Beating botulism
How Tule Lake Refuge avoided disaster this summer
by Alex Schwartz, Herald and News 11/16/21

Stakeholders decided they needed to do something to avoid a situation similar to last year, when more than 60,000 molting ducks died of botulism on Tule Lake Refuge. They consolidated water and instituted unprecedented operations, at one point draining an area of open water that hadn’t been dry in millions of years.

“The thought of dealing with another summer like we did last summer, it was terrifying,” said John Vradenburg, supervisory biologist for the Klamath Basin National Wildlife Refuge Complex.

Even after draining Tule Lake’s Sump 1A and putting that water into its smaller Sump 1B, everyone braced for an inevitable outbreak. Evaporation and irrigation diversions began drying up the remaining wetland faster than expected, just as ducks began molting their feathers and losing their ability to fly. Everyone braced for impact.

By late July, the staff of nonprofit Bird Ally X’s Duck Hospital on Lower Klamath Refuge sat on edge, waiting for the inevitable call from refuge biologists that the first botulism patient of the summer had been picked up. January Bill, co-director of the Bird Ally X Botulism Response, said it was a very stressful time.

“I was waiting on pins and needles until night temperatures started dipping,” Bill said. “If one bird is rescued, we need to be available to drive to the refuge within hours to provide treatment. I didn’t let my guard down.”

But as summer rolled on, Bill and her team continued to wait in suspense, and refuge crews still hadn’t picked up any sick birds. By October 8, once nighttime temperatures had dropped low enough to neutralize the botulism bacteria and the fall migration had begun, Vradenburg gave the OK to close the duck hospital for the season. They never had to treat a single patient.

“We didn’t receive any birds this year,” Bill said.

Beating botulism

Astonishingly, a botulism outbreak didn’t occur in the Klamath Basin despite abysmal conditions on the refuges in 2021. Luck certainly played into it, but the adaptive management employed by stakeholders could prove a blueprint for mitigating disease outbreaks in the future.

For Vradenburg, draining Sump 1A in May and June steered Tule Lake away from a repeat of last summer’s massive outbreak, which was mainly concentrated there.

Without water deliveries from the Klamath Project, the 9,000-acre sump would have evaporated to mud puddle in no time, attracting thousands of birds who would contract botulism released from the lakebed. And because it would’ve been so shallow, refuge crews wouldn’t be able to access large swaths of the sump to collect sick and dead birds and contain the outbreak.

By putting the water contained in Sump 1A into the comparatively lush Sump 1B, stakeholders gave the smaller wetland a leg-up on evaporation by raising its water level. A dry Sump 1A would, in turn, jumpstart wetland plant growth to make that unit more productive once it could be refilled. Beyond that, the draining and pumping effort was a collaboration between the Fish and Wildlife Service, Ducks Unlimited and Tulelake Irrigation District, which physically delivers water to the refuge.

“That management action stands out as the best before-outbreak action that we all took,” Vradenburg said. “That definitely took a tremendous amount of flexibility out of [TID’s] operations.”

In July, above-normal temperatures had accelerated evaporation from Sump 1B. Irrigators farming on the adjacent refuge leaselands exacerbated the water loss by diverting some water out of the sump. The water level dropped precipitously, stranding grebe nests and exposing mud flats that would become botulism hotspots. TID placed a limit on the water its patrons could extract from the sump and began replacing part of the diversions with well water.

Though she bemoaned irrigators drawing down one of the only remaining wetland strongholds in the basin, California Waterfowl Association Waterfowl Programs Supervisor Caroline Brady said that infusion of cooler, fresher groundwater ultimately kept Sump 1B from turning into a botulism breeding ground by maintaining circulation and lowering water temperatures.

“If no one had ever drained the sump for irrigation, there definitely would’ve been an outbreak,” Brady said.

