A focus on endophyte and mycorrhizal enhancement of switchgrass growth and stress tolerance, as well as other plants, requires the establishment of a stable plant-microbe interaction. Hence, the initial microbial infection and subsequent colonization of the plant is requisite for the eventual beneficial impact of the microbe on plant performance. While the focus of this chapter is on switchgrass, little work has been carried out to describe microbial infection and colonization processes with switchgrass systems. Therefore, literature relating to the mechanisms of infection and colonization of other plant species forms the bulk of this section, with the assumption that similar mechanisms are operational during switchgrass-beneficial microbe interactions.

Endophytic microbes and mycorrhizal fungi can inhabit various parts of the plant, such as the root, stem and leaves, and can also be found in flowers, fruits and seeds (Zakria et al. 2008; Rodriguez et al. 2009; Compant et al. 2011; Kim et al. 2012). However, most efforts have focused on microbes located within the soil compartment, and more specifically the beneficial bacteria living in this region and their interactions with the root system of the plant. As we explore the steps associated with bacterial infection and colonization, it is worth noting that many studies have followed these processes through the use of readily visible tags in the bacteria of interest, such as GFP (Compant et al. 2008; Prieto and Mercado-Blanco 2008; Kim et al. 2012; Weyens et al. 2012). However, care must be taken when using such tagged microbes, as it has been shown that GFP-tagging can modify the natural behavior of the microbe (Weyens et al. 2012).