The U.S. government's latest report on the mysterious disappearance of honeybees points to a parasitic mite as the biggest factor behind colony collapse disorder — and downplays the role of controversial pesticides that European officials are planning to ban.

Thursday's report from the Environmental Protection Agency and the U.S. Department of Agriculture says there should be further research into the effects of those nerve-agent pesticides, known as neonicotinoids. But it says the studies so far have not shown it to be the biggest hazard facing the bees.

Last month, beekeepers and environmentalists filed a federal lawsuit calling for an immediate ban on two kinds of neonicotinoids — clothianidin and thiamethoxam. One of the attorneys bringing that suit, Peter Jenkins of the Washington-based Center for Food Safety, told NBC News that his group was "very disturbed" by the way the report was presented, but he also said some of the problems cited in the report supported his case.

'Complex problem'
The report says that a complex combination of causes is behind colony collapse disorder, or CCD, a term that applies to the difficult-to-explain losses that have hit U.S. honeybee colonies since 2006. In the worst cases, entire colonies have disappeared within a few weeks. That's a big problem, because the government says an estimated one-third of all food and beverages are made possible by pollination, mainly by honeybees. Pollination is said to be worth more than $20 billion in agricultural production annually.

The relatively light bee colony losses during the winter of 2011-2012 gave some experts reason to hope that the CCD situation was getting better, but experts say that last winter's losses look as if they were worse than ever.

"The decline in honeybee health is a complex problem caused by a combination of stressors, and at EPA we are committed to continuing our work with USDA, researchers, beekeepers, growers and the public to address this challenge," acting EPA Administrator Bob Perciasepe said in a statement.

Deputy Agriculture Secretary Kathleen Merrigan promised that "key stakeholders will be engaged in addressing this challenge."

Scott Bauer / USDA via AP

A worker bee carries a Varroa mite, visible in this close-up view.

The report draws upon a gathering of officials and stakeholders that took place in Alexandria, Va., last October. It says that the parasitic Varroa mite is the "major factor" behind CCD in the United States and other countries. Varroa mites latch onto the bees and feed on their fluids, weakening the insects. The mites have developed widespread resistance to the chemicals that have been used to control them. The report says more attention should be given to breeding bees that can weather the mites, and notes that gene-sequencing projects focusing on honeybees as well as Varroa mites may provide fresh insights.

Beekeepers have long known about the mite problem, as well as the other causes listed in the EPA-USDA report: poor nutrition, reduced genetic diversity, the Nosema gut parasite, emerging viruses and a bacterial disease called European foulbrood. But figuring out the role played by pesticides has posed the biggest challenge for researchers as well as policymakers.

What to do?
Recent research studies have focused on the effect of neonicotinoids, a neurotoxic type of pesticide that has become widely used because they have little effect on mammals. Most of the studies suggest that the pesticides can scramble a bee's brains — but at what level of exposure?

Some say the exposure levels used in those studies may not accurately reflect the levels that bees experience in the fields. That's the tack taken in Thursday's report: "The most pressing pesticide research questions lie in determining the actual field-relevant pesticide exposure bees receive, and the effects of pervasive exposure to multiple pesticides on bee health and productivity of whole honeybee colonies," it said.

The report says residues from a different class of pesticides, known as pyrethroids, could pose three times as much risk to bees as neonicotinoids.  

The Center for Food Safety's Peter Jenkins complained that the effects of neonicotinoids were being downplayed, but he also called attention to some of the shortcomings mentioned in the federal agencies' report. "They admitted that their labeling is inadequate," Jenkins said. "They admitted that past risk assessments and data requirements were inadequate."

He said some of the proposed policy changes — including, for instance, the introduction of better equipment for coating seed corn with pesticides — would have a positive impact. "What they don't say is that it's going to take years and years to achieve those changes," Jenkins said.

Jenkins called for an immediate tightening of regulations of pesticides. "The one factor that EPA actually has control over is the one that they refuse to regulate," he said.

The EPA is working on a new round of risk assessments for pesticides, but the results of those assessments have not yet been released. Meanwhile, the agency is due to file its response to the environmentalists' lawsuit later this month. Jenkins said Thursday's report would have "no real effect" on the legal action, which could go on for years.

More about the bee die-off:

• Rise in bee deaths stirs up a buzz
• Neonicotinoids tied to crashing bee populations
• Mites and virus team up to wipe out beehives

Alan Boyle is NBCNews.com's science editor. Connect with the Cosmic Log community by "liking" the log's Facebook page, following @b0yle on Twitter and adding the Cosmic Log page to your Google+ presence. To keep up with Cosmic Log as well as NBCNews.com's other stories about science and space, sign up for the Tech & Science newsletter, delivered to your email in-box every weekday. You can also check out "The Case for Pluto," my book about the controversial dwarf planet and the search for new worlds.

This past winter has been exceptionally rough for honeybees — and although it's too early to say exactly why, the usual suspects range from pesticides that appear to cause memory loss to pests that got an exceptionally early start last spring.

Friday marked the start of an annual survey that asks beekeepers to report how many bees they lost over the winter, conducted by the Bee Informed Partnership, the Apiary Inspectors of America and the U.S. Department of Agriculture. The advance word is that the results will be brutal.  The New York Times, for example, quoted beekeepers as saying the losses reached levels of 40 to 50 percent — which would be double the average reported last year.

One beekeeper in Montana was quoted as saying that his bees seemed health last spring, but in September, "they started to fall on their face, to die like crazy."

Dennis vanEngelsdorp, an entomologist at the University of Maryland who is one of the leaders of the survey team, said he can't predict what the past winter's average loss figure will be. The beekeepers' reports are being solicited online for the next two weeks, and the figures are due for release on May 7.

