Good post Doug,
I called several bacteria companies including one that I attended a training class with in Canada. They all stated that if one were to provide samples of both water and substrate (with muck) that they could engineer bacteria to match or (supplement) what is missing. Of course this is custom blending bacteria for every case and will be much more expensive.
I recall a project that had an old saw mill along the lake bank and train tracks that led to the middle of the lake. Every week the mill would send a train car full of saw dust and dump it in the lake. This was about 60 years ago.
Now the residents wanted to reduce the muck levels and we sent a bottom sample to the bacteria company to break down what the muck was composed of (wood pulp) and a bacteria was custom blended to work on these areas. Adding the bacteria with aeration was the only way this would work since a definate thermocline was present and oxygen level were below 1 mg/l
During my stint at Sea World, we used to add "donar" gravel from already established aquariums to jump start the bacteria cycle. I agree with Doug in that once the optimum carrying capacity has reached the bacteria will stop reproducing and the next strain of bacteria will beging to work. Case in point the cycle an aquarium during start up...fish are introduced and the ammonia builds up. The first strain of bacteria brings the ammonia down. Next Nitrites begin to spike. The next strain of bacteria take care of the Nitrites. Finally the Nitrates begin to rise which is not too dangerous for the fish as the other two and can be lowered by simple water exchanges (in a pond, rain and evaporation).
This topic should be one of those post that are archived. This has been a great conversation between everyone!