This would not be good to do mainly for 2 reasons. First, fish need oxygen in the water to live and oxygen gets in the water (and CO2 gets out) at the surface. It's a false myth that an air pump will add much oxygen to a tank. Studies have shown that very little gas exchange occurs on the surface of bubbles as they rise through the tank. It does help in that it brings water from the bottom of the tank to the top and constantly moves the refreshed water into the tank.
Secondly, with a small mouthed bottle it would be very difficult to feed and otherwise care for the fish.
Use a container with a large, open top for plenty of exposure to fresh air and you will have far better success with keeping fish. What you are suggesting would also certainly lead to killing fish needlessly.
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