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While the Caldwell Fire burned at the end of July, another warm weather woe began to manifest just north of Lava Beds National Monument.

Tule Lake National Wildlife Refuge’s main open body of water, Sump 1A, had been exceptionally low for weeks. The hot sun baked the shallow water during the day, and warmer nighttime temperatures ensured it stayed hot. Dormant bacteria awakened on the lake’s fringe wetlands, carrying with them a paralyzing and potentially fatal toxin. Beneath the cover of smoke began the refuge’s worst botulism outbreak in years.


Waterfowl have been hit particularly hard by this year’s botulism outbreak, mostly on Tule Lake. Refuge biologists estimate that approximately 15 percent of the molting birds on the lake have contracted the waterborne illness.

Normally, refuge staff are on botulism alert by July 4, when the peak of summer temperatures begins and they begin to survey all wetland habitat in the Klamath Basin for the disease’s avian victims.

But by the time crews contained the Caldwell Fire and it was safe enough for biologists to take airboats out on Tule Lake in early August, they met an outbreak that had already claimed thousands of victims.

“It blew up really fast,” said refuge biologist John Vradenburg. “I’ve never seen the sump as low as it got down to.”

Botulism is a natural occurrence in most wetland systems, especially those whose environments heat up significantly during the summer. The waterborne outbreaks originate with the bacterium Clostridium botulinum, which lies inactive in wetland soils throughout most of the year.

Once temperatures get hot enough, oxygen concentrations in the water get low enough and aquatic invertebrates begin to die as a result of the harsh conditions, the bacteria begin to go through their life cycle and multiply. They release a highly potent toxin that binds to nerve endings and inhibits muscle movement, effectively paralyzing their victims.


Most birds who have contracted botulism have already died, but those still alive are taken to the duck hospital on Lower Klamath Refuge.

The toxin bioaccumulates in the invertebrates, which are often food for birds. It only takes a single bird to consume a toxin-laced meal and succumb to botulism to start an outbreak. Flies lay eggs on the carcass, and the maggots that hatch from them accumulate the toxin. Other birds consume those maggots for food and ingest the toxin, and a deadly cycle takes off.

This year, with the basin’s refuges receiving little to no water to maintain wetland habitats, a considerable amount of waterfowl set up shop to molt in the open waters of Tule Lake. When birds molt, they’re flightless for at least a month, making it impossible for them to escape the outbreaks on their own.

Vradenburg said shallow water provides the optimal environment for C. botulinum to spread. Because so little water flowed into Tule Lake this summer, much of the sump essentially became one massive mud flat. Combined with the molting waterfowl, it was a perfect storm.

“There’s just a huge area that is ripe for infection right now,” he said.

Typically, botulism appears in hotspots, with a group of sick or dead birds congregated near a couple of rotting carcasses. When biologists first got out onto Tule Lake, they saw one vast array of affected birds. In Vradenburg’s five years working on refuges in the Klamath Basin, he’s never seen anything like this. Some refuge staff who have been there for 20 years or longer agreed.

“All those hotspots are bleeding together,” Vradenburg said. “It’s sort of one big hotspot at this point.”

Tule Lake wasn’t the only refuge touched by botulism. Lower Klamath National Wildlife Refuge had an outbreak on Unit 3, one of its two permanent wetlands, more than a month ago. Staff found one dead bird on July 15. The next day, they found two. The following day, they found seven. Day 4 saw 150 carcasses.

There are only a few ways to manage botulism outbreaks of this magnitude, Vradenburg said. You can flush the area with more water to cool temperatures down and increase oxygen, making it harder for the bacteria to survive. Or you can drain the area entirely. In an exceptionally low water year like 2020, draining Unit 3 was the only option refuge managers had, and it worked.

Every day, biologists pick up sick and dead birds to help contain the spread. So far, they’ve picked up about 16,000 with the outbreak about halfway over. In 2018, which had a considerably sizeable outbreak, they picked up about 10,000 the entire summer.

