It could just be that the bees are stressed out. Bees are being raised to survive a shorter offseason, to be ready to pollinate once the almond bloom begins in February. That has most likely lowered their immunity to viruses.

Mites have also damaged bee colonies, and the insecticides used to try to kill mites are harming the ability of queen bees to spawn as many worker bees. The queens are living half as long as they did just a few years ago.

Researchers are also concerned that the willingness of beekeepers to truck their colonies from coast to coast could be adding to bees’ stress, helping to spread viruses and mites and otherwise accelerating whatever is afflicting them.

Dennis van Engelsdorp, a bee specialist with the state of Pennsylvania who is part of the team studying the bee colony collapses, said the “strong immune suppression” investigators have observed “could be the AIDS of the bee industry,” making bees more susceptible to other diseases that eventually kill them off.

Growers have tried before to do without bees. In past decades, they have used everything from giant blowers to helicopters to mortar shells to try to spread pollen across the plants. More recently researchers have been trying to develop “self-compatible” almond trees that will require fewer bees. One company is even trying to commercialize the blue orchard bee, which is virtually stingless and works at colder temperatures than the honeybee.

Beekeepers have endured two major mite infestations since the 1980s, which felled many hobbyist beekeepers, and three cases of unexplained disappearing disorders as far back as 1894. But those episodes were confined to small areas, Mr. van Engelsdorp said.

Today the industry is in a weaker position to deal with new stresses. A flood of imported honey from China and Argentina has depressed honey prices and put more pressure on beekeepers to take to the road in search of pollination contracts. Beekeepers are trucking tens of billions of bees around the country every year.