In pegmatites from Ukraine Precambrian fossils between 1.5 Ga and 1.76 Ga were preserved in cavities connected to the surface in a geyser system. The fossilization process is silicification of the outermost rim of the fossils, stabilizing the remaining part of the organisms. The variety of organisms points to an ecosystem of several microorganisms which was active in the continental environment, and igneous rocks such as the pegmatites seem to be an ideal habitat for the deep biosphere.

Over 95 % of the microbial communities in isolated groundwater in Olkiluoto bedrock, Finland, is composed of only a few common species. The remaining rare microbiome contains over 3- and 6-fold more microbial diversity. The rare microbiome is an unlimited source of genomic functionality in the ecosystem. These microorganisms can respond to change caused by physical or biological factors that may lead to alterations in the diversity and function of the microbial communities in crystalline bedrock.