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I have a planted Fluval Mega Flex. It is an AIO tank with a heater, media and pump in the last compartment. I am running CO2 with an inline diffuser similar to this one on the output hose
https://images.app.goo.gl/EusRTuoio1zkTJuA6 . I also added extra bio media in a media sock in the last compartment.
Should I add an air stone in the last compartment also. I feel that it is not getting enough aeration as the water looks stagnate and Im seeing some protein build up. Is that a good idea or will it gas off all my CO2?
 

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It will off gas your co2. It's not protein on the surface it's bacteria. You can aim the nozzle at the surface to create a little surface agitation and when you do your weekly water change use a cup to skim the surface for part of the change.
 
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