Although it looks like your shingles are breaking down, those dark stains are actuallyliving organisms- bacteria, mold, and fungi
These organisms have infested your roof and are feeding on the components of your shingles
The main culprit for the dark stains is a cyanobacteria called gloeocapsa magma, sometimes called blue-green algae or just algae
Once you see the dark stains, there is a significant infestation of this bacteria and this infestation creates a great environment for mold and other fungi to quickly populate
The bacteria, mold, and other fungi are airborne and can present a health risk, especially for the elderly, younger children, and people who suffer from asthma or other respiratory problems
Additionally, the organisms can make their way into the interior of a structure, including the HVAC systems/ductwork, via the air and tracking by pets and people
In order to completely clean your roof, all of these organisms must be exterminated with a targeted biocide and then thoroughly removed, along with their dark stains