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For the whole yeast set up, I've seen putting an air stone on it, or just putting the end of the tube near the filter intake, which way is more effective?
 

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Putting the end of the tube near the filter intake and allowing the bubbles to be smashed up by the filter impeller is more effective in getting CO2 dissolved into the water.
Yep, I agree. Also, by adding the CO2 bubbles to a filter or powerhead you don't get a slimy buildup that you would get if you connected the tube to an airstone. Eventually the airstone gets totally clogged up and then bad things can happen to your DIY CO2 setup.
 
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