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At the beginning of the 20th century Louis Pasteur laid the foundations of classical microbiology, based on the cultivation of microorganisms. Microbiology ceased to be an exclusive concern in matters of health or food conservation and extended to almost all fields in Nature. Microbes were recognized as the catalysts of all the cycles of the elements in our planet. In this context, agricultural microbiology works as a catalog of curiosities that offers the possibility to isolate particular microorganism and convert them into modern additives of agriculture. However, this paradigm vanished not many years ago, after a big anomaly in bacterial counts. Biochemical tools allow us to see the new unculturable microbes and a new scenario of soil microbiology is under construction at present. The new concept of microbiome expands the complexity of the soil where any macroscopic form of life develops. Analyzing the soil microbiology at a soil microaggregates scale suggests that agricultural managements are the way of shaping soil microbiomes to improve soil quality and improve crop production and soil services without harming the environment. The integration of soil microbiomes knowledge into the other levels of the soil food web is the future of soil science and could be one of the clues to mitigate the global climate change.