More than 40% of U.S. honeybee colonies died in a 12-month period ending in April, extending a troubling trend that has scientists scrambling for a solution and professional beekeepers struggling to stay in business.

The Agriculture Department said in its annual honeybee survey released Wednesday that beekeepers are starting to lose large numbers of bees during both the summer and winter—presenting scientists with a new wrinkle since die-offs had generally occurred during the cold winter months.

“I think the situation is changing,” said Dennis vanEngelsdorp, an expert on honeybees at the University of Maryland. “It remains bad but I don’t know if we can assume the same thing is happening year to year.”

For the first time since the survey began five years ago, the summer loss rates exceeded the winter loss rates, suggesting bees are becoming vulnerable during a time of the year they were thought to be healthy and robust. The most recent summer loss rate reached 27%, up from 20%.

While the precise cause of the honeybee crisis is unknown, scientists generally blame a combination of factors, including poor diets and stress. Some bees die from infestations of the Varroa mite, a bloodsucking parasite that weakens bees and introduces diseases to the hive.

Environmental groups also point to a class of pesticides known as neonicotinoids. In April, the Environmental Protection Agency said it would stop approving new outdoor uses for those types of chemicals until more studies on bee health are conducted.

During the one-year period ending in April, beekeepers lost 42% of their colonies, according to the survey, marking the second-highest rate of loss since the Agriculture Department began tracking annual statistics in 2010. The loss rate was up from 34% during the previous 12-month period.

Bee deaths present a considerable challenge to professional beekeepers, who spend substantial amounts of time and money to replenish their colonies. Many beekeepers, already in their 50s and 60s, are considering early retirement or are being forced out of the business due to the expense. 

Beekeepers have said they start to feel a financial pinch once annual loss rates rise above 19%.

“It’s just tough because [high loss rates] seem like the new norm today,” said Blake Shook, owner of Desert Creek Honey in Texas. “And that’s challenging because it’s not sustainable.”

A dwindling supply of beekeepers is problematic for the agriculture industry, which relies on honeybees to pollinate more than $15 billion of crops each year. Almond growers in California, already dealing with the state’s crippling drought, rely almost exclusively on honeybees for pollination.

“If beekeepers are going to meet the growing demand for pollination services, researchers need to find better answers to the host of stresses that lead to both winter and summer colony losses,” said Jeff Pettis, an entomologist at the Agriculture Department’s bee research lab.

The White House created a task force last year to study ways to prevent honeybee losses. It is expected to issue a national plan in coming weeks.

The honeybee crisis dates back to at least 2006, when beekeepers first reported a troubling phenomenon known as colony collapse disorder. Adult bees were simply vanishing from their hives, leaving behind the younger bees, the queen and the honey.

Beekeepers are witnessing fewer instances of colony collapse disorder but the overall high losses are still “very troubling,” Mr. Pettis said.

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