A Disease Outbreak in California Has Killed an Estimated 40,000 Birds

Avian botulism is a regular issue at the sprawling wetlands of the Klamath Basin Wildlife Refuges, but in a dry and hot year, it's gotten out of control.

First, an infected bird may lose the ability to walk. Its wings often go next. Finally, its neck goes limp and it drowns. 

This is the sad scene that Caroline Brady, a biologist with the California Waterfowl Association, has observed often this summer. As wildfires burn across the state, temperatures hit record highs, and communities cope with the COVID-19 crisis, she is helping respond to a different disaster: the worst avian botulism outbreak that anyone can remember at the Klamath Basin National Wildlife Refuge Complex.

There, thousands of acres of wetland and marsh that should be rich and verdant havens for millions of migrating waterfowl and shorebirds have become a wasteland of dried-up mud ponds strewn with dead ducks, geese, and other victims of avian botulism. Caused by toxin-producing bacteria, the disease—which is different than the botulism that can infect canned foods—tends to affect wetlands lacking flowing water that is cool, clean, and aerated. Thanks to drought and limited water deliveries, that's exactly what's missing this summer from much of the refuge. 

To make a bad situation worse, a wildfire storm stalled the botulism response effort. Because firefighting helicopters were scooping water from the refuge to dump on the nearby Caldwell fire, refuge staff were barred from entering even as the disease began to spread. “The disease outbreak had two weeks to fester before anyone was allowed to go in at all,” Brady explains.    

Avian botulism is a regular problem of the Klamath system, which comprises six refuges managed by the U.S. Fish and Wildlife Service. A local wildlife care center handled 494 sick birds in 2018 and 233 last year, according to January Bill, founder of the organization Bird Ally X, which runs the refuge’s so-called “Duck Hospital.” But this summer, between mid-July and early September, her facility had received more than 2,750 birds of several dozen species, including Mallard, Green-winged Teal, Gadwall, Northern Pintail and Northern Shoveler. “So, this year is out of control,” she says.

Bill and her team, working in the makeshift field hospital of PVC-framed tents and shallow swimming pools for the birds, have successfully rehabilitated at least 90 percent of their patients and returned them to the wild in botulism-free parts of the refuge. However, the death toll of both waterfowl and shorebirds that don’t make it to the facility is soaring off the charts. Field surveyors have collected about 20,000 dead birds, and they guess at least twice that many have perished.

“Back in the tule reeds, there’s sometimes 10 dead birds all on top of each other,” says Brady, who has personally collected several thousand birds since July. Removing the carcasses is important; if left in place, they quickly produce fly larvae which carry the disease and can spread it to other birds that eat the small worms. The disease thrives in warm temperatures, and refuge managers don’t expect it to disappear until autumn brings subfreezing nighttime lows.

The disaster comes after a dry spring and summer and highlights challenges in sustainably and equitably using the Klamath River’s water. Fish, birds and other wildlife depend on the resource. So do thousands of local farmers, who grow crops like potatoes, horseradish, hay, and barley.

To provide water for these users, the U.S. Bureau of Reclamation releases flows from southern Oregon’s Upper Klamath Lake, a natural waterway that serves as the basin’s major holding pond. The agency also must retain enough water in the lake to support two species of endangered suckers. This arrangement, Bureau critics argue, hasn’t helped the fish much, and it has many stakeholders feeling shortchanged. In the lower reaches of the watershed, salmon runs have dwindled in part for lack of water, creating dissent among tribal communities and fishing interests. Farmers often want more water, too. In late spring, Klamath Basin growers staged a protest of the Bureau’s plans, announced in April, to reduce agricultural allocations.

But, as in many river basins in the arid West, the Klamath’s water has been overallocated to users, leaving insufficient flows for the basin’s aquatic ecosystems. Climate change, which is worsening drought conditions and diminishing the mountain snowpack that feeds the Klamath’s tributaries, is likely to aggravate the situation.  

Amid these challenges, birds are also having a tough time. The Klamath’s water allocation system places the basin’s refuges last in line to receive flows, which can magnify impacts in dry years like 2020. This summer, the shrinkage of the refuge’s wetlands has forced flocks of passing birds to aggregate tightly in warm stagnant water—perfect conditions for a botulism outbreak.

To try and stave off disaster, the Bureau of Reclamation in August released an emergency delivery of 4,000 acre-feet of water, following a 4,600-acre-foot release in July, according to Mary Lee Knecht, a public affairs officer with the agency. It wasn’t enough, though, and as the crisis escalated in early September, the Bureau announced it would release another shot of 5,400 acre-feet water for the refuge. All together, the releases were but a trifle in the grand scheme of Klamath's water equation. Farmers, for instance, are receiving 147,000 acre-feet this year.

At the U.S. Fish and Wildlife Service, Greg Austin, the manager of the Klamath Basin refuge complex, said in an email that he and his agency “appreciate every drop of water that [the Bureau of] Reclamation can make available.” The water, he explains, will help keep portions of the refuge wet for a few more weeks as they wait for freezing temperatures to halt the disease’s life cycle.  

Meghan Hertel, Audubon California’s director of land and water conservation, visited the plague-stricken refuge in late August, when daytime temperatures peaked around 100 degrees. “It was almost totally dry out there,” she says. “There were a few waterholes crammed with birds.”

Hertel and colleagues have been advocating for allowing more water onto important bird refuges for years, both here in the Klamath system and farther south, in the San Joaquin Valley, where refuges are chronically shortchanged the water they’re supposed to receive. As droughts, heat waves, and a growing human population add extra strain to water-dependent ecosystems like the Klamath Basin’s wetlands, Hertel worries that, unless water allocation policies change, crises like the one now affecting the Klamath refuge will recur with greater frequency and intensity.

“This die-off should be a wakeup call for all the local stakeholders to sit down and think about how we can get more water out to the refuges,” she says. “Putting water out on this landscape is not wasting water.”