There are lab checks that can be done and are done to check bulk fuel installations for fungus.
Good care of the tanks of fuel, i.e. ensuring water drain checks are done on a daily basis. Here at my location we fill from tank-tainers containing 20 thousand litres that have been at sea. The fungus and quality lab checks are done on receipt of a new container, before going into bulk storage.
Boron compound treatments have been successful in the past in treating bulk fuel and affected aircraft fuel tanks and for prevention of fungus development.
However, some engine manufacturers have limits of how much boron from these compounds can be tolerated by the turbines of their particular engine during its working life.