The poisoning of Dungeness crab off the California coast by a mysterious algae bloom may be bad news for the seafood industry, but to marine biologists and climate scientists, it is a frightening omen of future distress to a vibrant ecosystem.

Experts say the toxin in the algae, which likely flourished in this year’s record-high ocean temperatures, is one symptom of a wholesale shift in the physical and biological makeup of the Pacific Ocean — a transformation so abrupt and merciless that it is endangering species and forcing migrations before our eyes.

“We are talking about a whole ecosystem change — including a lot of changes besides just the blooms,” said Raphael Kudela, a professor of ocean sciences at UC Santa Cruz. “It’s really restructuring the way California looks.”

Tissue samples of Dungeness and rock crabs last week showed contamination by domoic acid, a neurotoxin known to cause seizures, coma and even death when consumed by animals or humans. The finding prompted California wildlife officials to delay the $60 million commercial crab season, which was supposed to start Nov. 15.

The poisonous algae, multiplying since April, is now estimated to be 40 miles wide, in some places reaching down as far as two football fields, marine biologists say. It is the biggest and most toxic bloom researchers have ever seen.

Back to Gallery Toxin in crab among impacts of warm sea that alarm... 2 1 of 2 Photo: Paul Chinn, The Chronicle 2 of 2 Photo: Paul Chinn, The Chronicle



The primary culprit, the experts say, is consistently high ocean temperatures caused by climate aberrations that are being reinforced by a strengthening El Niño weather pattern in the tropics.

“This El Niño is building up to be quite a doozy, but we also have a series of other changes going on,” said Steve Palumbi, director of the Hopkins Marine Station at Stanford University. “We are having changes in wind patterns, changes in upwellings along the coast. It’s like your whole basic ecosystem is being shifted around in different ways.”

The waters off the West Coast are hovering at as much as 6 degrees warmer than normal. The anomaly began a couple of years ago when the wall of atmospheric pressure over the Pacific that blocked storms from hitting California — and kicked off the drought — also kept cold, stormy air from stirring the ocean and moderating water temperatures.

“If you want to cool off a bowl of soup, you blow on it. With that ridge of high pressure, the winds were a lot weaker than normal,” explained Nick Bond, the climatologist for the state of Washington who watched a 1,500-mile-long patch of water in the northern Pacific heat to record levels, which he famously dubbed “the blob.”

Effect in, out of water

Since then, ocean currents have pushed the blob against the coast between Baja California and Alaska. A lack of winds from the north limited upwellings of nutrient-rich water, driving surface temperatures even higher.

Scientists say the soupy warm sea is having an effect in and out of the water. Weather in California and much of the Pacific Northwest has been balmier than normal, while the ocean has carried a mix of marine life more typical of the tropics. The conditions are exacerbated by spring arriving an average of 20 days earlier than it did in 1970, according to climate scientists.

“It’s like looking out your office window and watching a flamingo walk by,” said Bill Peterson, a senior scientist with the National Marine Fisheries Service in Newport, Ore. “We’re seeing stuff we never would have guessed we’d see.”

The changes have been devastating for cold-water critters like salmon, squid and crab, but everything from microscopic plankton to giant whales has been forced to adapt, migrate or die.

“The local marine life is being affected because their food sources are in places where they don’t normally go, and all these organisms are coming up from the south that the local animals don’t know what to do with,” said Francisco Chavez, a biological oceanographer at the Monterey Bay Aquarium Research Institute.

Marine biologists have been seeing many exotic species, including ocean sunfish and Guadalupe fur seals, roaming waters far north of their normal hunting grounds in Mexico and Southern California. Nonnative species such as common dolphins, which are normally seen in Mexico, as well as booby birds and flying fish, have been spotted in large numbers.

Not all of the recent shifts are negative — or well understood. Researchers were surprised to see humpback and blue whales thriving this summer off San Francisco and Monterey.

“It almost seems like every time you turn around someone is saying, ‘Wow, I’ve never seen this before,’” Palumbi said.

Chavez believes the whales benefited from a burst in the anchovy population, an unusual circumstance given that the schooling fish have been in decline for 15 years and prefer cold water.

“You wouldn’t expect that anchovies would be doing so well during El Niño,” Chavez said. “It is a conundrum, and we aren’t sure why.”

