When you treat the irrigation water to kill pathogens with quaternary ammonium compounds, for example, won't the residual present in the water kill the good microflora in the pots?

We are not aware of any research on that question. We do know that oxidizers such as chlorine are rapidly broken down as they contact peat or other organic components in growing media.  The organic matter would also deactivate a quaternary ammonium product. However, there is a possibility that a chemical with residual activity may have some impact on soil microbes - we just do not have any data.

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