Computers can decipher information from DNA and match pieces of genetic code with particular organisms. Luckily, a project to sequence some 11,000 genes of the honeybee was completed late last year at Baylor University, giving scientists a huge head start on identifying any unknown pathogens in the bee tissue.

"Otherwise, we would be looking for the needle in the haystack," Cox-Foster said.

Large bee losses are not unheard of. They have been reported at several points in the past century. But researchers think they are dealing with something new — or at least with something previously unidentified. "There could be a number of factors that are weakening the bees or speeding up things that shorten their lives," said W. Steve Sheppard, a professor of entomology at Washington State University. "The answer may already be with us."

Scientists first learned of the bee disappearances in November, when David Hackenberg, a Pennsylvania beekeeper, told Cox-Foster that more than 50 percent of his bee colonies had collapsed in Florida, where he had taken them for the winter.

Cox-Foster, a 20-year veteran of studying bees, soon teamed with Dennis vanEngelsdorp, the Pennsylvania apiary inspector, to look into the losses.

In December, she approached W. Ian Lipkin, director of the Greene Infectious Disease Laboratory at Columbia University, about doing genetic sequencing of tissue from bees in the colonies that experienced losses. The laboratory uses a recently developed technique for reading and amplifying short sequences of DNA that has revolutionized the science. Lipkin, who typically works on human diseases, agreed to do the analysis, despite not knowing who would ultimately pay for it. His laboratory is known for its work in finding the West Nile disease in the United States.

Cox-Foster ultimately sent samples of bee tissue to researchers at Columbia, to the Agriculture Department laboratory in Maryland, and to Gene Robinson, an entomologist at the University of Illinois. Fortuitously, she had frozen bee samples from healthy colonies dating to 2004 to use for comparison.

After receiving the first bee samples from Cox-Foster on March 6, Lipkin's team amplified the genetic material and started sequencing to separate virus, fungus and parasite DNA from bee DNA.

"This is like C.S.I. for agriculture," Lipkin said. "It is painstaking, gumshoe detective work."

Lipkin sent his first set of results to Cox-Foster, showing that several unknown micro-organisms were present in the bees from collapsing colonies. Meanwhile, vanEngelsdorp and researchers at the Agriculture Department lab in Maryland began an autopsy of bees from collapsing colonies in California, Florida, Georgia and Pennsylvania to search for any known bee pathogens.