When my toilet is not being used, I hear air bubbles. What's going on with it?

Do those bubbles happen when another plumbing fixture is draining like a sink , tub or shower? If so its likely a clogged ventstack which is now trying to vent itself back through your toilet.

No... I took the top off and I see bubbles coming from the tall black tower.

I tightened and loosened the screw at the top before. Could that have something to do with it?

Does it look anything like either one of these https://www.askmehelpdesk.com/attach...-ballcocks.jpg If so that screw is the tank level adjustment. It would not cause this issue but tell me why you are doing anything to it?

Yes and the bubbles are coming from maybe number 4

Months ago the flap wouldn't close so I took the top off to see why. I check the chain and... I honestly don't know why I messed with anything. Now I see and hear the bubbles and a water bill increase, I'm seeking help.

That is the fill tube. Only 2 ways I can think of for air to come out of that tube: air in your cold supply or a broken diaphram in the valve. To check for air in your supply disconnect the supply line as it exits the stop valve below the toilet. Let me know if you do not have a stop valve, if so tell me where you can close off the supply

You know it might be easier and not that expensive to just replace the fill valve and flapper. Fluidmaster has a nice kit Fluidmaster 400C | Toilet Fill Valves | Westside Wholesale is the one I'd recommend.