Interaction of Ag with communities of soil saprotrophic organisms was studied in two different soils using a metagenomic approach. Three levels of Ag were applied to the soil samples: 0, 0.008 and 0.505 μg Ag/g soil. Silver was applied in mineral form as well as naturally bound in dry fruit-body biomass of the Ag-hyperaccumulating ectomycorrhizal fungus Amanita solitaria. Contrasting behavior of fungi and bacteria in reaction to Ag dosages was observed. The majority of bacterial ribotypes tended to prefer the soil with low doses of Ag, the ribotypes of fungi were more abundant in untreated soils and soils treated with the highest Ag concentration. Organically bound and mineral forms of Ag did not differ substantially in their effects on microbes in samples. The results indicate that decomposing Ag-rich fungal biomass can significantly alter the soil microbiota. This can contribute to formation of spot-like non-homogeneities in soil microbial distribution.