Understanding how the bacteria works can help here. They reproduce by dividing. So what causes them to divide? The answer is they will do so when there is more ammonia or nitrite than they need to thrive. When this is the case they reproduce. The other side of this coin is when there is less of these things than the colonies need to thrive, they reproduce less or not at all.
Next, the bacteria live inside a bio-film they create which allows them to attach to hard surfaces in a tank. This also means that everything they need to live and thrive must be delivered to them.
Finally, the bacteria will colonize anywhere the things they need are available. They will reproduce the most where they are left alone and where the get the most of what they need.
So, the bateria can be in flters in the substrtae on any hadr surface in a tank that meets the above conditions. The last condition is that the bacteria are somewhat photophobic so they tend to do best in the dark or in area without bright light.
In an established tank lok for the most bacteria to be where the conditions are most optimal for them. For most, this is in filter medias and substrate. So when we rinse out media or vacuum the first inch of substrate we may be removing some of the good bacteria. However, it takes a lot to remove much of it. So what happens when we do maintenance?
Lets assume we accidentally remove or kill 10% or even 20%, I have no reason to believe we do this, but for this explanation we will work with these amounts. We know that the ammonia bacteria can double in about 8 hours and the nitrite ones in close to 11. These bacteria can up or down regulate the amount of nuritents they use before they change their reproductive habits. This means they can do OK in a bit more or a bit less without any issues. So, the 10% or 20% numbers are actually a few points less.
Next, if it takes 8 hours (480 minutes) for the ammonia bacteria to double then it would be more like 48 to 96 minutes for those bacteria accidentally removed to be replaced by reproduction. The nitrite ones would be a bit longer. Those times do not account for any upregulation. So in many cases the deficit of bacteria from a rough cleaning will self correct in anywere from 20 to maybe 75 minutes.
What the above is telling us is that it is not easy for us to cause an ammonia and/or nitrite spike from doing routine maintenance and water changes. And even if we do so, we have to be pretty quick to test it or it will self correct before we see it.
The greatest problems can occur when we remove media and substrate from a tank and in so doing, we remove too much bacteria. Bear in mind that, unless one has a substrate with ive plant roots, only the top 1/2 inch or so has enough oxygen to support nitrifying bacteria. At one inch there are none.
Here is one good clue about the effects one's maintenance has on the fish. Water changes and our hands in the tank tend to stress fish. They hide until we are done and the tank is refilled. How they behave after that offers a pretty good clue to knowing if there is a problem or not. In an established tank oince the new water is in, the fish come out and are usually pretty active. However, if there is ammonia or nitrite in the water they will not do so. They will tend to hide or are at the surface. They may hang out in the filter return. But they will not behave in their normal manner.
