Beekeeper James Doan first began finding empty hives last fall. Entire bee colonies seemed to have up and vanished, leaving their honey behind. Noting the unusually wet fall in Hamlin, N.Y., he blamed the weather. Unable to forage in the rain, the bees probably starved, he reasoned.

But when deserted hives began appearing daily, "we knew it was something different," he says. Now, at the beginning of the 2007 pollination season, more than half of his 4,300 hives are gone. "I'm just about ready to give up," says Mr. Doan from his honeybee wintering site in Ft. Meade, Fla. "I'm not sure I can survive."

The cause of the die-offs has yet to be determined. Its effect on the food supply may be significant. Longer-term, it may also force a rethinking of some agricultural practices including our heavy reliance on human-managed bees for pollination.

Scientists call it "colony collapse disorder" (CCD). First reported in Florida last fall, the problem has since spread to 24 states. Commercial beekeepers are reporting losses of between 50 and 90 percent, an unprecedented amount even for an industry accustomed to die-offs.

Many worry that what's shaping up to be a honeybee catastrophe will disrupt the food supply. While staple crops like wheat and corn are pollinated by wind, some 90 cultivated flowering crops – from almonds and apples to cranberries and watermelons – rely heavily on honeybees trucked in for pollinization. Honeybees pollinate every third bite of food ingested by Americans, says a Cornell study. Bees help generate some $14 billion in produce.

Research is only beginning and hard data is still lacking, but beekeepers suspect everything from a new virus or parasite to pesticides and genetically modified crops. Scientists have hastily established a CCD working group at Pennsylvania State University. Last week, the US House of Representatives' Committee on Agriculture held hearings on the missing bees.

For many entomologists, the bee crisis is a wake-up call. By relying on a single species for pollination, US agriculture has put itself in a precarious position, they say. A resilient agricultural system requires diverse pollinators. This speaks to a larger conservation issue. Some evidence indicates a decline in the estimated 4,500 potential alternate pollinators – native species of butterflies, wasps. and other bees. The blame for that sits squarely on human activity – habitat loss, pesticide use, and imported disease – but much of this could be offset by different land-use practices.

Moving away from monoculture, say scientists, and having something always flowering within bee-distance, would help natural pollinators. This would make crops less dependent on trucked-in bees, which have proved to be vulnerable to die-offs.

The stress on honeybees grew as native and wild pollinators diminished and farmers came to rely more on honeybees. We've put "all of our pollination eggs in the honeybee basket," says Mace Vaughan, conservation director of the Xerces Society for Invertebrate Conservation in Portland, Ore. "We need more baskets."

An immune-system disorder?

Meanwhile, beekeepers are seeing hives empty in a matter of weeks, sometimes days. The entire adult bee population vanishes, except for a few juveniles. This makes CCD difficult to study. "You have a crime scene, you know a crime happened here, but you don't really have evidence," says Medhat Nasr, provincial apiculturalist in Alberta, Canada. Eerily, the stored honey in the hive remains untouched. Raiding bees from nearby colonies never materialize, as is common.

Records of suddenly empty hives go back as far as the late 1800s, but never on this scale. Beekeepers dubbed it "autumn collapse," "spring dwindle," or "disappearing disease." But Dennis vanEngelsdorp, the acting Penn State apiarist, calls this manifestation the AIDS of bees. The remaining juvenile bees appear to be rife with disease. To him, "It's clear that there is an immune suppression," he says.

What might suppress a bee's immune system is anyone's guess. But many ascribe to a tipping-point theory: A variety of factors may have accumulated until a single straw finally broke the bee's back.

A review of honeybee history shows many suspects. The Varroa mite, native to Asia, came to North America in the late 1980s. Since then, yearly losses of between 15 and 20 percent have become the norm. "Before the mites, you could be a bee-have-er," says Mr. vanEngelsdorp. "Now you have to be a bee-keep-er."

Beekeepers are the first to acknowledge the stress of migratory pollination. Carted on flatbed trucks from wintering sites in the South, the bees crisscross the continent, first to California's almond groves, which rely entirely on honeybees for pollination, and then northward throughout the country, following the spring flowering season. Farmers have come to rely increasingly on honeybee services, says May Berenbaum, head of the department of entomology at the University of Illinois, Urbana-Champaign. "Given its economic importance, beekeeping really hasn't gotten the attention it deserves," she says.

Poor nutrition may be another factor, says Mr. Vaughan. To prepare them for winter, bees are fed high-fructose corn syrup and protein supplements. In the fields they've pollinated, meanwhile, more often than not they've gathered only one kind of pollen. Maybe, like other animals, they need a diverse diet, he says. "If you only ate McDonald's every day, you'd be just like that guy in 'Super Size Me,' " he says. "And he didn't feel that good."

Others, like Doan, suspect pesticides.

Similar problem in 1990s France

In the 1990s, France experienced a precipitous honeybee decline from "mad bee disease." Honey production dropped by nearly one-third, to 25,000 tons. French beekeepers blamed a newly introduced pesticide marketed under the name Gaucho. From the same family as nicotine, the chemical targeted aphids' navigational systems. And when the honeybees weren't finding their way home, either, French beekeepers protested. The French government banned the product in 1999. Though subsequent studies haven't found a strong link, bee populations still haven't rebounded to previous levels.

Others point to genetically modified crops – specifically, those with a gene for a bacterial toxin called Bt. Initial studies indicated that it didn't affect bees. But some beekeepers argue the trials didn't last long enough to determine the long-term effects. (Doan says the same about the nicotinelike pesticides.) A German study supports this. Scientists at the University of Jena found that while Bt food had no direct effect on bees, when fed to bee populations infected with parasites, they quickly became diseased. Alone, Bt may do nothing. But in the presence of a parasite, it may facilitate infection.

"Maybe these toxins weaken the immune system," says John McDonald, a retired biologist and hobby apiculturalist in Spring Mills, Pa., who wrote an editorial on the topic for the San Francisco Chronicle

But the shrinking of our so-called "pollination portfolio" is of more concern to many entomologists than a die-off in commercial beehives. A 2006 National Academy of Sciences report declared that there was "direct evidence for decline of some pollinator species in North America" – species responsible for pollinating three-quarters of flowering plants. Europeans have documented a parallel decline in their natural pollinators for years.

On the US East Coast, where a more ecologically diverse farming landscape enhances species diversity, studies have shown that wild pollinators were doing about 90 percent of the pollinating anyway, says Neal Williams, an assistant professor of biology at Bryn Mawr College in Pennsylvania. "It seems a little bit silly from a whole-country perspective, even from a farmer perspective, that we would place so much emphasis on one species. We don't do that with any other part of the economy," he says.

Meanwhile, a Canadian study suggests that if canola farmers leave 30 percent of their land fallow, they will increase their yields. Wild land provides habitat for native pollinators, improving pollination and increasing the number of seeds. "If we cultivate all the land, we lose ecosystem services like pollination," says Lora Morandin, lead author on the study. "Healthy, sustainable agricultural systems need to include natural land."