For the smaller bottles (airpump method) I use black stockings to keep them dark, for the larger ones, black plastic bags work well.
Still trying to figure out how to minimize degradation of the fluid over time. The macro bottle develops a bad smell, the micros grow some stuff. I'll look into adding HCl and see if that helps with these issues.
Dry dosing with an automatic feeder or such would work good, plus an Eheim Liquidoser for the fluids... if money isn't an issue. Of course you are losing the top-off capability that comes with the bottles.
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