Microbes secrete enzymes that break organic compounds(paper,plastic,food leftovers,..) down in to their inorganic components, which can be absorbed by the soil.
Microbes break down nondegradable material they secrete enzymes and digest them.A scientist called Anad Chakrabarthy has developed a genetically modified form of pseudomonas called superbugs that can degrade complex toxic oils.This technique is also used during space travel and also in sewage treatment so that sewage water is recycled.
Is it any element or compound in particular your talking about?