A fish-kill mystery in a remote Alaska village takes a toxic turn

A foul chartreuse sea of cyanobacteria drove researchers to learn more about Arctic water quality.
Yellow-green cyanobacteria bloom in Upper Klamath Lake, Oregon. Events like these can cause mass fish dieoffs.
Cyanobacteria, sometimes also called blue-green algae, are fairly common in lakes, such as in this image taken at Upper Klamath Lake, Oregon, but they can also grow in brackish water and the ocean. Photo by Christopher Boswell/Alamy Stock Photo

This article was originally featured on Hakai Magazine, an online publication about science and society in coastal ecosystems. Read more stories like this at hakaimagazine.com.

Dead fish were everywhere, speckling the beach near town and extending onto the surrounding coastline. The sheer magnitude of the October 2021 die-off, when hundreds, possibly thousands, of herring washed up, is what sticks in the minds of the residents of Kotzebue, Alaska. Fish were “literally all over the beaches,” says Bob Schaeffer, a fisherman and elder from the Qikiqtaġruŋmiut tribe.

Despite the dramatic deaths, there was no apparent culprit. “We have no idea what caused it,” says Alex Whiting, the environmental program director for the Native Village of Kotzebue. He wonders if the die-off was a symptom of a problem he’s had his eye on for the past 15 years: blooms of toxic cyanobacteria, sometimes called blue-green algae, that have become increasingly noticeable in the waters around this remote Alaska town.

Kotzebue sits about 40 kilometers north of the Arctic Circle, on Alaska’s western coastline. Before the Russian explorer Otto von Kotzebue had his name attached to the place in the 1800s, the region was called Qikiqtaġruk, meaning “place that is almost an island.” One side of the two-kilometer-long settlement is bordered by Kotzebue Sound, an offshoot of the Chukchi Sea, and the other by a lagoon. Planes, boats, and four-wheelers are the main modes of transportation. The only road out of town simply loops around the lagoon before heading back in.

In the middle of town, the Alaska Commercial Company sells food that’s popular in the lower 48—from cereal to apples to two-bite brownies—but the ocean is the real grocery store for many people in town. Alaska Natives, who make up about three-quarters of Kotzebue’s population, pull hundreds of kilograms of food out of the sea every year.

“We’re ocean people,” Schaeffer tells me. The two of us are crammed into the tiny cabin of Schaeffer’s fishing boat in the just-light hours of a drizzly September 2022 morning. We’re motoring toward a water-monitoring device that’s been moored in Kotzebue Sound all summer. On the bow, Ajit Subramaniam, a microbial oceanographer from Columbia University, New York, Whiting, and Schaeffer’s son Vince have their noses tucked into upturned collars to shield against the cold rain. We’re all there to collect a summer’s worth of information about cyanobacteria that might be poisoning the fish Schaeffer and many others depend on.


Huge colonies of algae are nothing new, and they’re often beneficial. In the spring, for example, increased light and nutrient levels cause phytoplankton to bloom, creating a microbial soup that feeds fish and invertebrates. But unlike many forms of algae, cyanobacteria can be dangerous. Some species can produce cyanotoxins that cause liver or neurological damage, and perhaps even cancer, in humans and other animals.

Many communities have fallen foul of cyanobacteria. Although many cyanobacteria can survive in the marine environment, freshwater blooms tend to garner more attention, and their effects can spread to brackish environments when streams and rivers carry them into the sea. In East Africa, for example, blooms in Lake Victoria are blamed for massive fish kills. People can also suffer: in an extreme case in 1996, 26 patients died after receiving treatment at a Brazilian hemodialysis center, and an investigation found cyanotoxins in the clinic’s water supply. More often, people who are exposed experience fevers, headaches, or vomiting.

When phytoplankton blooms decompose, whole ecosystems can take a hit. Rotting cyanobacteria rob the waters of oxygen, suffocating fish and other marine life. In the brackish waters of the Baltic Sea, cyanobacterial blooms contribute to deoxygenation of the deep water and harm the cod industry.

