I posted this response in the Chemistry Forum and thought I would add it here for remarks:
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Jason,
Thanks for the link.
The remarks that Agathos has made in the posted thread above tells it pretty much the way I believe from the research I have read regarding populations of bacteria studied in the ocean, though this information can't be directly correlated to a reef tank.
For example scientists have taken samples from the ocean surface water at various spot and then analyzed the bacterial populations present in one gallon of ocean water. They have found that there are literally tens of thousands of types of bacteria in one gallon of ocean water found within the top 30'. If I were to use this knowledge and try to transfer what to expect to find in an average reef aquarium I would expect to find at least thousands, if not a lot more types of bacteria in a reef tank.
Other research completed on bacteria introduced into reactors used on tanks has shown that introduced bacteria do not compete in general with native species for the nitrogen cycle purposes. The research shows that usually several species of bacteria end up dominating the nitrogen cycle and the bacteria species will shift when the concentrations of nitrate, nitrite and ammonia are changed. Further research has demonstrated that the bacterial species will shift with changes in dissolved organic carbon content and type. Further research has demonstrated that the bacterial species will change if the heavy metal content changes in amount and type. Further research has demonstrated that the bacterial populations will shift with temperature changes. These bacterial shifts in species does not mean the the other species go away. To the contrary they still survive, but not in dominate numbers. Recent research has shown that bacterial species have survived for many tens of thousands of years, many in very reduced numbers, but still available if the need presents itself to make a come-back.
One might extrapolate from this research that every change we make in food, vitamins, organic carbon dosing, supplement dosing (heavy metals), temperature changes........etc can cause shifts in bacterial populations in the water column, substrate, rock, inside the coral tissues and in the secretion layers around the coral. Thankfully, these changes in bacterial populations in most situations are not a bad thing and the bacteria that replace the others are actually more effective at the job for nitrogen cycle purposes.
However, hobbyists do notice bad things happening occasionally from these bacterial specie shifts, IMHO. For example, some hobbyists will dose carbon sources (like vodka, vinegar, sugar, vit. C and amino acids) and notice problems starting. What kind of problems to expect from bacterial specie shifts would be tissue necrosis in coral. What happens according to research, is the new bacterial species that take over can (in some cases) produce toxins that actually kill the coral. Some of the toxins can be sulfur compounds or other organic sources that are very toxic. In other cases, the new bacterial will start physically eating the coral tissues and beneficial bacterial species. In many cases it is impossible to stop the new bacteria from killing the coral. Perhaps fragging the coral may help.
IMHO, the moral of the story is that every change we make in a reef system can cause bacterial population shifts, either for the better or worse. So, one should be careful in what they add, and make changes very slowly and carefully watch for noticeable changes in the coral color, polyp health and signs of tissue necrosis. One should only change one variable at a time.
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FWIW, to add to what I have posted above, the same applies to other micro-organisms found in a reef tank, especially the cyanobacteria, algae, symbiotic algae within coral tissues and dinoflagellates. These other micro-organisms can change in populations for the same reasons that bacterial populations change and these other micro-organisms can in some cases, produce toxins that harm the coral. In other cases, the changes in bacterial & other micro-organism populations can cause color changes in coral that many hobbyists seem to like.
When playing with carbon sources, vitamins, amino acids, higher temperatures, heavy metals (micro-nutrients), changing food types, making major changes in water parameters, introducing new things into your tank and many other aspects of our hobby, we are playing with fire. Sooner or later someone is going to get burnt, which is seen occasionally in this forum.
I have been burnt several times, since I like to experiment more than anything else.