Vradenburg said the diversions ramped down at the perfect time to dry up the exposed mud flats, which eliminated botulism risk in those areas but also further reduced the amount of available habitat on Sump 1B. Additionally, he said the benefit of the added well water was “a tough pill to swallow” given that the Klamath Basin — and the Tulelake area in particular — is in a serious groundwater deficit.

“It’s hard to balance groundwater reductions with the benefits, but without a doubt that definitely played into us avoiding an outbreak,” Vradenburg said.

Right as TID began stabilizing the sump level, thick smoke from the Bootleg Fire and other wildfires in California descended on the Tule Lake Basin. TID Manager Brad Kirby said the smoke’s arrival put an additional damper on evaporation at exactly the right time. Under orange skies, he watched the sump level slow its decline even before the district began adding additional water.

“That was significant enough to show an effect that you wouldn’t even think you’d be able to notice,” Kirby said.

By mid-August, the U.S. Fish and Wildlife Service, DU and TID were able to ‘borrow‘ roughly 10,000 acre-feet of water from the PacifiCorp reservoirs on the Klamath River to send to Sump 1B. It didn’t change the water level much, but it may have also kept the wetland circulating as adjacent farmers continued diverting water. In the roughly three weeks between the rapid decline of the sump level and the arrival of that water, Kirby remembers trying to “make water out of nothing.”

“I was holding on by a string here operationally,” he said. “I found myself saying and doing and directing things — I would’ve thought I was crazy two years ago.”

Jeff McCreary, director of operations for DU’s Western Region, said the creative solutions devised to solve the botulism problem this summer are proof that stakeholders can continue adaptively managing the system in the future to benefit both farmers and wildlife.

“It also sets the table for all parties involved to continue sharing their logistical and scientific expertise as we work toward a more permanent solution for the Klamath Basin Refuge Complex’s water woes going forward,” he said.

But Brady is skeptical of relying on that same flow-through setup in future years when botulism risk is high. While their actions actually helped the situation, she felt it was selfish of irrigators to take Sump 1B’s water after making a big deal of their commitments to saving waterfowl. Either way, she said it’s a management action the refuge can keep in its back pocket for the future.

“I think it’s hard to say you want to give TID an inch, because they’ll take 10 miles,” Brady said. “In drought years like this, maybe it does benefit both parties if you irrigate X number of acres using X number of acre-feet of water, and you put groundwater back in so you can prevent those big disease outbreaks. I think that’s something you could do in the future, but I don’t think anyone wants to have that conversation with TID, because they’re not trustworthy.”

In a general sense, Vradenburg said collaboration was crucial to saving refuge birds this summer. Because they all made avoiding a botulism outbreak a priority, stakeholders were able to devise creative ways to change operations and mitigate the risk as best they could.

“Everybody finally started to understand that botulism is related, in some way, to how we manage this system, and everybody took it serious,” he said. “We’re going to have botulism outbreaks again, and there are going to be big ones and small ones, but we learned a lot on how to tip the scale in our favor to minimize those this year.”

Ultimately, human actions had only delayed the onset of a disease outbreak — Mother Nature picked up the baton from there. Vradenburg said signs of botulism eventually started to appear on the refuge, but a somewhat early start to autumn brought frost and wetter weather much sooner than last year, when summer never seemed to end. The change in weather effectively ended the threat of an outbreak.

“An outbreak was starting. It was prime to go, and we started to see affected birds at the end of September and early October. We got lucky,” Vradenburg said. “There’s a big part of nature that plays into the likelihood of these outbreaks.”

Concerning future

But the relative success around botulism in the Klamath masks an even more pressing problem for the refuges and for all avian travelers along the Pacific Flyway: There’s a chronic lack of birds in the basin, stemming from a chronic lack of wetland habitat.

Depending on the year, Tule Lake Refuge can support as many as 200,000 molting birds. Though biologists couldn’t conduct an aerial survey, Vradenburg said recapture rates during duck banding in August suggested there were between 20,000 and 30,000 birds molting on the sump. Last year, biologists estimated between 150,000 and 200,000 birds had been molting there when botulism broke out.

