Tree species influence soils through direct and indirect inputs above- and belowground through leaf litter and root inputs. Soil microbial communities can in turn influence tree growth and development through processes such decomposition and chemical transformation of nutrients in soils. In this chapter we will provide an overview of the mechanisms by which trees influence soil microbial communities and nitrogen cycling processes. Specifically, we explore the effects of tree species on ammonification and nitrification processes in forest floor soils, and relate those to functional genetic markers for ammonia-oxidation by archaea and bacteria (amoA AOA and AOB) bacterial denitrification (nirS and nirK). We will cover the use of complementary laboratory methods used to investigate these relationships, including the use of molecular techniques such as quantitative polymerase chain reaction (qPCR) to target gene abundances in soils, and 15N tracing experiments to understand the production and consumption of nitrogen. We will also address some of the benefits and drawbacks of these approaches, with special focus on the types of research questions that can be answered using these approaches. The chapter will wrap up with an example study in a common garden tree species trial in Vancouver, B.C., Canada, which demonstrated tree species effects on soil microbial communities and nitrogen cycling dynamics.