How about something along the lines of;
What happens if you change it from a clear bottle to a colored bottle?
If the bottle is currently capped; what happens if it is capped, or vice-versa?
What happens if you make the dirt more acidic/basic?
What happens if you increase the pressure in the bottle?
etc, etc
What method of torturing the plant most interests you? And not just the few ideas I listed, come up wit your own.