The black stains are caused by a cyanobacteria frequently referred to as algae (Gloeocapsa Magma) that feeds on organic material (Typically crushed lime stone) now used in composition roof shingles. Algae growth on roofs occurs to varying degrees in all regions of the country, especially those subjected to warm humid conditions.
The Sacramento area has a particular problem with dirty roofs due to the consistent marine layer that often covers the coast and certain inland areas. Nearly all types of roofing are susceptible to staining and discoloration. It is, of course, most visible on lighter colored roofs and less visible on darker shades of roofing.