December 1, 2023

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Why disease is killing California’s wild ducks and shorebirds

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Nothing Wild

Click the arrow below for more stories in Nothing Wild, a Sacramento Bee series on California’s broken relationship with its wild places.

Even through my face mask, I could smell botulism and decay as the mallard baked under the midday sun. The duck floated on its back near a patch of tules. It was writhing with maggots.

I reached over the side of the airboat to pluck it out of the muddy water with a pair of four-foot grippers, trying not to gag. I dropped it into a garbage bag at my feet filled with a half-dozen ducks and shorebirds. Maggots, mud and viscera splashed my chest waders.

“That’s what we’re looking for,” shouted the pilot, John Vradenburg, over the roar of the engine powering the airboat’s propeller. “The ones with the maggots are the problem.”

By the time I got there in early September, Vradenburg, a biologist with the U.S. Fish and Wildlife Service, had been picking up dead birds at the Tule Lake National Wildlife Refuge along California’s border with Oregon for more than a month. The signs of drought were all around: Brush growing in ponds that once held knee-deep water, scaly cracks at the bottoms of dry irrigation canals, a fog of wildfire smoke obscuring the hillsides.

For three months, Vradenburg, his colleagues and a team of volunteers in airboats collected close to 25,000 dead and dying shorebirds and waterfowl, most of them on Tule Lake’s Sump 1A, a 9,000-acre pond that turned into a mud flat after one of the driest winters and springs on record in the Klamath Basin.

The birds they collected represent only a fraction of the body count. It’s likely that more than 60,000 birds died miserable deaths.

While avian botulism outbreaks happen nearly every summer on the refuges, it’s usually just a few thousand birds at most.

This year was by far the worst avian botulism die-off on record in the Klamath Basin thanks to the refuge and its adjacent sister property, Lower Klamath National Wildlife Refuge, having their supply water cut off earlier this year.

I was in the middle of it for two days, collecting as many birds as Vradenburg and I could find to try to slow the outbreak’s spread and to save what few survivors we could catch.

I was there to tell this story, but I also wanted to help save these wetlands and these birds, an important part of my life since childhood. I grew up in Siskiyou County. I’ve hunted these wetlands since I was a boy. I still spend a couple of weeks each fall hunting ducks here.

They were once two of the West Coast’s premier waterfowl refuges — all that was left of marshes that were drained for farming during the last century. Recognizing its special place, President Teddy Roosevelt made Lower Klamath the nation’s first federal waterfowl refuge in 1908. Twenty years later, President Calvin Coolidge designated 39,116 acres of Tule Lake as a national wildlife refuge.

Just a few decades ago, the refuges drew nearly 7 million birds each year as they made their spring and fall migrations.

Over the past couple of decades, I’ve watched as these critical wetlands have been drained by drought and environmental regulations. Those rules have kept more water upstream and downstream to protect endangered fish on which struggling Native American communities depend.

The refuges are at the bottom of a federal water-rights pecking order that allocates Klamath River water first to fish, then to farms.

But it didn’t have to be this way. Tens of thousands of birds didn’t have to die like this. These refuges could have had a reliable water supply.

A decade ago, a diverse coalition of tribes, farmers and conservationists hashed out water-sharing settlements that would have given the refuges a steady supply of water each year, and in the process stopped years of lawsuits, protests and acrimony.

But Congress killed their efforts. Now the refuges — and Lower Klamath in particular — are at risk of drying up. And the fighting over water will only continue as the watershed grows increasingly dry from climate change.

The more than 400 species of birds and animals that depend on these places I love are only going to suffer for it.

U.S. Fish and Wildlife Service supervisory park ranger John Fitzroy steps from the airboat and reaches into a tule patch to collect a dead duck at Tule Lake National Wildlife Refuge in early September in northeastern California. Wildlife refuge specialist Steven Jensen, left, piloted the airboat as they worked to collect dead and dying birds sickened by avian botulism. Xavier Mascareñas [email protected]

Wetlands without end

This entire region was once a body of water that stretched from the California border into Oregon over 1,000 square miles. As the ice age ended, the lake drained off to become three primary lakes, Upper Klamath, Tule, and Lower Klamath — giant marshes connected to rivers and springs that swelled and contracted with the seasons, through droughts and floods.

The mazes of open water and channels, and miles upon miles of tules and cattails, sustained native peoples who hunted the millions of migratory birds drawn to the water and the deer, elk and pronghorn antelope around the marshes. They caught suckers that swam in the wetlands and the salmon and steelhead that migrated from the Pacific Ocean to spawn in the tributaries.

“Even the Klamath name Ewksiknii means ‘People of the lake,’ ’’ said Don Gentry, the chairman of the Klamath Tribes, the federally recognized nation made up of the Klamath, Modoc and Yahooskin band of Northern Paiute Indians.

