Lethal cyanobacteria are creeping into rivers—no one knows exactly why

In the clear shallows of Utah’s Virgin River, a slimy brown glob clings to the streambed. Hannah Bonner stands shin-deep in the water, eyeing the goo. It looks like Microcoleus, a toxic genus of cyanobacteria that was first detected in the river four years ago. Microcoleus doesn’t pose much risk underwater. Occasionally, though, a clump gets dislodged and floats to the surface, where a dog or child might eat it. Ingesting even a tablespoon can deliver enough neurotoxin to kill a toddler.

Researcher Hannah Bonner conducts a visual monitoring survey of benthic cyanobacteria in North Creek, a tributary of Utah’s Virgin River. Image credit: Emily Butko (photographer).

Bonner, an ecologist with the state’s division of water quality, hikes the rocky banks of the Virgin River regularly, surveying the riverbed for toxic cyanobacterial mats. When she finds a big one, Bonner asks any downstream waders to get out of the river, then walks over and stomps on the goo. Her heavy boots dislodge the cyanobacteria and break open its cells, releasing toxins and tissue into the water. Bonner dips a 5-gallon bucket into the churning soup and collects a sample, which she sends out to be tested for concentrations of several toxins, the deadliest of which is anatoxin-a. The method mimics the worst-case exposure scenario, Bonner explains—a kid splashing and playing on the riverbank disturbs an area of mat and accidentally takes a drink.

That worst-case scenario hasn’t happened yet. But in Utah and other states, managers are worried, as detections of toxic cyanobacteria continue to rise. In California, the Santa Rosa regional water board has reported growing concerns along the Russian, Snake, and Eel rivers since 2015, with incidents, most often dog deaths, as far back as the early 2000s. At least 19 nations worldwide now report at least one detection (1).

What’s odd is that Microcoleus and other toxic river cyanobacteria are not turning up in polluted waterways, notes ecologist Joanna Blaszczak at the University of Nevada, Reno. Indeed, the reasons for the uptick in sightings are still a matter of some debate—and concern.

A Tragic Mystery

Utah has been monitoring Microcoleus in the Virgin River monthly since 2020, when a puppy died over July 4th weekend after snapping at floating cyanobacteria along a riverside trail in Zion National Park. The incident caught the state by surprise. “It wasn’t something we were even worried about or thinking about,” Bonner says. Zion attracts more than 5 million visitors a year—many of whom come to hike The Narrows, a pinch point in Zion Canyon where visitors wade in the water—so there was immediate concern that other families might be at risk.

The Park Service and Utah Department of Environmental Quality quickly mobilized. They collected toxin samples and surveyed for dangerous cyanobacteria in popular areas of the park. Three tributaries, they found, were lined with mats of Microcoleus and several other toxic genera. Today, Zion National Park and an interagency collaborative team including the Utah Division of Water Quality and the recreational water program continue to monitor the Virgin River monthly, surveying the riverbed for potentially toxic cyanobacterial mats. Laminated paper signs are mounted at popular river access points, warning swimmers not to dunk their heads, drink the water, or let their dogs splash. When toxin concentrations are high, additional signage warns visitors not to touch the water at all.

Most well-studied cyanobacterial species drift as plankton in lakes and estuaries, where populations typically explode in response to nitrogen and phosphorus runoff from agriculture, Blaszczak explains (2). But river-bottom species, rather than drifting in dirty water, hide in plain sight, clinging to rocks and cobbles in sparkling clean, nutrient-poor ecosystems. And they don’t release their toxins unless disturbed. Part of what makes benthic river cyanobacteria so dangerous, Blaszczak says, is that they lurk in the most inviting places to swim or fill a water bottle. And no portable backpacking water filter has been shown to remove cyanobacterial toxins from a thermos of creek water.

In California, Oregon, Utah, Kansas, and Virginia, there’s growing vigilance for Microcoleus and other dangerous river bottom-dwellers. What researchers don’t yet know is how to forecast that a bloom is coming. Blaszczak is now leading research on the South Fork of California’s Eel River, searching for predictive factors of population booms. The goal is to post warning signs before toxin loads are high. One thing’s clear, Blaszczak says: The risk of toxic mats peaks in late summer to early fall, at least in Mediterranean climates. But so far, she says, “there isn’t conclusive research on a certain individual factor that causes their growth.”

While three greenish strains of Microcoleus (Left) are nontoxic, the others produce anatoxin and dihydroanatoxin and are used in the lab to study growth rates and toxicity over time. Image credit: Rosalina S. Christova (George Mason University, Woodbridge, Virginia).