Dark green cyanobacteria in the ocean, seen from NASA satellite
With the right combination of nutrients, light, and temperature, cyanobacteria can reproduce quickly or “bloom.” NASA

As climate change reshapes the Arctic, nobody knows how—or if—cyanotoxins will affect Alaskan people and wildlife. “I try not to be alarmist,” says Thomas Farrugia, coordinator of the Alaska Harmful Algal Bloom Network, which researches, monitors, and raises awareness of harmful algal blooms around the state. “But it is something that we, I think, are just not quite prepared for right now.” Whiting and Subramaniam want to change that by figuring out why Kotzebue is playing host to cyanobacterial blooms and by creating a rapid response system that could eventually warn locals if their health is at risk.


Whiting’s cyanobacteria story started in 2008. One day while riding his bike home from work, he came across an arresting site: Kotzebue Sound had turned chartreuse, a color unlike anything he thought existed in nature. His first thought was, Where’s this paint coming from?

The story of cyanobacteria on this planet goes back about 1.9 billion years, however. As the first organisms to evolve photosynthesis, they’re often credited with bringing oxygen to Earth’s atmosphere, clearing the path for complex life forms such as ourselves.

Over their long history, cyanobacteria have evolved tricks that let them proliferate wildly when shifts in conditions such as nutrient levels or salinity kill off other microbes. “You can think of them as sort of the weedy species,” says Raphael Kudela, a phytoplankton ecologist at the University of California, Santa Cruz. Most microbes, for example, need a complex form of nitrogen that is sometimes only available in limited quantities to grow and reproduce, but the predominant cyanobacteria in Kotzebue Sound can use a simple form of nitrogen that’s found in virtually limitless quantities in the air.

Cyanotoxins are likely another tool that help cyanobacteria thrive, but researchers aren’t sure exactly how toxins benefit these microbes. Some scientists think they deter organisms that eat cyanobacteria, such as bigger plankton and fish. Hans Paerl, an aquatic ecologist from the University of North Carolina at Chapel Hill, favors another hypothesis: that toxins shield cyanobacteria from the potentially damaging astringent byproducts of photosynthesis.

Around the time when Kotzebue saw its first bloom, scientists were realizing that climate change would likely increase the frequency of cyanobacterial blooms, and what’s more, that blooms could spread from fresh water—long the focus of research—into adjacent brackish water. Kotzebue Sound’s blooms probably form in a nearby lake before flowing into the sea.


The latest science on cyanobacteria, however, had not reached Kotzebue in 2008. Instead, officers from the Alaska Department of Fish and Game tested the chartreuse water for petroleum and its byproducts. The tests came back negative, leaving Whiting stumped. “I had zero idea,” he says. It was biologist Lisa Clough, then from East Carolina University and now with the National Science Foundation, with whom Whiting had previously collaborated, who suggested he consider cyanobacteria. The following year, water sample analysis confirmed she was correct.

In 2017, Subramaniam visited Kotzebue as part of a research team studying sea ice dynamics. When Whiting learned that Subramaniam had a long-standing interest in cyanobacteria, “we just immediately clicked,” Subramaniam says.

Environmental scientists in waterproof gear on a boat full of gear off of Kotzebue, Alaska
Alex Whiting, the environmental program director for the Native Village of Kotzebue, left, and Ajit Subramaniam, a microbial oceanographer from Columbia University, New York, right, prepare water-monitoring equipment for deployment. Photo by Saima Sidik

The 2021 fish kill redoubled Whiting and Subramaniam’s enthusiasm for understanding how Kotzebue Sound’s microbial ecosystem could affect the town. A pathologist found damage to the dead fish’s gills, which may have been caused by the hard, spiky shells of diatoms (a type of algae), but the cause of the fish kill is still unclear. With so many of the town’s residents depending on fish as one of their food sources, that makes Subramaniam nervous. “If we don’t know what killed the fish, then it’s very difficult to address the question of, Is it safe to consume?” he says.

I watch the latest chapter of their collaboration from a crouched position on the deck of Schaeffer’s precipitously swaying fishing boat. Whiting reassures me that the one-piece flotation suit I’m wearing will save my life if I end up in the water, but I’m not keen to test that theory. Instead, I hold onto the boat with one hand and the phone I’m using to record video with the other while Whiting, Subramaniam, and Vince Schaeffer haul up a white-and-yellow contraption they moored in the ocean, rocking the boat in the process. Finally, a metal sphere about the diameter of a hula hoop emerges. From it projects a meter-long tube that contains a cyanobacteria sensor.