Downstream, the Klamath’s lower reaches once teemed with fish including coho and chinook salmon, lamprey and steelhead trout, providing sustenance for three river tribes — the Yurok, the Karuk and the Hoopa Valley — who lived along the Klamath and its tributaries, the Trinity, Scott and Shasta rivers.

Centuries of native culture and traditions were nearly stamped out when settlers began to arrive in the mid-1800s.

In 1864, in the middle of the Civil War, the native people who lived around the Klamath marshes signed a treaty with the United States that ceded their lands in return for a reservation north of Klamath Falls, Ore. While some of the Modocs agreed to live on the reservation, others did not. In 1872, the U.S. Army dispatched troops to send them back.

After the first battle, the Modocs retreated across Tule Lake and holed up for months, fending off seven times their number of U.S. troops in the lava fields of what’s now known as Lava Beds National Monument along Tule Lake National Wildlife Refuge’s southern border.

During a peace talk, the Modocs killed U.S. Army Gen. Edward Canby and members of his retinue. Months later, the Modoc leader Keintpoos, also known as “Capt. Jack,” surrendered and was executed, ending the Modoc War, and allowing these marshy waters to be “reclaimed” without resistance or agriculture.

These marshlands make excellent farmland. The loamy dirt that now sticks to Klamath farmers’ tractors was created by centuries of decaying plant and animal life compacting and decomposing under all that murky water.

Around the turn of the last century, the federal government began to systematically drain Tule and Lower Klamath lakes to grow crops, and Upper Klamath Lake was used as a reservoir that could meter out water to a series of canals and pumps to irrigate the lands the homesteaders took. The project cut Lower Klamath Lake off entirely from the Klamath River, and it dammed the Lost River, which drained into Tule Lake.

Downstream from the marshes on the Klamath River, the power company that eventually became known as PacifiCorp built large hydroelectric dams — three in California and one in Oregon — blocking migratory fish from their spawning grounds.

Legislation known as the Kuchel Act in 1964 allowed local farmers to lease portions of the refuges for growing crops. To this day, farmers graze cattle and grow wheat, potatoes and other crops on portions of the refuges. Migrating geese and ducks gorge on the farmers’ leavings.

In-N-Out Burger fries come from potatoes grown here. Go out to dinner at any fancy steakhouse, and the beef you eat might have grown fat on Klamath Basin alfalfa. The garlic and onions seasoning your meal could have been grown in this peaty soil. The horseradish in the sauce you dip your prime rib almost certainly was.

Your beer might contain Klamath Basin barley, and your bread might be dough from wheat grown on Lower Klamath National Wildlife Refuge.

U.S. Fish and Wildlife Service wildlife refuge specialist Steven Jensen, left, steers an airboat along a shore at Tule Lake National Wildlife Refuge, as supervisory park ranger John Fitzroy keeps an eye out for birds affected by avian botulism during a botulism outbreak at Tule Lake National Wildlife Refuge in northeastern California. Xavier Mascareñas [email protected]

‘Showing up with a garden hose’

An appetite for beer and beef did not kill these ducks by the tens of thousands. But it’s easy to draw a straight line from decades of bureaucratic infighting and shifting allegiances over California’s increasingly scarce water resources.

Levee-lined sumps, ponds and fields in both refuges are now almost entirely flooded by the turn of an irrigation canal headgate. For much of the last century, the refuges and the farms had nearly unlimited water.

Then came a major drought in 2001. Farmers had their water shut off. The next year, thousands of Klamath River salmon died. Amid protests and lawsuits, the various groups came together and agreed to compromise. Farmers would retire some land, and the government would fund habitat restoration.

The biggest win for the tribes: The four aging hydroelectric dams downstream of the irrigators and refuges would come down. But Republicans who controlled the U.S. House of Representatives at the time refused to sign off.

“Tearing down four perfectly good hydroelectric dams when we can’t guarantee enough electricity to keep your refrigerator running this summer is lunacy,” U.S. Rep. Tom McClintock, whose district stretches from Alpine to Tuolumne counties, said as the accords were about to expire in 2015. He called the settlements a “greens-gone-wild episode.”

U.S. Rep. Doug LaMalfa, a rice farmer from Butte County, also refused to sign them, even though Tulelake farmers in his district were part of the deal. “No one has shown me that taking down the dams is beneficial to fish or people,” he said in 2015.

Their resistance to dam removal quickly became pointless. The states of Oregon and California agreed to tear the dams down on their own. Just last month, the power company that owns them, Warren Buffett’s Berkshire Hathaway, agreed to relinquish their licenses to the states in the hopes of clearing regulatory hurdles and meet a 2023 demolition date.

