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The book contains research articles and reviews recently published online for the MDPI journal Diversity, in the Special Issue "Genetic diversity of soil bacterial communities". The issue aimed to collect up to date information from the international scientific community to get insight in the "black box", as soil has been defined in the last decades, focusing in detail on the role that the microbial communities have in soil processes such as carbon and nutrient fluxes and on their genetic and functional diversity. The book meets the interests of scientific communities directly involved in the topics investigated, as well as of PhD students, scholars, professional organizations interested in improving their knowledge on a group of organisms considered vitally important to the maintenance and sustainability of the biosphere, where soil has a key role as an important natural resource.