to the first
year’s data, only 4 of 200 reached the bridge.

Mr. MacFarlane said it was possible that a diversion dam on the upper
part of the river, around Redding and Red Bluff, created calm and deep
waters that are “a haven for predators,” particularly the pike minnow.

Farther downstream, he said, young salmon may fall prey to striped
bass. There are also tens of thousands of pipes, large and small,
attached to pumping stations that divert water.

Jeff McCracken, a spokesman for the federal Bureau of Reclamation,
which is among the major managers of water in the Sacramento River
delta, said that in the last 18 years, significant precautions have
been taken to keep fish from being taken out of the river through the
pipes.

“We’ve got 90 percent of those diversions now screened,” Mr. McCracken
said. He added that two upstream dams had been removed and that the
removal of others was planned. At the diversion dam in Red Bluff, he
said, “we’ve opened the gates eight months a year to allow unimpeded
fish passage.”

Bureau of Reclamation records show that annual diversions of water in
2005 were about 8 percent above the 12-year average, while diversions
in June, the month the young Chinook smolts would have headed
downriver, were roughly on par with what they had been in the
mid-1990s.

Peter Dygert, a NOAA representative on the fisheries council, said,
“My opinion is that we won’t have a definitive answer that clearly
indicates this or that is the cause of the decline.”