The Devil You Know

Fifteen years before the incident at Zion, New Zealand faced a similar crisis. At least five dogs died while walking along the Hutt River on the lower North Island (3). Owners saw their pets “dying suddenly, frothing at the mouth and experiencing paralysis,” recalls Susie Wood, a freshwater scientist at the Cawthron Institute, New Zealand’s largest independent science organization.

Veterinary necropsies ruled out an attack on the pets—for example, with rat poison. “So we started looking in the river,” Wood says. Working with local authorities, her lab surveyed the Hutt in the days after several of the deaths and found rafts of cyanobacteria lumped at the river’s edge. The rafts had a musty smell that attracted animals. Back in her lab, Wood poked through stomach contents from the dogs and found the telltale hair-like filaments of cyanobacteria. Samples from the dogs and from the river contained the same bacteria, and both tested positive for anatoxin-a.

Anatoxin-a is a fast-acting small molecule that causes sudden death as the toxin travels directly from the stomach into the bloodstream, explains César Mattei, a toxicologist at the University of Angers, in France. The toxin flows through the body, attacking the muscular and nervous systems by outcompeting acetylcholine to bind that neurotransmitter’s normal receptor molecule (4). Nerves in the muscles become overstimulated, Mattei adds, causing paralysis and eventually stopping the heart and lungs. A handful of cyanobacterial species are known to produce anatoxin-a. And while there is no US national database recording when and where incidents occur, anatoxin-producing species may turn up in freshwater or saltwater, as well as in hot springs (5).

Nobody had really studied river cyanobacteria before the incidents in New Zealand in 2005. The literature consisted of three or four case studies, including one dog death in Scotland (6). Ecologists identified the organism as belonging to the clade Phormidium (a designation that’s since been reclassified into the genus Microcoleus). But other than that, “there was very little guidance internationally for us to draw on,” Wood says.

To understand why mats were forming, Wood’s lab began a series of field studies around New Zealand, comparing the water quality of rivers with and without benthic cyanobacteria. These studies have since identified that Microcoleus generally blooms in clean water with low phosphorus and slightly elevated nitrogen (7). How mats survive in relatively nutrient-poor conditions has been something of a mystery, Wood says. But cyanobacteria have been evolving for some 3.8 billion years—long enough that plenty of cyanobacterial species have adapted to extremes, including hot springs and Antarctic ice (8).

Genomic analyses and lab cultures are beginning to provide hints to at least one way that benthic river cyanobacteria are surviving: The mats are communities of multiple bacterial and algal species, each contributing essential nutrients to their microhabitat, “almost like microbial cities,” Wood says. Essential nutrients become concentrated inside these tiny cities, at high levels relative to the outside water (9, 10).

New Zealand still has one or two dog deaths a year, but the public is now much more aware of the risk, Wood notes. Signs along the Hutt and other rivers warn of toxic cyanobacteria, though mats are patchy and only occasionally wash ashore. Hundreds of rivers worldwide have experienced similar explosions of benthic bacteria recently, Wood says, and many places are caught by surprise. To prevent future tragedies, she’s eager to better understand how to predict where riverbed cyanobacteria will explode next.

A Microcoleus mat grows over a rock in California’s Eel River watershed. The trapped bubbles, a product of oxygen-producing photosynthesis, and veiny appearance are telltale signs of this cyanobacteria. Image credit: Keith Bouma-Gregson (University of California, Berkeley).

Toxic Insights

Sunken water sensors, each the size and shape of a flashlight and mounted to a cinderblock about 6 inches up off the bottom, may offer a sort of crystal ball to foresee these blooms. Blaszczak deployed several such sensors in the South Fork of California’s Eel River, as well as in the Salmon and Russian rivers in 2022 and 2023, to passively monitor changes in dissolved oxygen and temperature in the water. Twice a month during the field season, she waded into the rivers to download sensor data and to scoop up samples of any benthic cyanobacteria, which were tested for toxin concentration. Blaszczak is capitalizing on those data to model localized benthic cyanobacterial hotspots. The dissolved oxygen and temperature that these sensors track are two of many variables (including light, streamflow, and nutrient concentration) known to affect the photosynthetic productivity of rivers.

Algae and aquatic plants, not cyanobacteria, do most of the photosynthesizing in rivers. The question is whether cyanobacterial population expansion follows growth trends in the community, or if it deviates in some predictable way, Blaszczak says. Preliminary results suggest that mat growth and toxin loads peak a few weeks after photosynthesis. Data collection will continue for at least another year, and Blaszczak estimates at least another decade before the field has full forecasting models.

“The ultimate goal is to understand and predict what controls the magnitude and timing of the toxin production in these mats, as well as where they occur.”