"What I can say is, when we were in California this year, the strength of the colonies that were there was significantly lower than it was in previous years," vanEngelsdorp told NBC News. 

Pesticides at issue
That's consistent with a mysterious ailment known as colony collapse disorder, which has stirred scientists' concern for the past decade. The malady almost certainly due to combination of factors — including the Varroa mite, a single-celled parasite known as Nosema, several varieties of viruses, and pesticides. Researchers point to one particular class of pesticides, known as neonicotinoids, as a prime suspect.

Neonicotinoid-based pesticides are commonly applied as a coating on corn seeds, but the chemicals can persist in the environment. Although they have low toxicity for mammals, they've been found to have a significant neurotoxic effect on insects, including bees. Several European countries have banned neonicotinoids, the European Union has been looking at a wider ban, and the Environmental Protection Agency is considering new limitations as well. Just last week, a lawsuit called on the EPA to suspend the use of two types of neonicotinoids immediately.

Two recently published studies add to the concern: This week, researchers report in Nature Communications that neonicotinoids block the part of a bee's brain that associates scents with foods. They suggest that without that functionality, the bees effectively forget that floral scents mean food is nearby, and thus die off before they can pollinate. A study published in January in the Journal of Experimental Biology found a similar link to problems with scent-related learning and memory.

Mild winter, dry summer
Although neonicotinoids are currently front and center in the debate over colony collapse disorder, they're not necessarily the primary reason for this winter's dramatic dip in bee colonies.

VanEngelsdorp noted that the winter of 2011-2012 was easy on the bees: Losses amounted to just 21.9 percent, compared with a 2006-2011 average of 33 percent. However, the mild winter was kind to the bees' pests as well. VanEngelsdorp speculated that Varroa mites may have gained an early foothold in the hives last spring. By the time beekeepers started their treatments on the usual schedule, it was too late to keep the mites from weakening the colonies. That would help explain why the past winter's losses were worse than usual.

Scott Bauer / USDA via AP

A worker bee carries a Varroa mite, visible in this close-up view.

California beekeeper Randy Oliver, who discusses industry trends on the Scientific Beekeeping blog, said the past summer's drought was also a factor: "When there's a drought, the bees are in poor shape with the food," he told NBC News. He said he and other beekeepers predicted that there'd be heavy winter losses last July, when the scale of the drought became clear.

Heavy losses are bad news, and if bee colonies are becoming progressively weaker, that's worse news. It's not just because of the honey: The Department of Agriculture says that bee pollination is responsible for more than $15 billion in increased crop value each year. A bee scarcity increases costs for the farmers who need them for pollination, and that could lead to higher food prices. But Oliver said it's important to keep a sense of perspective about the bad news.

"The situation with the bees is not dire," he said. "The bees are doing OK. There's no danger that the bees will go extinct. ... That's just not true."

More about bees:

• Neonicotinoids tied to crashing bee populations
• Zombie bees spread to Washington state
• Mites and virus team up to wipe out beehives

Alan Boyle is NBCNews.com's science editor. Connect with the Cosmic Log community by "liking" the log's Facebook page, following @b0yle on Twitter and adding the Cosmic Log page to your Google+ presence. To keep up with Cosmic Log as well as NBCNews.com's other stories about science and space, sign up for the Tech & Science newsletter, delivered to your email in-box every weekday. You can also check out "The Case for Pluto," my book about the controversial dwarf planet and the search for new worlds.

Is a widely used pesticide to blame for making bees disappear? The debate over a class of chemicals known as neonicotinoids was the focus of a spot on NBC's "Nightly News" tonight, and NBC News' Anne Thompson has supplemented her TV report with a couple of Web-only videos presenting the pro and con arguments on neonicotinoids.

There's little question that pesticides play a role in the malady known as colony collapse disorder, in which whole colonies of honeybees leave their hives abruptly and never return. Most experts would say pesticides are among a host of bee-debilitating factors that also include viruses, mites and fungi. However, in recent months a number of studies have highlighted neonicotinoids as a particularly worrisome threat to bees.

So far, the Environmental Protection Agency has not acknowledged a link between colony collapse disorder and the reported problems with neonicotinoids. The chemicals are attractive to farmers, particularly for corn crops, because they are much more toxic to insects than they are to mammals. The stuff is sprayed on corn seeds as well as plants in the field.

One of the bonus videos is an interview with Steve Ellis, owner of the Old Mill Honey Company in Minnesota. "The quantity of neonicotinoid systemic insecticides that are being used in the country is mind-boggling," he says. Ellis is one of the backers of a petition campaign calling on the EPA to suspend further use of a type of neonicotinoid known as clothianidin.

In the other video, David Fischer, chief ecotoxicologist for Bayer CropScience, contends that neonicotinoids don't kill off bee colonies as long as they're used properly. He contends that in the studies linking the chemicals to colony collapse disorder, the bees were exposed to "unrealistically high levels" of the chemicals. Bayer CropScience markets clothianidin in brand-name pesticides that include Poncho and Prosper.

Watch the three videos, then feel free to weigh in with your vote and/or your comments.

More about the bee debate:

• Two studies link neonicotinoids to bee crash
• Fungal threats are a growing concern
• New bee viruses found attacking healthy hives
• Bees feel the sting of huge population plunge

Alan Boyle is msnbc.com's science editor. Connect with the Cosmic Logcommunity by "liking" the log's Facebook page, following @b0yle on Twitter and adding the Cosmic Log page to your Google+ presence. You can also check out "The Case for Pluto," my book about the controversial dwarf planet and the search for new worlds.