Genetically engineered microbes (GEMs) have the potential to revolutionize agricultural techniques by facilitating crop protection and increased productivity. However, there has been widespread concern regarding the potential impact these microbes may have on the environment. Here we mathematically model the dynamics of GEMs in an agricultural setting, focusing on parameters that can be used to summarize the potential of modified microbes for persistence and spread. First developing a comprehensive model for the dynamics of GEMs which includes mobile and stationary classes of GEMs as well as competition from indigenous microflora, we then analyse a sequence of simplified mathematical models with a view to answering two fundamental questions: (1) will the GEMs spread (or invade), and if so how quickly? and (2) what are the best strategies for containing the spread of GEMs in a spatially varying environment?