—Joanna Blaszczak

In the meantime, scientists are scratching their heads, wondering why encounters with riverbed cyanobacteria are on the rise. Are these bacteria new to certain rivers, more abundant than they were in the past, or simply becoming easier to detect?

Wood, for one, thinks the cyanobacteria have always been there, but changes in the rivers are boosting the bacteria’s growth. While the mats thrive in clean, unpolluted habitats, studies in New Zealand suggest that they respond well to sediment inputs, especially near development sites (11). “Because of land-use change, we’re seeing a real increase in sediment in our rivers, and so a real increase in the problem,” Wood says. Downwind of clearcutting forestry and farms, fine soil rushes off the land and into waterways. That small amount of sediment is generally rich in nutrients, she says, and, anecdotally, seems to trigger blooms. “These blooms tend to occur in rivers with very low phosphorus and slightly elevated nitrogen, but still extremely good water quality,” Wood explains. A slight uptick in nutrients from agricultural and urban runoff may be enough to help mats establish.

Keith Bouma-Gregson, a research biologist with the US Geological Survey in Sacramento, California, led one of the earliest genomic analyses of riverbed cyanobacteria in 2019. He scooped dozens of mucilaginous samples out of the Eel River and sequenced them. “There wasn’t that much diversity,” Bouma-Gregson says. He identified just four species, all in the genus Microcoleus, and all closely related to species in New Zealand (12). The genetic similarity hints that geographically distant species may have occupied the same rivers beginning millions of years ago when those land masses were connected.

More recent dispersal is also a possibility, Bouma-Gregson says, but how recent is hard to say. The cyanobacteria could have crossed the Pacific from New Zealand to California, or vice versa, a few thousand years ago—for example, on the foot of a pan-Pacific migrating bird. Or the cyanobacteria could have hitched a ride on some fly fisherman’s waders on a return trip from New Zealand in the last couple of decades. “We don’t have enough monitoring data and documentations to confidently say that these [cyanobacteria] have ‘invaded,’” Bouma-Gregson says. Most likely, he says, the cyanobacteria have been around, but then something changed in the environment to drive the uptick in growth. “For example, as summers are warming up and winters are getting milder,” he explains, “we might see it in new places within a watershed.”

Research technician Taryn Elliott assesses the percent cover of benthic cyanobacterial mats on the south fork of the Eel River, using a bucket with a clear Plexiglas bottom to peer at the riverbed. Image credit: Joanna Blaszczak (University of Nevada, Reno).

Warning Signs

Although predicting river-bottom blooms isn’t yet possible, the California Water Board maintains a public map, available online, with a pin in each location tested for benthic cyanobacteria in the calendar year. There’s a hotline for the public to report concerns about any stretch of river. Managers drive out to reported sites, visually inspect the river for any cyanobacteria, collect samples if they can, and send them out for toxin testing, says Rich Fadness, coordinator of California’s north coast Surface Water Ambient Monitoring Program, which keeps an eye on watersheds in the far north of the state. If the managers detect toxins, the Water Board alerts the county’s health department and provides free PDF templates of warning signs that the county can print and post.

Counties’ limited funding could go further—for instance, toward monthly monitoring at high-risk sites—if managers had models or other early warning signals to predict where incidents are likely to spread. The “ideal,” Blaszczak says, would be using sensor data and other environmental information to predict when mats will spread and toxins will spike, “and then notify the folks responsible for posting signage.”

“In the rivers, we’re still in the stage of learning and developing capacity to monitor,” says Rosalina Stancheva Christova, a freshwater ecologist specializing in benthic algae at George Mason University in Woodbridge, Virginia. “We’re still collecting data to be able to predict the blooms.”

Christova, the first to culture toxin-producing Microcoleus in California (13, 14), is part of an NSF-funded project that began in January 2023 in collaboration with Blaszczak and others. They’re collecting information about Microcoleus biology, physiology, genetics, and ecology. “We are trying to understand what triggers the toxin production, what controls the magnitude of the toxin production, and we’re getting at that from a physiological, genetic, and ecological perspective,” Blaszczak says.

One goal: To expand Blaszczak’s existing time-series dataset tracking the cadence and magnitude of riverbed cyanobacterial populations in California, compared to temperature, streamflow, and other environmental variables. The researchers are assessing RNA and DNA data from mat samples taken near the sensor sites to understand what’s happening inside the mats themselves—for example, how toxin concentrations respond to nitrogen loads in the water.

“The ultimate goal is to understand and predict what controls the magnitude and timing of the toxin production in these mats, as well as where they occur,” Blaszczak says, alluding to the project, which will collect data until at least 2026. “We need an understanding of the true underlying triggers that cause this toxin production.”