The Why Files The Why Files --

Bee virus discovery shows fast-track to the heart of biology

It's not easy being a bee
Bee colonies in the United States are mysteriously dying: The bees leave the hive, and never return. At some beekeeping operations, "colony collapse disorder" has damaged or destroyed 90 percent of the hives.

Black and yellow bee stands above a yellow honeycombHGRI-supported researchers have sequenced the genome of the domestic honey bee. Photo Courtesy Scott Bauer, USDA, /ARS

Colony collapse matters even if your sweetener of choice is aspartame rather than honey. Bees are necessary for pollinating crops, including almonds, apples, blueberries, and citrus fruits, that are worth $14.6 billion a year in the United States. Without a bee to transfer the pollen, the fruit cannot develop.

Bees are an unusual type of migrant worker. Large beekeepers get paid by the hive for pollination, and many truck their colonies long distances to follow the blooming schedule of various crops.

After honey bee colonies started collapsing in 2004, a hundred theories blossomed to explain mass die-offs: cell phone radiation, a new pesticide, the combined impact of multiple parasites and pathogens, the stress of long-distance trucking, or some witches' brew of the above.

Since bees are infected by many parasites, bacteria, viruses and fungi, it was not immediately clear that the syndrome was actually anything new. But one factor strongly implicated infection: Bees did fine in colonies whose former occupants had died -- if the hive box had been sterilized with radiation.

Bee real
Last week, a large group of researchers pointed a finger at Israeli Acute Paralysis Virus (IAPV; see #1 in the bibliography) as a possible cause of the collapse disorder. Their study relied on modern, high-speed gene sequencing machines and a technique called metagenomics, which analyzes all the DNA present in a sample.

A "gene sequence" lists the individual bases (A, C, G or T) on the DNA, in order. The sequence shows a gene's heritage and may suggest its biological function.

Metagenomics can attack phenomenally complex jobs like counting the types of microbe in the gut of a person, a handful of soil, or sample of water. By sidestepping many of the limits on conventional microbiology, metagenomics can quickly produce data on the genetic makeup of a sample. Metagenomics cannot, however, actually identify unknown microbes or explain their ecological role.

Beekeeper kneels next to box full of swarming bees
Honey bees suffer plenty of diseases and parasites. These materials are used to take samples from hives. Image courtesy ARS/USDA Jay D. Evans

Bee careful
The colony-collapse analysis, headed by Diana Cox-Foster, professor of entomology at Penn State, Jeffery Pettis of the U.S. Department of Agriculture's Bee Research Laboratory, and W. Ian Lipkin of Columbia University, first compared DNA from colonies with and without colony-collapse disorder, using the metagenomic technique we'll describe on the next page.

The researchers next removed honey bee genes from their analysis. "The genome of the honey bee had just been completed," said Cox-Foster in a press release. "So it was possible to do the sequencing and then eliminate the genetic material of the bees."

No bacteria were linked with the collapse disorder, but the data did point a finger of suspicion at two of the seven viruses detected in the mixed-up DNA: IAPV and the related Kashmir bee virus.

A further analysis found IAPV in 25 of 30 collapsing colonies, but in only one of 21 healthy ones. The Kashmir virus was judged innocent because it appeared more or less equally in healthy and collapsing hives.

Tellingly, IAPV was also detected in bees that the researchers ordered from Australia. Honey bee imports have been tightly regulated to prevent the introduction of diseases, but apparently World Trade Organization rules have forced the United States to allow imports from countries that may harbor new pathogens.

Bee wary
Overall, the researchers said IAPV is "strongly correlated" with colony-collapse disorder. They did not say it "causes" the collapse. The virus may simply be a "marker" for a disease that has another cause. Researchers are testing whether IAPV causes the disorder by infecting healthy colonies with the virus.

If IAPV does cause colony collapse, we're encouraged that Ilan Sela, the Israeli plant virologist who identified it in 2002, has found some bees in Israel that are evolving resistance to it. It may be possible to breed IAPV-resistant bees (see #2 in the bibliography).

But many questions remain at this early stage. For example, if IAPV did come from Australia, why doesn't it kill Aussie bees? That could reflect, as some Australian scientists think, a case of mistaken identity; IAPV did not reach the United States from Australia. Or it could reflect the absence of the varroa mite in Australia. This common parasite inhibits the immune system of the bees it afflicts in the United States.

Small black mite hangs on to the furry collar surrounding head of honeybee
Honey bee worker carrying a parasitic Varroa mite. Could a co-infection with these mites help explain the mysterious colony-collapse disorder? Image courtesy ARS/USDA Scott Bauer

Bee sure
The explanation for the disparity could also reside in genetic difference between the American and Australian strains of IAPV, and here is another place that fast, cheap genetic tools could be helpful, says Janet Koprivnikar, assistant professor of biology at the University of the Pacific (Stockton, Cal.). The new tools "allow us to identify pathogens in a way we could not before." Using metagenomics and rapid sequencing, "It is going to be easier to track the spread. When a specific strain or a particular pathogen pops up, we can see how it is different genetically from other strains, and can start to pinpoint why it may be so pathogenic."

Koprivnikar, who studies the interaction of amphibians and flatworm parasites, says metagenomics would be "really excellent" for understanding the effects of genetically distinct parasites, and how they work in various environmental conditions. "A lot of parasites can be really cryptic, it's often hard to tell exactly which species or strain we are dealing with and what they are doing."

Long  primordial tale extends out of the tiny half formed body of a frog
Studies of amphibians highlight the interaction of multiple parasites, pathogens and environmental stresses. Metagenomics allows us to understand how different genetics lead to different outcomes. Photo: Northern leopard frog tadpole, courtesy Janet Koprivnikar, University of the Pacific.

Rapid sequencing and metagenomic analysis may represent a watershed for environmental ecologists, Koprivnikar says. "A lot of people are becoming more and more interested in gene flows and population variances.... It will enable us to look at a lot of new questions."

Bee smart
Rapid sequencing and quick identification of unknown pathogens -- the hallmarks of the colony-collapse project -- are critically important as ever-more humans, goods and diseases move across the globe at the speed of a jet plane. But the new metagenomic technology is also helping address other biological issues:

Faster, cheaper sequencing of individual human genomes.

Rapid counting of all types of organism in a sample of soil, water or rock.

Quick identification of particular variants of a pathogen, to help make treatment decisions.

Metagenomics is useful far beyond human genomics, and one of the most exciting places is in environmental microbiology: the study of microbes in the environment. We asked Mitchell Sogin, of the Marine Biological Laboratory in Woods Hole, Mass., who has used the modern sequencing technology to explore the microbiology of ocean water. "This allows us to do very fine-scale population structure maps, meaning we can determine with remarkable sensitivity the differences in environmental samples." The ocean, Sogin has found, may house a limitless amount of biodiversity.

Fast sequencing has countless other applications, Sogin added. One concerns the vast bacterial zoo living in the mammalian gastrointestinal tract. "We could go into an animal treated with an antibiotic and see how the gut community changes, or compare yours to mine, or compare a fat person to a skinny person."

So how does this super-sequencing work?


Megan Anderson, project assistant; Terry Devitt, editor; S.V. Medaris, designer/illustrator; David Tenenbaum, feature writer; Amy Toburen, content development executive

©2017, University of Wisconsin, Board of Regents.