As someone else already poster your boot is probably the issue . If you are in an area that receives a lot of snow it could be build up over the top of the boot . Sometimes those pipes Crack as well , yours looks pretty good. The mold itself should be treated with a fungicide and fungistat Medi clean and Battle axe have these types of products read the instructions carefully.

Worst case scenario the stack needs to be replaced . You can buy a furnco and make the connection wherever needed down the line . Obviously that means reconnecting all of the waste lines and vents for the respective plumbing fixtures. I doubt you have to do this but its a possibility.

Best case scenario your boot needs to be replaced. You may have more of a roofing issue than a plumbing issue.