Moving northward

Marine scientists have found as many as 20 new species of zooplankton — tiny organisms such as krill, marine worms and sea urchin larvae — along the Northern California coast. Red pelagic crabs, normally seen in Baja California, have also come north in large numbers, drawing bluefin tuna north as well to dine on them.

“They are up here because the water is moving northward when it normally goes the other direction,” Chavez said. “They think they are in Baja. There is a lot of that happening.”

While the Pacific has seen warm patches before, the current heating is confounding scientists. There’s little consensus in the research community on when it might dissipate and whether it may represent a new normal in an era of climate change.

Climate scientists believe global warming has already bumped up ocean temperatures and increased acidity. How warm it gets over the next 50 to 100 years depends on how much greenhouse gas is spewed into the atmosphere.

“We usually make guesses about what’s going to happen based on our experience, and with this, we don’t have any experience,” Peterson said. “At best, it’s what the world might look like 50 years from now. At worst, it might be the beginning of a trend, where it stays warm because of global warming.”

While the whales have thrived, huge numbers of fish, birds and marine mammals have suffered. The common murre, a native fish-eating seabird with a large nesting population on the Farallon Islands, is in an unprecedented die-off. Thousands have been found dead on the beaches of California, Oregon, Washington and Alaska.

Guadalupe fur seals, listed as threatened under the U.S. Endangered Species Act, have been dying in such large numbers that the National Oceanographic and Atmospheric Administration recently declared an “unusual mortality event,” triggering special protections.

Most of the fur seals were suffering from domoic acid poisoning. Dangerous levels of the toxin were also found in anchovies this year, forcing the closure of that fishery. Officials in California, Oregon and Washington have also implemented warnings or closures for sardine fishing.

The microscopic algae, or diatom, that produces domoic acid is itself a strange, otherworldly creature. The plankton species forms blooms on the surface and later sinks to the bottom, where it covers itself in a tiny glass house made out of silicon, Chavez said.

The algae, which Chavez said breaks down and forms most of the petroleum at the bottom of the ocean, doesn’t always produce domoic acid, though scientists don’t know why.

“It may be they produce more when they are under stress,” Chavez said. “That stress may occur because there aren’t enough nutrients produced by upwellings.”

Whatever the cause, a lot of toxin is now being produced. It has accumulated in fish, shellfish and mussels and poisoned the marine mammals, birds and other creatures that eat them. When it is sufficiently dense, it attacks the hippocampus, the brain’s memory center, and can cause memory loss, tremors and convulsions.

The plumes, which one researcher called “toxic plankton soup,” have killed harbor porpoises, fur seals, sea otters and sea lions. Although whales don’t seem to be dying in large numbers, researchers in Monterey Bay have reported strange behavior by humpbacks and other whales.

Trying to find food

California sea lions have suffered the most. More than 1,300 sick or dying juvenile sea lions washed ashore this spring and summer, many convulsing with seizures.

Shawn Johnson, the director of veterinary science for the Marine Mammal Center in the Marin Headlands, believes the pinnipeds couldn’t find enough food early this year, then discovered the anchovy bonanza and are now being hit by domoic acid poisoning.

He said 180 sea lions have been treated for domoic acid poisoning at the clinic. Recent studies have shown that the toxin can even affect the fetuses of pregnant animals, which may explain why so many sea lion pups died this year.

“We continue to rescue animals affected by this toxin every day and realize we may continue to see the impacts of this bloom for months to come,” Johnson said. “As ocean conditions continue to deteriorate, this is just one of the many challenges facing marine life.”

The algae isn’t the only plankton bloom forming in the ocean. A couple of months ago, beachgoers began noticing a brilliant powder-blue tint in the water along the Monterey Bay shoreline. It turned out to be a different type of bloom, which, fortunately, did not create domoic acid. The chalky blue bloom also formed in the Santa Barbara Channel.

“That’s never been seen before,” said Kudela of UC Santa Cruz.

The human toll, so far, has been a loss of livelihood for crabbers and a hit to the holiday tradition of slurping up fresh local crab. Unanswered yet is the cost to life as we know it.

“My hunch is that this kind of variation is the new normal,” Palumbi said. “Because of climate change, the planet is beginning to have stronger weather patterns. All of those things feed into the coastal ocean.”

Peter Fimrite and Kurtis Alexander are San Francisco Chronicle staff writers. E-mail: pfimrite@sfchronicle.com, kalexander@sfchronicle.com Twitter: @pfimrite, @kurtisalexander