How are discoveries made in microbiology?

Slowly.

I have a cousin who is in cancer research on a microbiology level. In general they start out with a hypothesis – with Condition X, knowing how organisms usually react, trying Compound Y and Compound Z ought to have the following effect.

Then they set up a couple of hundred samples, apply the compounds to the organisms, wait (weeks, maybe months) and see if their hypotheses are correct. If not, they adjust amounts, levels, temperature – various variables, and try again.

To me, it’s painstakingly frustrating, but ultimately it’s how science is done – you try something, see why it failed, try something else, and so on.

There are many different ways to drill down to the cellular level, that one can use together to triangulate. By and large, the structural issues (which organites are where) are explored with microscopes and the chemical ones with NRM, mass spectometers and a batery of enzymes which behavior is already well known.