Organic-rich laminated shales and limestones from the Monte San Giorgio (Lugano Prealps, Switzerland) are known as famous fossil lagerstätten for excellently preserved fossils from the Middle Triassic Period. The various bituminous shales from Monte San Giorgio are thermally immature and rich in diverse organic compounds, which provide unique substrates for active soil microbial communities. We selected the Cava superior beds of the Acqua del Ghiffo site for this study. To investigate its microbial structure and diversity, contig assembly, Operational Taxonomic Units (OTUs) clustering, and rarefaction analysis were performed for bacterial 16S rDNA preparations from bituminous and non-bituminous limestone strata with the MetaAmp pipeline. Principal coordinates analysis shows that the microbial communities from the bituminous strata differ significantly from limestone samples (P < 0.05 Unifrac weighted). Moreover, metagenomic tools could also be used effectively to analyze the microbial communities shift during enrichment in specific growth media. In the nutrient-rich media, one or few taxa, mainly Proteobacteria and Firmicutes, were enriched which led to the drastic diversity loss while oligotrophic media could enrich many taxa simultaneously and sustain the richness and diversity of the inoculum. Piphillin, METAGENassist and MicrobiomeAnalyst pipeline also predicted that the Monte San Giorgio bituminous shales and oligotrophic enriched microbiomes degrade complex polycyclic aromatic hydrocarbons.