Soil microbial ecology deals with the study of the influence of the soil microbial community on the functionality of soil ecosystem. From the agricultural point of view, it is very important issue due to the effect of such microbial community on maintaining soil fertility and health. Such condition is produced as a result of the role of microorganisms on the biogeochemical cycles, the improvement of soil structure, the natural control of plant diseases and the degradation of organic pollutants. The process related with the functions carried out by the microorganisms in the environment are not completely understood. Therefore, different research groups in the world, have been focused on the application of diverse approaches, to try to identify specific biomarkers at different taxonomic levels that allow the design of crop management strategies to improve the performance of soil microbial community, for the benefit of plant growers. Knowing that it is still a long term target, the aim of this course will be to give an up to date state of the art of the techniques, approaches and concepts that have been developed recently to understand the role of the microbial community, on the soil agricultural environment, with emphasis in three main subjects: the understanding of the role of rhizosphere microbiome on biogeochemical cycles, and recycling of nutrients; the bacterial-bacterial and interkingdom communication to improve symbiotic plant microbial relationship; and ecology and function of endophytic bacteria. These notions will be developed, in order to contribute to the understanding of the implications of applying concepts of microbial ecology, for the development of strategies of agricultural management including the application of inoculants for the improvement of the nutrition of plants of agricultural interest.