Beneficial microbes are indispensable for environment and agriculture. They provide plants with more accessible nutrients and protect them from pathogen infection. To understand how plants and microbes communicate, it is important to identify the chemical mediators and to characterize their physiological functions. This knowledge will provide us with better strategies for modern agriculture. In this thesis, the interaction between Arabidopsis thaliana plants and a Trichoderma species, Mortierella hyalina, and Piriformospora indica was investigated.