A Mysterious Salmon-Killing Affliction is a Mystery No More

Scientists have conclusively identified the cause of a lethal vitamin deficiency that is driving the demise of one of California’s unique salmon populations. In a recent paper, a team of 37 biologists, physiologists, and fisheries experts show that a severe, widespread vitamin B1 deficiency plaguing the winter run of Sacramento River chinook (Oncorhynchus tshawytscha) is linked to an extreme dietary imbalance caused by the spread of northern anchovy (Engraulis mordax) up the coast.

Historically, some 200,000 winter-run chinook returned each year to spawn in the Sacramento River. Already stressed by rising temperatures in a river divided by dams and overdrawn by farmers, this federally-endangered salmon population has been listed as endangered under the U.S. Endangered Species Act since 1994, and is bolstered by hatchery-raised fish. Now, with as few as one thousand spawners returning to California’s Central Valley each year, the added strain of severe vitamin deficiency could drive the population extinct.

In early 2020, as the onset of the global COVID-19 pandemic disrupted life on land, managers in salmon hatcheries across California’s Central Valley were faced with the arrival of a different affliction. Hatchery workers were reporting juvenile fish, or fry, swimming in erratic, corkscrew patterns—a characteristic reaction of fish to a vitamin B1 deficiency. They were also suffering a soaring death rate.

From 2021 through 2024, says Nathan Mantua, a researcher with the National Oceanic and Atmospheric Administration (NOAA) Southwest Fisheries Science Center in Santa Cruz, California, roughly 40 to 50 percent of the salmon fry may have died. That’s according to estimates based on modeling. He added that in 2025 about 36 percent of winter-run fry may have died from their vitamin deficiency.

Also known as thiamine, vitamin B1 is essential to cellular-level metabolic processes and is a vital building block of life. Without enough of it, animals suffer neurological disorders, reproductive failure, and eventually death. And for a range of suspected reasons, thiamine deficiency is an emerging problem in aquatic and marine ecosystems across much of the world. The problem has been especially apparent in fish, mussels, and birds in North America’s Great Lakes and in the waters of northern Europe. In some of these cases, researchers have been unable to explain the cause of the deficiency.

Now, for California’s Sacramento River winter-run chinook, at least, scientists know what’s going wrong—and it has everything to do with northern anchovy. 

Rich in vital fats, protein, and calories, northern anchovies seem like a fine meal. But these fish also contain high concentrations of a uniquely problematic enzyme called thiaminase. Scientists believe that in their own bodies, fish may use thiaminase to help synthesize thiamine. However, when a predatory fish eats an animal rich in thiaminase, the enzyme enters the predator’s digestive tract where it destroys thiamine before the critical vitamin can be absorbed by its body. For salmon eating an anchovy-centric diet high in thiaminase, this process can lead to severe thiamine deficiency.

Though winter-run chinook return to the Sacramento River each winter and spring, the animals spend one to three years before that feeding in the open ocean along several hundred kilometers of the northern California coast, mostly between Monterey and San Francisco.

Before 2014 or so, Sacramento River chinook dining in the Pacific would gorge themselves on a diverse diet of forage fish. But from 2014 to 2021, the population of northern anchovy in their feeding grounds surged. Though they can’t say exactly why, Mantua and his colleagues write that it likely has to do with changes that are taking place “closer to the base of the food chain—perhaps driven by physical or chemical changes in the California Current Ecosystem.” At the same time, Mantua and his coauthors found, species that young salmon would otherwise eat—including krill, squid, and rockfish—declined in the same region.

As the proportion of northern anchovies in the salmons’ diets increased, so too did the problems. Notably, this thiamine deficiency can be passed down to a salmon’s offspring, which is how it winds up in newborn fish. 

Over the past several years, as Mantua and his colleagues pieced together the puzzle of California’s thiamine-deficient chinook, state and federal hatchery managers developed a way to treat the condition. After they capture adult fish from a nearby river, but before they collect the fish’s sperm and eggs and mix them in incubation trays, they inject females with thiamine, which prevents the problem from spreading to the next generation.

Though this intervention is effective, Mantua and his team warn that it comes with the risk that it could disrupt potential evolutionary responses by the chinook to persistently low thiamine levels. And, of course, these injections can generally only be given to fish that have been captured and delivered to the hatchery; chinook that carry out natural spawning in the Sacramento River go untreated. For the offspring of these natural spawners, thiamine deficiency poses “a huge bottleneck” against survival, Mantua says. 

Better than thiamine treatments, Mantua says, would be to help diversify the food web by rebuilding populations of less-troublesome prey species like rockfish, Dungeness crab, and Pacific herring. Mantua says observations from as far back as the 1950s show herring were a key food source for winter-run chinook. So helping these fish recover by tackling issues such as water pollution, overfishing, and the loss of shallow-water eelgrass beds and other herring spawning sites could in turn elevate salmon numbers.

“Herring would be a great vitamin pill,” Mantua says. “If there were a lot of herring out there, would the [salmon] diversify their diet?” he wonders. “Would they get better nutrition? Would they be relieved of this?”

The problem is not limited to California’s salmon. Scientists are investigating the possibility that thiamine deficiency is driving chinook declines farther north in British Columbia’s Fraser River and in the Yukon River, which wanders through the Yukon and Alaska before emptying into the Bering Sea. In the Yukon River, scientists measuring thiamine levels in salmon eggs showed concentrations low enough to kill newborn fish. But unlike farther south, says Cody Pinger, an Alaska-based chemist with NOAA Fisheries who has been studying thiamine deficiency in the Yukon River since 2022, “there is no smoking gun like anchovies.” 

“We don’t see the lack of diversity in the food web like they see in California, where they’re seeing salmon packed with one thing,” Pinger says.

Across the planet, animals are suffering a surprising and severe lack of vitamin B1. For many wild populations, scientists are just beginning to understand what is at the root of the problem. Now, for some of California’s salmon, at least, we know what’s gone wrong. The question now is what to do about it.