Many of the technology within the field of fluorescence microscopy has been developed from the medical science field. A natural use for this technology is studying organisms that naturally have fluorescence characteristics.
There are two main strategies used in medical sciences for studying non-fluorescing organisms. The first is using antibodies that bind to proteins of interest. These antibodies can be conjugated (joined) with a fluorescing protein. This allows for the protein of interest to be illuminated by the conjugated antibody, and you can then measure and observe through fluorescence microscopy.
The second strategy is to insert a gene that codes for a fluorescing protein into an organism's genome. This is particularly useful in studying specific bacteria of interest.
These methods can be applied to studies in the laboratory and can be used to diagnose certain diseases such as tuberculosis, meningitis and malaria.
Fluorescence microscopy is primarily used in environmental monitoring. Usually air and water samples are passed through membrane filters, and these filters are examined using fluorescence microscopy to determine if there is bacterial contamination.
There are many possible uses of fluorescence microscopy within a variety of industries. A very common example is the use of this technology within the food industry. You can directly count microbes in many food products and thus determine the contamination of the food in question. This method is far more sensitive than standard bacterial culturing.