For decades, the unwritten motto at shellfish hatcheries in the Pacific Northwest was “Better oysters through science.”

Scientists mated the heartiest, fastest-growing stock to produce plumper, sweeter oysters for slurping raw on the half-shell or frying up to dip in tangy sauces.

They probed the genetic code to select for the most desirable traits of the Pacific oyster, an import from Japan that now weighs in, pound for pound, as the No. 1 aquacultured crop in the world: 4.5 million tons a year (shells included) valued at $3 billion.

They even bred out sexual organs that at certain times of the year can take up more than a third of an oyster’s body weight and give it a soft, mushy texture.

With selective breeding and genetic fingerprinting, they were on their way to developing a super oyster resistant to summer mortality, keeping one step ahead of a warmer, more polluted planet. Or so they thought.

Suddenly, oyster research bogged down as a riotous bloom of bacteria went on a West Coast killing spree, wiping out billions of oyster larvae.

The outbreak first shut down an oyster brood stock program run by Oregon State University in Newport, Ore., in 2005. “All we saw was our larvae were dying,” said fisheries professor Chris Langdon, “and we couldn’t put our finger on why.”

Then the microscopic culprit overran commercial hatcheries in Washington and Oregon, crippling production over the last couple of years and causing a shortage of oyster “seed” needed to replant tideland farms from Southern California to Canada.

“It’s pretty scary,” said Sue Cudd, owner of Whiskey Creek Shellfish Hatchery in Netarts, Ore. The hatchery, she said, has been drowning in costs and failing to produce sufficient oyster larvae for West Coast shellfish farmers. “We almost decided to close, and people panicked. I realized if I go out of business, I take a lot of people with me.”

Science has identified the culprit, a strain of bacteria called Vibrio tubiashii, which is harmless to humans but fatal to baby oysters. It attacks them in their vulnerable, free-swimming larval stage before they settle to the seafloor, latch onto rocks or other oysters and grow thick shells.

The Vibrio blooms appear to be linked to warmer waters in estuaries and the oxygen-starved “dead zones” that have showed up this decade off the coast of Oregon and Washington, researchers said.

These low-oxygen waters correlate with stronger winds coming from a warming planet.

Scientists note that Vibrio tubiashii has an advantage over other microscopic life in the sea. This bacterium thrives in oxygen-starved dead zones, feasting on decaying plant and animal matter littering the seafloor. And when brought to the surface with water welling up from the deep, it can switch survival strategies to flourish in warm, well-oxygenated waters.

Researchers were not surprised to find this type of bacteria in seawater but were stunned that it had become so dominant over other microbes: It was nearly a pure concentration of this one bacteria, one that happens to be deadly to oyster larvae.

“It seems to be logical that the dead zone is playing a role,” said Ralph Elston, who runs a veterinary medical practice in Sequim, Wash., that offers advice to shellfish farmers. “It’s the perfect bacterial setup, and we get these explosive blooms along the coast.”

Edmund Jones removed a pinch of brown silt and smeared it across a glass slide. Tanks of seawater gurgled in the background. A salty tang hung in the moist air.

Jones, who manages Taylor Shellfish Farms’ hatchery here on Dabob Bay, fiddled with a knob, bringing into focus a dozen or more 9-day-old oyster larvae.

He pointed out a few healthy ones, dark round discs scuttling around, propelled by hair-like cilia. Most didn’t move at all. Light shined through them, revealing empty insides. They hadn’t been feeding. If they weren’t dead already, they were dying.

“When your job is to grow larvae and you see that on the screen,” Jones said, “it’s extremely frustrating to see. Unfortunately, what this tells me is we’ll probably be dumping that tank tomorrow.”

That meant jettisoning 30 million larvae.

Failures of this kind have become so regular that Taylor’s hatchery is producing less than a quarter of its capacity, far short of what is needed to reseed its oyster beds or to sell to other shellfish farmers looking to do the same.

The shortage of oyster seed, or “spat,” will have its greatest effect in several years, when oyster beds left fallow would otherwise be ready for harvest. That may set the stage for shortages and economic upheaval in the West Coast’s $110-million-a-year shellfish industry, said Bill Dewey, a division manager at Taylor Shellfish.

“We don’t have the seed to replace these crops you see here,” Dewey said, standing on a Samish Bay tidal flat in hip-waders, watching a work crew fill baskets with 4- and 5-year-old oysters.

Shellfish growers, Dewey said, often provide “the first indication that there’s a problem out there, because the animals we are farming are telling us that.”

What the dead larvae are saying is that something is wrong with coastal waters, he said. “Whether it’s climate change” or something else, he said, “it’s likely something that man has done to our environment that is creating this problem for us.”

Alan Trimble, a researcher at the University of Washington, has noticed similar problems in the wild. Sampling seawater in Willapa Bay, Wash., he found that the oyster and clam larvae had disappeared in the last two years from waters where bacteria counts had been high.

Hatchery operators inadvertently pump in the bacteria along with seawater they use to bathe their infant oysters and grow the green algae used to feed larvae. The microbes even drift in on the sea breeze, launched into the air by bubbles bursting at the ocean’s surface.

The shutdown of Oregon State’s experimental hatchery prompted university officials to develop a multistage filtering system that blasts seawater with ultraviolet light to kill bacteria, skims the harmful bacteria’s lingering toxins and then reinoculates the cleaned water with a healthful balance of microbes.

The Whiskey Creek Hatchery has adopted the same filtering system, which helped revive half of its larvae production. The hatchery run by Taylor Shellfish, the largest grower in the country, is experimenting with similar techniques to get its production going again.

Growers have sought the help of university researchers and asked Congress for emergency funds to look for solutions.

The U.S. Department of Agriculture, which funds the Molluscan Broodstock Program at Oregon State’s hatchery, is exploring microbial warfare.

Gary Richards, a USDA researcher at the University of Delaware, has been screening seawater samples to find a virus, or bacteriophage, that would seek out and destroy Vibrio tubiashii. Marine bacteria often have such natural enemies. An intervention, such as releasing the right “phage,” as they are called, could avoid “an ecological disaster of monumental proportions,” Richards wrote in an e-mail to scientists and hatchery managers.

As filter feeders, shellfish clean seawater of excess algae and nutrients, maintaining healthy coastal waters. When oysters disappear, as they did in the Chesapeake Bay, an estuary’s water can turn murky and foul.

“With the loss of oysters, the water in the Chesapeake became more turbid, restricting light penetration to plants and sea life, and the higher nutrient levels made algal blooms more common,” Richards wrote. “The West Coast needs to avoid this at all cost.”

So scientists like Donal T. Manahan and Dennis Hedgecock at USC, among others, have spent decades hovering over bubbling tanks of oysters to improve on nature. They’ve been selecting stocks with more productive pedigrees that offer the double benefit of cleaning coastal waters and multiplying the bounty of this gastronomic treat.

“Our hybrids do better than wild oysters,” producing two to three times more oyster meat per acre of shellfish beds, Hedgecock said. Yet as the bacterial outbreak reminded them, the first step of any successful breeding program is to make sure oysters don’t die.

The episode has moved disease resistance to the top of the list of characteristics researchers want to tease out of the mollusk’s genetic code, said Langdon, from Oregon State’s hatchery.

“We need to find those oysters that are most resistant to this bacterium,” he said. “This whole problem has created a new target for the selective-breeding program.”

ken.weiss@latimes.com