In the future, the honeybees are dying, dead. Even the clones cannot survive. The narrator has been traveling time, even stealing almonds and raspberries from places about to be destroyed so they can recreate recipes otherwise impossible.
The honeybees from the past are transported to the future. It's not explicitly stated, but perhaps the time-traveling--transporting the bees from past to the future--is responsible for their demise. Ah, the meddlesome-ness of human nature.