And you thought, we would live in a clean world. Let me tell you, you do not even want to know, what is on chicken eggs.......
Bacteries are everywhere. They only start to pose a problem if the conditions allow them to grow more than what they should. Consider your skin for example, tons of bacteries of all kind. Under normal conditions, the "good" range of bacteries (flora) is balanced with the "bad" flora. The bad bacteries do not do us harm, unless they get to a place they should not be, e.g. inside the skin with a cut or a sliver. Then you get infections...
Here in this case with the aquarium, we have to change the conditions for the nitrosoma and nitrobacter in order to make them grow and make our fish happy.