Devils garden map

Even if the dams come down, the Klamath Basin farmers and the refuges will continue to have no guarantee of a reliable water supply. They receive no water from the four Klamath River dams slated for demolition.

In the years since the agreements collapsed, environmentalists and the tribes have continued to prevail in court. That has forced the federal government to send more water to the Klamath River and Upper Klamath Lake, to try to protect the fish that are sacred to the tribes’ cultural practices, ceremonies and livelihoods.

To some tribe members, the entire system is based on the subjugation and the pillaging of the natural world, so it doesn’t come across as being particularly neighborly when farmers argue that when they get water, it also keeps the refuges flooded.

“It’s kind of like lighting your neighbor’s house on fire and showing up with a garden hose and patting yourself on the back,” said Clayton Dumont, a Klamath Tribes councilman.

Perfect conditions for an outbreak

The federal government threatened to shut off water deliveries this spring, prompting local farmers and their allies to rally in a miles-long tractor protest. The Trump administration sent local farmers some water so they could grow the crops they’d already planted, but there was hardly any left to go to the refuges.

Sump 1A on Tule Lake was drawn down to its lowest levels in decades, exposing to the sun much of its nearly 14-square miles of thigh-deep mud, covered in a sheen of water. There wasn’t enough water for refuge managers to flood other ponds on the two refuges to help draw birds away from Sump 1A’s botulism mudflats.

Clostridium botulinum — a type of bacteria — is found in the mud at the bottom of the Klamath Basin marshes. When the mud is exposed to the sun in low water levels and high heat, the bacteria emerge from dormancy. The microbes release a neurotoxin that’s absorbed by various types of invertebrates.

Maggots are the real killer. As carcasses quickly decompose in the summer heat, flies land on them and lay eggs, which grow into wriggling maggots, some of which float away.

As birds eat those maggots, they get poisoned and their bodies shut down. In less than 24 hours, their wings and legs stop moving, then they can’t pick up their heads. Then they drown.

Waterfowl and shorebirds are social creatures, so when they see a group of partially paralyzed birds and recently dead corpses in the water, they fly or swim over to join what to them looks like a normal flock. They eat the maggots and the cycle continues.

It’s why Vradenburg, the biologist, and his team of refuge employees and volunteers spent weeks on airboats collecting up to 500 dead birds a day. They were trying to end what he calls “the maggot cycle.”

Collecting all those muddy, wet carcasses leaves the airboats and the people on them covered with foul-smelling gunk that clings to your clothes, your hair and gets under your fingernails, even if you wear gloves. (This particular strain of botulism isn’t toxic to humans, luckily.)

And the gruesome job continued day after day until nearly the end of October.

“You can clean up an area, and you’re out there the next day at the same time in the morning,” Vradenburg said, “and you’ve got sick and affected birds out there.”

After a morning on the airboats, Vradenburg’s crews drove over to a pair of incinerators and heaved the heavy, soggy bags of dead birds inside to burn them.

U.S. Fish and Wildlife Service supervisory park ranger John Fitzroy reaches over the side of an airboat to rescue a botulism-sickened bird at Tule Lake National Wildlife Refuge’s Sump 1A in early September. Biologists took the surviving birds to wildlife rehabilitators who tried to nurse them back to health. Xavier Mascareñas [email protected]

‘It’s pretty heartbreaking to be out there’

But they did save some. The crews chased down and captured live birds that had been sickened from the toxins, using nets for the livelier ones or by reaching over the boat to grab the sickest with their hands.

They were placed in cages on the airboats and taken to a makeshift bird hospital set up on Lower Klamath refuge. There, a team force-fed them fluids and vitamins, and they were given injections of anti-toxins into their breast muscles. The sickest ones went on an IV.

If they survived the night, the birds were placed into wading pools converted into makeshift duck ponds filled with clean well water. They were fed mealworms, dried insects and marsh plants until they were healthy enough to be released to a local lake off the refuge lands that’s deep enough to prevent botulism growth.

The birds that make it through the first night had a nearly 80 percent survival rate.

By the time collections concluded in late September the hospital had rehabbed 3,125 birds — a mix of 42 different species. That was 10 times the numbers they took in during the outbreak the year before.

“It was extremely overwhelming,” said January Bill, co-director of Bird Ally X, a group that has worked with Focus Wildlife and the U.S. Fish and Wildlife Service to save the birds.

At first, the large numbers of live birds the airboat crews delivered were too much for Bill’s small team to handle. They had just one wading pool and not enough staff to deal with them all. They didn’t have nearly enough funds to gear up.

One day in August, the hospital was so overwhelmed, the airboat crews were forced to wring the necks of some of the sickened birds they found that day to save them from a slow death.

