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Nitrospira and the correct organisms for the nitrogen cycle do not do well at such low pH. I do not know if it is actually the pH or the lack of minerals that is common at that pH.

Here is what I have done to fix exactly that problem:
Add enough baking soda to raise the KH to 3 German degrees of hardness or more.
Add enough GH booster to make the GH at least 3 degrees.
Add fertilizer (Macros and micros) per the EI method.
Higher levels of GH and KH are just fine. These organisms were originally cultured in water a lot like the Rift Lakes. Lots of minerals.

That will ensure the water has the carbonates these organisms need, (They get their carbon from carbonates) and any other minerals they need.

Check these levels daily, I know some substrates remove the KH pretty fast.
 
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