The CO2 controller doesn't know what time it is. It's operating completely based on pH. If pH rises above your set point, it turns on the CO2 to lower it.
There is some debate about the best way to do it. But the consensus based on what I've read is that CO2 does no good at night and since your plants will already off-gas CO2 at night, your fish don't need to be exposed to any more. Further, it has been said that pH fluctuations day to night from CO2 concentrations alone are not a problem for fish. And you can run with more CO2 during the day when the plants need it, than you might otherwise by not adding it at night.
I operated for several years using pH controllers 24/7 and recently switched to keeping the controller but putting a timer on the powerstrip that controlled the CO2 so it would prevent it from coming on at night. I found no adverse effects and when one of my solenoids stopped closing the valve, I rebuilt my rig (which serves 3 tanks) so one solenoid turns all on and off and runs only on a timer. I also increased water circulation in the tanks and bumped up CO2.
I read that while not all plants pearl equally, for those most likely to pearl, assuming you start CO2 1 hr before lights on, you should see pearling within an hour after lights on, otherwise you can increase CO2. And in theory you can keep increasing CO2 unless your fish show distress (hanging out at the surface.) Tom Barr said that based on the charts, he has run levels that should be more than fatal without a problem. It's one of those things that's kind of fuzzy. He asserts that if you're getting algae, you need more CO2 in almost every case, and my experience seems to confirm that so far. (more CO2 can also mean better water circulation as it might just be uneven throughout the tank.)
Michael
