Wow there are really a lot of questions and interest in this topic. Maybe I can help a little.
What happens to bacteria after you put them in a pond? They multiply or they die. Bacteria require soluble nutrients for rapid assimilation, growth and performance. In addition, the presence of trace elements such as potassium, calcium, magnesium, sulfur, sodium, chloride, zinc, iron, manganese, and many more are required for biological activity. If these things are present, the bacteria thrive and consume sludge. If they're not present they die. This is why the most effective sludge consuming bacterial products require "activation" meaning that you provide the bacteria with nutrients and carbon source, heat, and oxygen for 24 hours before applying to your pond. That's not to say that other products aren't effective. There is a caveate to this life or death situation...larger organisms feed on bacteria and larger organisms feed on those organisms so essentially, in a perfect pondmeister world, the bacteria keep reproducing and eventually become fish food. Biolgical activity is also very dependent on temperature and pH.
There are no direct effects on other organisms. There are not even direct effects on the vegetation itself. The idea is to consume the soluble nutrients via bacterial digestion so that we starve the algae of nutrients. The bi-products of this process are mainly CO2 and inert ash. There are some other greenhouse gasses but they are nominal in abundance.
Indeed there are different types of bacteria that thrive in different environments. Some of these "snake oil salesman" might have told you that their bacteria function in both aerobic and anaerobic conditions. This does not appeal to our intuitions. However the bacteria they are referring to are called facultative bacteria and do in fact live in aerobic, anoxic and anaerobic conditions. However they thrive and consume nutrients best in aerobic conditions. The organisisms that are the driving force of sludge digestion (really we're talking about the nitrogen cycle) are Nitrosomonas, Nitrobacter, Pseudomonas, and Clostridium.
You can enhance the effect of bacteria by providing more surface area for them to live in a process called "fixed film media" we can install growth media such as a product called Aquamats or even the popular Floating Islands that have been discussed on this forum. The idea is to have a media in which layers of bacteria grow on. Aerobic bacteria grow on the outermost portion of the media while anaerobic bacteria grow closest to the media and anoxic bacteria in between. In a Floating Island, the roots extending down into the water column provide this growth media.
The effects of bacterial sludge and nutrient digestion are well documented and some pond products can consume up to an inch per week of organic sludge. I've personally seen it happen. Bacteria is responsible for treating our wastewater, creeks, ponds, and virtually any surface water. If you really want to bore yourself to death on this topic (as if I haven't done so already
) pick up a copy of Metcalf & Eddy's
Wastewater Engineering; Treatment and Reuse. This is the bible for wastewater engineers and has invaluable information on bacterial water treatment.
