As the article you linked will note, what you're seeing is delamination...not damage caused by algae or other microbes.
A poor gelcoat (or porous gel coat, as the case may be) can cause this as can pitting and damage in the coat. A properly poured and painted coat should prevent it, but where polyester resins and a gelcoat are used, the aging of the resin, hull (or airframe flexing), and the inevitable cracking of the gelcoat will allow in moisture. It's the moisture that's causing your problem. Not microbes.
An epoxy underlying structure with something other than a polyester coat will make a big difference, but it's more expensive, and not widely used. It's largely used on aircraft, however, where fiberglass and composite structures are involved.
Gelcoat issues are largely cosmetic issues, not structural ones.
These have nothing to do with aircraft fuel tanks, however, as most fuel cells are not fiberglass, nor gen coated on the inside.