Honey bees are critical to U.S. agriculture, which depends upon them to pollinate 130 different crops, representing more than $15 billion in crop value each year and roughly one-third of the human diet, according to the U.S. Department of Agriculture.

For the California almond crop to be successfully pollinated, DeRisi said, roughly half of the honeybees in the country – about 1.3 million honeybee colonies – must be in the Central Valley by the first week in February, when the trees begin to bloom. That need is echoed throughout the country, as different crops come due for pollination, resulting in semis traversing the nation for most of the year, each bearing hundreds of hives.

Since 2006, however, the bee industry has reported a mysterious phenomenon involving the sudden disappearance of most of a hive’s worker bees, which leaves the queen and young bees without enough workers to support them. The disorder is one factor in the growing decline of U.S. honey bees – an estimated 30 percent of the population is lost each year and some beekeeping operations cite 90 percent losses, the USDA reports.

Researchers nationwide have identified various possible causes of that collapse, mainly based on pathogens found in the affected hives. While this study did not identify the cause of colony collapse, it did offer a measurement of the normal levels of pathogens.

In addition to viruses, the research revealed six species each of bacteria and fungi, four types of mites and a parasitic fly called a phorid, which had not been seen in honey bees outside California. One of the new viruses, a strain of the Lake Sinai virus, turned out to be the primary element of the honey bee biome, or community of bacteria and viruses.

“Here’s a virus that’s the single most abundant component of the bee biome and no one knew it was there,” DeRisi said, noting that hundreds of millions of these viral cells were found in each bee in otherwise healthy colonies at certain times of the year.

Flenniken jointly led the work with doctoral student Charles Runckel, in DeRisi’s lab. The team used a broad range of molecular detection tools for the study, including gene sequencing and a custom-designed microarray to detect insect pathogens. The microarray was designed using the same principles used for detecting human viruses, which DeRisi pioneered with UCSF professor Donald Ganem, MD. It was built in the Center for Advanced Technology on the UCSF Mission Bay campus.

The research was primarily funded by Project Apis m., which includes members of the American Honey Producers Association, the American Beekeeping Federation, the National Honey Board, California State Beekeepers Association and California almond farmers. DeRisi is supported by the Howard Hughes Medical Institute. Flenniken’s research was supported by the Häagen Dazs post-doctoral fellowship in honey bee biology, through University of California, Davis. Other funding sources and data can be found in the full paper.

Co-authors include Andino, in the UCSF Department of Microbiology and Immunology; Juan C. Engel, in the UCSF Sandler Center for Drug Discovery and UCSF Department of Pathology; and J. Graham Ruby and Donald Ganem, in the Howard Hughes Medical Institute and UCSF departments of Biochemistry & Biophysics, and Microbiology.

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