Planted Tank Guru
Join Date: Jan 2010
Location: Contra Costa CA
I think the nitrifying bacteria will be OK, but it will be a good idea to monitor the situation. Good on the prompt removal, keep it up. If you are suspicious that the nitrifying bacteria need to be replaced or supplemented look for a product with Nitrospira species of bacteria. When they are first added to the water it would be best if the ammonia is as low as possible (so another big water change) then give them a day or two (read the label) to get attached to things before doing another water change.
Had the bacteria been keeping up with your small additions of soil?
The 'non toxic' aspect of ammonium is not that it really is non toxic, but that fish can exclude charged particles from their cells. Ammonium is NH4+, a charged molecule. I have no idea if bacteria can do the same, but I would suspect they can.