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I have a 60 gallon tank that has been running for about 6 weeks. It is heavily planted and is being injected with CO2.

The pH prior to CO2 is about 7.5. With CO2 it is 5.7. The kH is 4 and I am fairly confident there is some other buffers in the water, including some Manzanita. It is 90% RODI and 10% tap (tap water is very, very hard 20ish dkH)

I am also dosing with the Seachem Flourish line, including excel.

My ammonia level has remained pretty constant at .25. I have yet to see a Nitrite reading, and my nitrate levels hover from 5 to 10.

My question is: is the drop in pH from the CO2 creating an environment that is not favorable to the beneficial bacteria? I have 2 danios that do not seem to be in any distress. If I understand correctly the drop in pH from CO2 injection is not a cause for osmotic shock for fish as the TDS does not actually change. But could it slow down or inhibit the nitrogen cycle?
 

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That is something I have not yet figured out.
The nitrifying organisms use carbonates for their source of carbon. In almost all set ups low carbonates = low pH. And the organisms grow slowly. But are the bacteria slowed for lack of carbonates? Or from the low pH? Or both?
All the other minerals you are adding (plant fertilizer, minerals from the tap water) are good.

Here is what I would do:
Slow the flow of CO2 so that there is no more than 1 unit of pH drop. In this case, from 7.5 to 6.5. This means you will have 30ppm CO2. This is plenty of CO2, no need to add more. pH of 6.5 seems to be the lower end of where these bacteria will be OK, though they are not growing very fast.
I would remove the fish and add more ammonia, see if you can get the fishless cycle off the ground. If there is not a quick response (the ammonia starts dropping immediately) I would next jump start the cycle by adding bacteria from some other source:
~Bottled bacteria that contain Nitrospira.
~Do the fishless cycle outside this tank (perhaps in a bucket) where you can use much harder water.
~Share media from another well established tank that you trust to be disease free.

I have seen a lot of posts from people who see that little trace of ammonia, and it may or may not really be there. At low pH this ammonia (if it is really there) is present in the ammonium (NH4+) form. This is not a problem for the fish.

Seachem Flourish Nitrogen is probably the source of the NO3 in this tank. Read the label, this product does not test correctly. There is other nitrogen in this product that does not make the NO3 test respond. Double the values you are getting from the test to see how much NO3 equivalent is available to the plants.

2 Danios in a 60 gallon do not contribute a significant amount of ammonia. Fish are not really the source of ammonia, anyway. Protein such as fish food is the source (when there are fish or other livestock in the tank)
If you are adding fish food like it was fully stocked, then the food is decomposing, then there would be more ammonia to feed the organisms.
 
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