The role of microorganisms as key components in the functioning of ecosystems and biodiversity is discussed. The latest methodologies developed to study microbial diversity and functioning of ecosystems are considered, as DNA extraction and isotope labeling, fluorescent in situ hybridization and microautoradiography, and tracking of a substrate labeled with a stable isotope. Investigations related to correlations between microbial diversity and functioning in situ are considered. An example is illustrated of a correlation of erosion of microbial diversity of natural microbial community in prairie soil and erosion of species diversity in an ecosystem.