The black “stains” on your roof are actually large colonies of airborne algae called Gloeocapsa Magma (Cyanobacteria). They affix themselves and eat away at the limestone filler found in shingles. As they eat and grow, they readily reproduce into more algae.
This 'plant' will take root on your roof.  As those roots spread to take hold of your shingles, they will wrap around and slowly lift away and separate the granules that protect your roof. SIGNIFICANTLY shortening the lifespan & waterproofing function of your shingle roof.

SHINGLE DETERIORATION

Like plants, fungi, and algae that are growing on a roof have root systems that can cause damage to shingles such as uplifting, spreading of shingles, and decomposition. Not to mention other forces are responsible for damaging a roof, such as erosion from nature or other, more harmful forms of roof cleaning. 

The roots that grow from these plants, open up tiny cracks in the shingles.
Many of these organisms growing on roofing surfaces do much of the same thing. They spread the shingle, like a fan. Because the shingle is attached from the backside, the front ends of the shingle flare and roll. 

These microorganisms, such as fungi and algae, will break down a surface and cause decomposition.