Protocols in Root-Microbe Interactions describes laboratory protocols that have been developed and optimized for scientists working in root-microbe interactions, specifically for those wanting to quantify immune responses in plant roots. The experiments are focused on cellular to whole-root scale and include molecular biology, biochemistry, and histology techniques. Written in an easy-to-understand fashion that is suitable for both early career and experienced scientists, the protocols were optimized for tomato roots but can easily be adapted to roots of other plant species, or if needed, to leaves. The book includes information on quantifying pattern-triggered immune (PTI) responses in plant roots and covers reactive oxygen species (ROS) burst, mitogen-activated protein kinase (MAPK) phosphorylation, root growth inhibition, and qualitative callose deposition. Other topics examined include transient expression of bacterial proteins in leaves and root sectioning (from a microtome and vibratome) and histology assays for both light microscopy and scanning electron microscopy. A variety of other protocols explored relate to the isolation of bacteria from the root endosphere and rhizosphere, and the extraction of DNA from root-associated bacteria. Protocols in Root-Microbe Interactions serves as an invaluable resource for those working in the root-microbe field and can be optimized for other laboratories' needs.