A prolonged and mysterious die-off of the nation’s honeybees, a trend worrisome both to beekeepers and to farmers who depend on the insects to pollinate their crops, apparently worsened last year.

In an annual survey released on Wednesday by the Bee Informed Partnership, a consortium of universities and research laboratories, about 5,000 beekeepers reported losing 42.1 percent of their colonies in the 12-month period that ended in April. That is well above the 34.2 percent loss reported for the same period in 2013 and 2014, and it is the second-highest loss recorded since year-round surveys began in 2010.

Most striking, however, was that honeybee deaths spiked last summer, exceeding winter deaths for the first time. Commercial beekeepers, some of whom rent their hives to farmers during pollination seasons, were hit especially hard, the survey’s authors stated.

“We expect the colonies to die during the winter, because that’s a stressful season,” said Dennis vanEngelsdorp, an assistant entomology professor at the University of Maryland who directs the survey for the bee partnership. “What’s totally shocking to me is that the losses in summer, which should be paradise for bees, exceeded the winter losses.”

Bees are not in danger of extinction, but their health is of major concern to agriculture, where honeybees’ pollination services are estimated to be worth $10 billion to $15 billion a year.

Nobody knows with certainty why honeybee deaths are rising. Beekeepers once expected to lose perhaps 10 percent of their bees in an average year. But deaths began to spike in the middle of the past decade, when a phenomenon in which bees deserted their hives and died en masse, later named colony collapse disorder, began sweeping hives worldwide.

Those mass die-offs have abated somewhat in recent years, experts say, but colonies remain in poor health, and overall death rates remain much higher than in the past.