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I just set up a DIY CO2 reactor (yeast and sugar, 2x2 liter bottles) on my 55 gallon planted tank. I have a small shrimp colony and moderately stocked with community fish. I have a fluval 407 canister and 2 sponge filters (shrimps love them).

In order to keep the CO2 from gassing off I put a timer on the air pump so the sponges kick on an hour before the lights cut out and shut off 2 hours before the lights come back on.

I'm sure the canister alone can handle the load, but it's nice having backup sponges for the shrimp to hang out on and comes in handy when I need to set up a quarantine/nursery on short notice. Figure the bubbles at night will also help keep overnight CO2 low as well.

Does this sound like a fair plan or should I ditch the sponge filters and replace with airstones? Is my beneficial bacteria in the sponges going to have daily die offs?
 

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The sponges should work. Remember that the air bubbles from an air stone do very little to the oxygenation of the water. Instead the bubbles create circulation through which gas exchange can occur over the large surface area at the top of the tank. I think your setup will be just fine as long as you don’t just pump up the co2.. a drop checker will be very helpful.
As for the beneficial bacteria, I’m not sure how they would react to the co2 on the sponge (if the co2 is coming out the sponges- I’m not clear on how the co2 is getting in the water) .. my guess is that it should be fine. Even with some bacteria daily die off.. a 55gal provides a massive amount of surface area and small die off would be quite negligible.
 

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Me, personally, I'd leave the sponges. You should still get enough agitation for o2 exchange and off gassing. Just keep an eye on the inhabitants as diy co2 can be unpredictable. If it seems like they're struggling after lights out then maybe consider ditching the sponges filters for air stones but I wouldn't try to fix something if it's not broken.
 
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