When normally harmless algae found off the West Coast make a deadly neurotoxin called domoic acid, casualties rocket up the food chain.

Fish and shellfish accumulate the neurotoxin, sickening those who eat them, including birds, marine mammals, and people. High levels of ingestion lead to amnesic shellfish poisoning, a potentially fatal illness causing seizures and short-term memory loss.

During a particularly intense domoic algal bloom in 2015, a sea lion female was found disoriented in Oceanside Harbor with a prematurely born pup. Mother and pup were taken to SeaWorld San Diego. The mother survived being poisoned; the pup did not.

A team led by scientists at UC San Diego’s Scripps Institution of Oceanography and the J. Craig Venter Institute report discovering the genes that causes domoic acid production. Their discovery may help provide early warning of these harmful blooms of algae in the genus Pseudo-nitzschia.


The study was published Thursday in the journal Science. It can be found at j.mp/domoicacid.

Monitoring for the activated genes could provide early warning of incipient algae blooms, said Frances Gulland, senior scientist at The Marine Mammal Center in Sausalito. In 1998, the center discovered the role of domoic acid in poisoning marine mammals.

“We could monitor water samples for domoic acid production by screening for the genes instead of the actual toxin,” said Gulland, who was not involved in the study. “It might be more sensitive and it might also help anticipate when the toxin is going to get produced.”

These harmful algal blooms, unrelated to the so-called “red tides,” have grown more frequent and extensive over the last two decades, Gulland said.


“The big one in 2015 extended from Baja right up to Alaska,” she said. “The earlier ones, 20 years ago, were just off Monterey Bay. So now every summer, all summer along most of the West Coast, there’ll be some bloom somewhere.”

The work builds on a 2011 study that found limited levels of phosphate and increased levels of carbon dioxide induce domoic acid production. That study was led by David Hutchins of the University of Southern California, also a co-author of the new study.

With that knowledge, the research team examined which genes were turned on during production, said Andrew Allen, a study author with joint appointments at Scripps Institution of Oceanography and the J. Craig Venter Institute. The two institutes contributed their respective expertises in marine biology and genomics to crack the code.

Such a genetic test could be done remotely, such as on a buoy or an underwater rover, Gulland said.


“It offers an opportunity to sample offshore and to get more information about what’s happening away from coastal sampling sites,” she said.

“For example, in San Diego, the main sampling is done from Scripps Pier, and that’s a fantastic long-term data series on algal species. But we know nothing about what’s happening 200 miles offshore.”

The work began five years ago, the brainchild of John K. “Patrick” Brunson, a graduate student and one of the study’s lead authors, Allen said.

It was a daunting challenge, he said, because the genetics of these algae are extremely complex.


“He hadn’t been around long enough to know just how hard the problem is,” Allen said. “I warned him, we need to plan the research because a lot of people have tried to tackle domoic acid and not made a lot of progress.”

But Brunson was temperamentally suited to the task because of his interest in medicine, Allen said. And Allen’s USC colleague, Dave Hutchinson, had recently published research on conditions that cause domoic acid production.

“Dave already done those experiments and you know, published this paper just on the physiology and amount of domoic acid,”Allen said. “He had samples in the freezer, you know, from those experiments.

“Dave and I were talking one day and said, maybe we should sequence those samples. We were kind of thinking it was a needle in the haystack.”


They sent Brunson the sequence data, and he went to work.

“He went away for about a month, and sent me an email that said, we’ve really got to talk about this. I think there’s something here,” Allen said.

“I was skeptical and we sat down and looked at it,” Allen said. “Lo and behold, the kinds of genes that we thought should be activated under domoic acid synthesis conditions were much higher than anything else.”

Other study authors included Shaun McKinnie and Bradley Moore of UCSD.


Study funders included the National Science Foundation, the National Institutes of Health, the Gordon and Betty Moore Foundation, and the U.S. Department of Energy.

Related reading

Southern California’s coast emerges as a toxic algae hot spot

Premature sea lion pup born at SeaWorld to rescued mom has died


SeaWorld caring for sea lion pup born to rescued, sickly mother

Sonoma Coast commercial crab season starts

Deaths of dolphins linked to natural neurotoxin

State mussel bans comes early after toxins found


State issues warning on Channel Islands seafood

Red Tides and Domoic Acid Toxicity

Climatic regulation of the neurotoxin domoic acid


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