“We killed more birds with botulism last year than we had on the refuge this year,” Vradenburg said. “The bird numbers are that bad.”

Because so little wetland habitat existed in the Klamath Basin, many birds simply skipped it altogether. Some stopped elsewhere in Southern Oregon, like Summer Lake, but others just kept going into the Central Valley.

Vradenburg said this year has seen the refuge’s lowest number of molting birds, lowest amount of food production and even the lowest fall migration counts. Just two decades ago, it supported 85% of the Pacific Flyway population. Now, to those who study and manage the flyway, the Klamath has been all but wiped off the map. That, he said, should be much scarier to people than the yearly threat of botulism.

“The number of birds we’re supporting is insignificant to continental management now,” Vradenburg said. “What we’re seeing now is far more catastrophic than the loss of 60,000 birds last year. The fact that this singularly most important wetland complex in the Pacific Flyway is completely offline this year and was 95% offline last year — it’s continentally the most significant wetland complex in North America, and it’s not functioning. There’s no birds, and nobody knows what that’s going to mean.”

What happens in the Klamath has ripple effects up and down the flyway. Brady said she’s observed abnormal behavior in birds who’ve arrived to the Central Valley for the winter, many of whom would typically stop at Lower Klamath or Tule Lake to rest and refuel before continuing their migrations.

“The birds showed up early simply because Klamath was offline,” she said. “And when they got here, they were really hungry.”

That spells concern for what the spring migration will look like, especially if the Klamath refuges don’t get water in time to grow invertebrate food and inundate crucial wetland habitat. Birds migrating back north from the Central Valley will likely be underfed when they return to the Klamath, emphasizing the need for plenty of food on the refuges.

If the Klamath refuges remain offline in the spring and more birds skip the basin a second time, no one really knows what will happen to the Pacific Flyway.

“We’ve never in the historical record seen a year where there’s this much wetland loss for both spring and fall migrating waterfowl,” Vradenburg said. “This is uncharted waters for continental waterbird management.”

Refuge advocates have requested that the Bureau of Reclamation deliver a surplus of 11,000 acre-feet of surface water in Upper Klamath Lake to Lower Klamath Refuge this fall to jumpstart invertebrate production, but the agency has said they plan to act conservatively heading into Water Year 2022, intending to keep as much water in the lake as possible. The water may show up in December, but Vradenburg said that’s a little late to get the wetlands producing enough invertebrates to feed birds in the spring.

There are also no current plans to deliver water to Tule Lake, and Vradenburg said refuge managers are operating under the assumption that Sump 1A will remain dry into next year unless hydrologic conditions drastically improve.

“It’s just scary, because the ball’s starting to unravel,” Vradenburg said.

As it did for every other piece of the Klamath puzzle, this summer demonstrated the need for a reliable water supply for Lower Klamath and Tule Lake Refuges. Stakeholders agree that while they learned a lot from an operations standpoint about how to collaboratively and adaptively manage the system in a critically dry year, it’s not sustainable to rely on groundwater or consistently running water uphill and backwards in future years.

“We can do everything we can operationally and come up with as many creative ideas as possible to move water effectively and efficiently, but when you have zero in the pot, there’s not much to work with,” Kirby said.

Though the threat of botulism has waned for 2021, birds in the Klamath Basin are far from out of the woods. Waterfowl numbers on the refuges are already less than 1% of what they were at their peak in the mid-20th Century. The last remaining wetlands in the basin remain under a near-constant threat of drying up for good.

“The birds are the canary in the mineshaft,” Vradenburg said. “If this basin can’t support waterfowl, when it was historically the most important place for waterfowl in North America, how can we expect to maintain a viable and sustainable agricultural program or viable and sustainable fisheries? They’re all linked to wetlands.”