Water and microbes in the form of bacteria and fungus (commonly called algae) is present in most diesel fuels, therefore it is best to buy the cleanest and freshest fuel from high volume dealers like Flying J.
There has been much discussion, as well as misunderstanding, of algae in diesel fuel. Algae require sunlight to live and grow. As there is no sunlight in a closed fuel tank, no algae can survive. However, some microbes can survive and feed on the diesel fuel.
These microbes form a colony that lives at the interface of fuel and water. They can grow quite rapidly in warmer temperature or even slowly over an extended tine (Steve's coach was stored in a heated warehouse and driven very little for years). Parts of the colony can break off and clog the fuel lines and fuel filters.
It is possible to either kill this growth with a biocide treatment, or eliminate the water, a necessary component of microbial life. There is a number of biocides on the market, which must be handled very carefully. If a biocide is used, it must be added every time a tank is refilled until the problem is fully resolved.
Biocides attack the cell wall of microbes resulting in lysis, the death of a cell by bursting. The dead cells then gather on the bottom of the fuel tanks and form a sludge, filter clogging will continue after biocide treatment until the sludge abates.
Given the right conditions, microbes will re-populate the tanks, and re-treatment with biocides will be necessary. With repetitive biocide treatments, microbes can form resistance to a particular brand. Trying another brand with a different antibiotic may resolve the problem.
Tank removal and internal cleaning is usually not necessary unless the problem is severe, as there are fuel additives available that will do the job much cheaper.
Gerald