Steve Albers, an intern with the U.S. Fish and Wildlife Service, lifts the carcass of a duck killed by avian botulism out of the water. Nate Schweber

An estimated 10,000 ducks and geese here, plus many others around the state, have been killed this year by outbreaks of avian botulism, a bacterial disease related to the deadly botulism that humans fear from improperly canned food. A third year of drought in California, this one the most extreme, has created what Beckstrand calls a perfect storm of an environment for botulism bacteria to explode. Worse, by shrinking reservoirs, ponds and wetlands, the drought has decreased the amount of surface water where waterfowl can spread out, thereby concentrating them in sloughs where this contagious disease is most severe.

“And the problem is, we don’t know how wide it’s going to spread or when it’s going to end,” he adds.

The colossal Central Valley of California is part of a vital bird migration route known as the Pacific Flyway. Before European settlement, the Central Valley gave wintering grounds for some 40 million waterfowl. In modern times, 95 percent of the wetlands were dried for agriculture, and now the valley grows about a quarter of all the food eaten in the United States. But the land still supports an estimated one-fourth of all the migratory birds in North America, biologists say. Starting in late summer and building to a crescendo by late fall, some 4 million to 7 million waterfowl course south down the Pacific Flyway, particularly ducks, geese and swans that summer in Alaska and on the prairies of Canada. These birds take rest breaks in all the waterways along their migration route.

While it’s a neurotoxin, avian botulism exists naturally, in nonlethal quantities, in the soil of waterways and wetlands, scientists say. It is not a threat to humans. The problem is that the bacteria turns virulent in water that is low, warm and sapped of dissolved oxygen — precisely the conditions created by drought.

“It creates this continuous cycle,” says Krysta Rogers, environmental scientist for the California Department of Fish and Wildlife.