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The only way to complete avoid algae is to be very sterile. You can also try to block light from getting to the water surface. In my emersed setup, 2.5 gallon with 25 watt spiral compact, I cut a piece of styrofoam that floats on the water surface. It is about 1/4 in smaller all around so it does not get hung up. I then cut holes for pots and put my plants in the pots. They wick up moisture through the soil/rockwool (I need to change the rockwool) and the raft prevents the light from reaching the water and allowing algae to grow. It also, along wiht the glass cover, help prevent evaporation. Maybe you could use ducttape to cover the bottum of the bottle up to the water level and a piece of black plastic, like a trash bag, over the soil with a hole poked in it for the plant. TO learn more about steralizing check this out
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