The best way to clear the waterborne bacteria is by UV. A UV is also very useful when putting new fish into the display or reducing the possibility of a disease outbreak should you have a temperature fluctuation.
There are a couple of other options but they are not as effective... ozone into skimmer and also Hydrogen peroxide dosing. You have to be very careful using either method as they can wipe out your tank.
The bacteria will lower your dissolved oxygen content of the water and also your redox potential. It is important to keep your skimmer running.
The upside is that the bacteria will consume nitrates.
Cheers,
Tim
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