Ok, just a quick thought.
http://www.**************.com/forum/library/water-filtration/aquariummicrobespart1/
Aquarium Microbs Part 1:
Says that ammonia is toxic at .35 ppm. That there will be problems for fish between .5 and 1 ppm ammonia. And death might occur at anytime above 1.5 ppm.
This is NOT true. I've seen higher than .5ppm in the "wild" where fish are thriving and breeding. I've also seen several populations of fish (of a range of species) do just fine after being exposed to over 2 part ammoinia. No loss in gill function, no elevated liver or renal function or any fluctuations in blood chemistry showing a problem.
The article also uses ***ue terms "could be" and "can be" are used alot. A big grey area for a lot. We also know there are other things fish die from while in water conditions like this, and can now pin point almost any death instead of using a blanket term like "New Tank Syndrome" to cover the loss.
Aside from seeing the chemical break down of the water, fully understanding the interworkings of fish blood chemistry and the fish's ability to process the ammonia is important when looking at the impact of water quality of any given species.
One thing I'd like to toss out for consideration:
The bacteria do live on surfaces (substrate, filter media, glass etc...). Many species of the bacteria aquarists want breed and live the early life stages in the water column. Doing big waterchanges will be effectively eliminating the growing colony.