Under normal circumstances, I would expect little in the way of direct microbiological activity in finished fuels, such as diesel or gasoline. What is more likely is the presence of a water layer on the bottom of a fuel storage tank that will provide a favorable environment for bacteria, especially anaerobic microbes such as sulfur reducing bacteria (SRB's). These organisms thrive in the fuel-water interface layer and can produce suspended solids/gums/sludge and acidic conditions in the water layer.
The best course of action is to physically remove free water layer if possible. This may require decanting out the fuel to a temporary tank, which will provide an opportunity for cleaning the tank as well. You may have to consider the periodic use of an approved fuel microbiocide additive on a regular basis to keep the problem under control either as an alterative to the tank work or as a post-tank preventative maintenance measure.
Good Luck.
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