This Seeking Tech guide will show you how to get the Beekeeper trophy and achievement in the Master Collection version of Metal Gear Solid 3: Snake Eater.
To unlock this, you need to “use bees to harass an enemy.”
During the opening section, if you managed to enter Dolinovodno without being in Alert or Caution status, then you should get a cut scene showing an enemy standing directly underneath a beehive.
Once you regain control, shoot the beehive to unlock Beekeeper. Use the following video as a reference:
While this is the easiest way to get the trophy and achievement, there should be other opportunities later on if you already passed through this area.