But an influx of donations from the nonprofit’s supporters, bird-watching groups, refuge boosters and duck hunting organizations allowed the bird rehabbers to buy 10 more wading pools and cattle troughs to turn to hospital ponds. Bill’s team also was able to bring in more people to help.

Though they saved some lives, those working on the airboats still had to endure day after day of maggoty carcasses and dying birds.

“If you have any connection to nature at all,” Vradenburg said, “it’s pretty heartbreaking to be out there.”

Longtime wildlife rehabilitator January Bill, co-director of Bird Ally X, collects a duck in early September recovering from botulism at a rehabilitation center at Lower Klamath National Wildlife Refuge in northeastern California. Xavier Mascareñas [email protected]

‘Turn the clock back 50 years’

A couple of days before I got to the refuge, Rep. LaMalfa spent a morning on the airboats as a volunteer collecting dead and dying birds. At one point, the tall, husky rice farmer got choked up.

“You think like, ‘Wow, how much of this could we have prevented, you know?’ ” he told me in a phone interview.

For him, it comes down to the farmers getting the same amount of water as they used to decades earlier. He called for “a new, stronger consensus on water allocations in the Basin” — never mind that for years he had a consensus sitting on his desk in the agreements he refused to sign.

Had Congress passed the agreement that LaMalfa refused to sign, this year, Lower Klamath alone would have received at least 48,000-acre-feet of water, delivered on-demand. Lower Klamath is only expected to get around a quarter of that this winter, long after most of the birds have flown past.

Under the agreements, farmers also would have received nearly three times more water than they received this year, runoff from which also would have gone to the refuges.

Over dinner one night in September in Klamath Falls, I asked a couple of Tulelake farmers what they thought about their congressman calling for a consensus after he killed their hard-fought compromise a few years earlier.

Rancher Gary Wright made a disgusted face over his bowl of chili. He said he has “no respect” for his congressman.

Scott Seus, who grows mint, horseradish, garlic, grain and onions, was more diplomatic. He said he understands why LaMalfa made the political choice to kill the agreements after seeing local Tea Party activists in his district come out vehemently against dam removal. Some local leaders who supported the accords got ousted from office because of their stance.

Seus said it’s also easy for LaMalfa, a farmer himself, to wish to go back in time before the Endangered Species Act, a time when farmers had an unlimited supply of water.

“To Doug’s point, he wouldn’t have been crying over dead ducks if he could turn the clock back 50 years to make it the run the way it was, and he’s not wrong,” Seus said.

But that hardline stance ignores the regulatory realities crippling the basin today, Seus said.

“That doesn’t give us a path forward to make it a sustainable thing for my kids to be able to farm,” Seus said.

Salmon numbers continue to be unsustainable below the dams that have yet to come down. Three years ago, the fall run was so small, river tribes couldn’t fish for the salmon. The tribes’ leaders told me at the time they were bracing for a rash of suicides.

The suckers in Upper Klamath Lake, which play a similar role in the Klamath Tribes’ cultural and spiritual lives, aren’t faring any better.

The long-lived fish are able to spawn, but the juvenile fish die before they grow large enough to breed. Without hatchery fish to supplement the aging adults’ numbers, the suckers in the lake are facing certain extinction.

Since the agreements collapsed, the tribes have grown more hardline in their belief that agriculture’s footprint in the Klamath Basin needs to shrink.

Gentry, the chairman of the Klamath Tribes, said the settlements that he supported at the time were “skewed toward irrigated agriculture,” but the tribes were willing to compromise. In the years since that goodwill has faded along with the local ecosystem from too much water going down irrigation canals.

“How could they support it now?” Gentry said.

With the various factions again dug in, it will take Congress to guarantee Lower Klamath and Tule Lake get the water that refuge managers need to flood ponds at critical times. Lower Klamath is in particularly bad shape.

Even in the best of years, it gets delivered less than half of what it needs to keep ponds flooded for waterbirds. As a result, much of the refuge’s ponds and nesting islands are overgrown with dry brush from not having seen water in a generation.

Without help, the sky-darkening clouds of ducks and geese I remember from my youth are likely to stay a distant memory, and those maggoty horrors LaMalfa and I saw this summer portend a grim future for my favorite hunting grounds.

Jenna Farmer, intern with Bird Ally X, releases a mallard along with a handful of other ducks in early September into Indian Tom Lake in Siskiyou County. The birds had been nursed back to health after being poisoned from avian botulism at Tule Lake National Wildlife Refuge. Xavier Mascareñas [email protected]

Related stories from Sacramento Bee

Profile Image of Ryan Sabalow

Ryan Sabalow covers environment, general news and enterprise and investigative stories for McClatchy’s Western newspapers. Before joining The Bee in 2015, he was a reporter at The Auburn Journal, The Redding Record Searchlight and The Indianapolis Star.

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