This document outlines a 3-credit PhD course on plant-microbe interactions exploring how beneficial microorganisms can improve crop productivity in a sustainable way. The course will be held at Makerere University in Uganda in 2014 and taught by professors from Makerere and the Swedish University of Agricultural Sciences. It involves lectures, seminars, practical laboratory and bioinformatics exercises, field trips, group discussions and a final student project presentation. The goal is for students to learn how microbes support crop production through beneficial interactions and development of stress management techniques as alternatives to agrochemicals.