Air holes are part of the design of your bottle system. The number, sizes, and shapes will depend on what you’re using your system for. In general, you’ll need to make air holes to provide adequate ventilation for plants, insects, and other life. And, it’s important that the holes be small enough to keep fruit flies and other small insects inside your system. One thing to remember is that the more holes you have, the faster the contents of your system will dry out, and the more you’ll need to provide water.
There are multiple ways to make air holes. Find the way that works best for you.

Using a nail poke
Simply push the push pin through the bottle being careful not to push so fast or hard that you crush the bottle.
Push just the very tip of the heated soldering iron through the bottle. Be careful to barely touch the bottle so that the holes are small enough to contain the organisms within.
Making Holes in Bottle Caps
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