Vradenburg estimates they’re only able to pick up about half of the total individuals affected by botulism, so this year’s number is likely closer to 30,000. That’s about 15 percent of the total population of molting birds on Sump 1A — and most of them are dead.

For the birds who are still alive when they’re taken onto the airboats, help is luckily available. Each afternoon, staff deliver about 50 of them to the duck hospital on Lower Klamath Refuge, run by nonprofit Bird Ally X. As of August 21, the hospital has treated 1495 patients, mostly waterfowl with some shorebirds sprinkled in. That’s more than double the past two years’ outbreaks combined.

Surrounded by makeshift pools of recovering birds, the haphazard-looking field hospital is set up specifically for treating botulism, and it’s gotten remarkably good at doing so.


The hospital may seem haphazardly set up, with these constructed pools to house the waterfowl, but they're an extremely effective operation.

“This is definitely M.A.S.H.,” said January Bill, who’s part of the hospital’s two-person management duo. They have three interns and a couple of longtime volunteers that come and go. Normally, volunteers are the lifeblood of wildlife rehabilitation, but because of COVID-19, the hospital has to hire more long-term interns to keep the total number of people coming in and out to a minimum.

Despite the skyrocketing cases of botulism this year, the hospital has achieved even more success than in previous responses. About 94 percent of birds that survive their first 24 hours in the hospital make a full recovery, the highest rate yet.


Some birds are so paralyzed from botulism that they can’t feed on their own. Hospital staff help nurse them back to health.

Bill said the hospital focuses on reducing the birds’ stress and providing them the support they need to flush out the toxin on their own. When a patient arrives, they’re given an intake exam, an antitoxin injection, vitamins and fluids to hydrate them and provide basic nutrients. Depending on the severity of their paralysis, birds are sorted into holding boxes based on three stages: Stage 1, for those who can’t escape capture but can still stand up; stage 2, for those who can move their head but not their legs or wings; and stage 3, for birds who are completely paralyzed.

“Some are so flat that you can’t tell whether they’re alive or not without listening with a stethoscope,” Bill said.

In the first 24 hours of care, the hospital’s goal is to get birds eating on their own. Food in the holding boxes is easily accessible: a combination of mealworms and duckweed, a wetland plant naturally found on the refuge. Once they survive to day two and are able to thermoregulate and hold their heads up without help, staff try to get them onto water where they’ll be most comfortable (spending too much time sitting in a dry box can give them bedsore-like lesions) and least stressed. That’s when they move to pools, where they can drink, eat and poop more normally.

On average, Bill said it takes a patient about four days to recover. Hospital staff choose which birds to release back onto the refuge based on their behavior in the pools. After they’re given physical examinations and a federal band that allows biologists to track them, they return to a part of the refuge not experiencing a botulism outbreak.


After a few days of treatment in the duck hospital, patients are released back into the refuge.

Bill has experience caring for birds in the immediate aftermath of oil spills, so the massive influx of patients isn’t too much of a concern. But she’s been running the hospital every day since the outbreak began, and funds that could secure interns and materials to build extra pools are scarce.

“We’re very familiar with how to expand our capacity and work with minimal resources,” she said. Grants from the Klamath Basin Audubon Society have allowed them to purchase incubators for birds that can’t thermoregulate and a computer system that lets them track patients in real time, but the hospital still needs more funding to make space for all the new patients.

Unit 2, Lower Klamath’s last remaining permanent wetland this year, has narrowly escaped a major outbreak, thanks to summer deliveries from the Klamath Project secured through the Bureau of Reclamation and the Drought Response Agencies.

Tule Lake also started receiving water a couple weeks ago, which Vradenburg said will take some time to improve environmental conditions and slow the outbreak. Water has gotten so low that airboats can’t access certain areas of the lake. Until nighttime frost conditions begin to set in sometime during September, botulism will still be a threat on both refuges.

“It’s kind of like a wildfire — right now we’re probably at 10 percent containment,” Vradenburg said. “We’ve got a long road ahead of us.”

Editor's Note: The second part of this story will look at how 2020 water deliveries have helped the refuge.