Microorganisms in Louis Pasteur's experiment of beans
So, where do microorganisms come from? Do they come from the environment?


Yes!

There is no spontaneous generations. Microorganisms (virus, bacteria, unicellular eukaryote, small multicellular eukaryotes) just like macroorganisms (big-enough to be seen by the naked eye multicellular eukaryotes) are not recreated out of nothing. Abiogenesis happened a long time ago and as far as we know, it is not happening today.

This means that if there is a micro-organism somewhere, it must have come from the environment. It did not pop up out of nowhere.