Soil is a complex environment that supports the largest, most diverse and resilient microbial community on the planet, essential for nutrient cycling and plant growth.  The details of many soil microorganisms remain unknown, but the recent improvements in molecular methods for microbial ecology have made it possible to view the soil microbiome as a whole, providing information on its responses to changes in land-use and microbially-mediated functions relevant to agricultural sustainability and major geochemical cycles.  This chapter discusses methods for investigating microorganisms in soil and the contribution of soil microorganisms to nutrient cycling in soil, as well as the impact on the soil microbiome of activities such as crop selection, land management and the use of agrochemicals such as fertilisers. The influence of the microbiome on crop health and yields is considered, and the potential for future exploitation of the soil microbiome is discussed.