Mechanisms in plant–microbiome interactions: lessons from model systems

The use of genetically tractable plant–microbe pairs has driven research in plant immunity and mutualistic symbiosis. Clear functional readouts for the outcomes of symbiosis or immunity have facilitated forward genetic screening and identification of signals, molecules and mechanisms that determine the outcome of these interactions. Plants also associate with beneficial microbial communities that form the microbiome. However, the complexity of the microbiome, combined with relatively subtle effects on plant growth and immunity, has impeded forward genetic screening to identify plant and bacterial genes that shape the microbiome. As a result, microbiome research has relied largely on reverse genetics approaches, based on what is known about plant nutrient uptake and immunity, to identify mechanisms in plant–microbiome research. Here we revisit the features of reductionist model systems that have made them so powerful for studying plant–microbe interactions, and how modeling microbiome research after these systems can propel discovery of novel mechanisms.