The sensor allows Whiting and Subramaniam to overcome a limitation that many researchers face: a cyanobacterial bloom is intense but fleeting, so “if you’re not here at the right time,” Subramaniam explains, “you’re not going to see it.” In contrast to the isolated measurements that researchers often rely on, the sensor had taken a reading every 10 minutes from the time it was deployed in June to this chilly September morning. By measuring levels of a fluorescent compound called phycocyanin, which is found only in cyanobacteria, they hope to correlate these species’ abundance with changes in water qualities such as salinity, temperature, and the presence of other forms of plankton.

Environmental scientists in waterproof gear drop water-monitoring equipment into the waters off Kotzebue, Alaska
Whiting, Subramaniam, and Vince Schaeffer, son of the boat’s captain, Bob Schaeffer, deploy the water-monitoring equipment. Information gathered from the device will help determine the conditions in which cyanobacteria tend to bloom. Photo by Saima Sidik

Researchers are enthusiastic about the work because of its potential to protect the health of Alaskans, and because it could help them understand why blooms occur around the world. “That kind of high resolution is really valuable,” says Malin Olofsson, an aquatic biologist from the Swedish University of Agricultural Sciences, who studies cyanobacteria in the Baltic Sea. By combining phycocyanin measurements with toxin measurements, the scientists hope to provide a more complete picture of the hazards facing Kotzebue, but right now Subramaniam’s priority is to understand which species of cyanobacteria are most common and what’s causing them to bloom.

Farrugia, from the Alaska Harmful Algal Bloom Network, is excited about the possibility of using similar methods in other parts of Alaska to gain an overall view of where and when cyanobacteria are proliferating. Showing that the sensor works in one location “is definitely the first step,” he says.


Understanding the location and potential source of cyanobacterial blooms is only half the battle: the other question is what to do about them. In the Baltic Sea, where fertilizer runoff from industrial agriculture has exacerbated blooms, neighboring countries have put a lot of effort into curtailing that runoff—and with success, Olofsson says. Kotzebue is not in an agricultural area, however, and instead some scientists have hypothesized that thawing permafrost may release nutrients that promote blooms. There’s not much anyone can do to prevent this, short of reversing the climate crisis. Some chemicals, including hydrogen peroxide, show promise as ways to kill cyanobacteria and bring temporary relief from blooms without affecting ecosystems broadly, but so far chemical treatments haven’t provided permanent solutions.

Instead, Whiting is hoping to create a rapid response system so he can notify the town if a bloom is turning water and food toxic. But this will require building up Kotzebue’s research infrastructure. At the moment, Subramaniam prepares samples in the kitchen at the Selawik National Wildlife Refuge’s office, then sends them across the country to researchers, who can take days, sometimes even months, to analyze them. To make the work safer and faster, Whiting and Subramaniam are applying for funding to set up a lab in Kotzebue and possibly hire a technician who can process samples in-house. Getting a lab is “probably the best thing that could happen up here,” says Schaeffer. Subramaniam is hopeful that their efforts will pay off within the next year.

In the meantime, interest in cyanobacterial blooms is also popping up in other regions of Alaska. Emma Pate, the training coordinator and environmental planner for the Norton Sound Health Corporation, started a monitoring program after members of local tribes noticed increased numbers of algae in rivers and streams. In Utqiaġvik, on Alaska’s northern coast, locals have also started sampling for cyanobacteria, Farrugia says.

Whiting sees this work as filling a critical hole in Alaskans’ understanding of water quality. Regulatory agencies have yet to devise systems to protect Alaskans from the potential threat posed by cyanobacteria, so “somebody needs to do something,” he says. “We can’t all just be bumbling around in the dark waiting for a bunch of people to die.” Perhaps this sense of self-sufficiency, which has let Arctic people thrive on the frozen tundra for millennia, will once again get the job done.

The reporting for this article was partially funded by the Council for the Advancement of Science Writing Taylor/Blakeslee Mentored Science Journalism Project Fellowship.