This course aims at elucidating the influence of the soil environment on settlement and activity of the microbial cenoses (microbiomes) in different pedological contexts. Within the completion of this course, students will have acquired a comprehensive overview of both the major phyla of microorganisms found in soil and the methods (including the new molecular high-throughput sequencing technologies) for their quantitative estimation as well as for the characterization of their physiological properties either in bulk soil or in the rhizosphere. Particular emphasis will be given to plant-microbe interactions, with a special attention to the multiple cross signaling mechanisms among plants and PGPR (Plant Growth Promoting Rhizobacteria) at the rhizosphere level. Symbiotic nitrogen fixation and different mycorrhizal associations will be discussed in deep details. Transformations of organic and inorganic pollutants mediated by soil microorganisms will be treated. Eventually, the understanding of soil microbial ecology principles will allow the students to correctly interpret environment-friendly strategies for improvement of crop productivity, biological control of plant pathogens and biodegradation/bioremediation of contaminated sites.