Algae: The black stains are called gloeocapsa magma or GM. GM algae is a bacterium that feeds off of both asphalt and limestone roofing in moist, cool and shaded areas of the roof. When there is minimal light, GM forms a blue-green color. The more shaded areas of the roof are more likely to have these algae, which can harbor various types of molds. This explains why some roofs are stained only on one side.