From Imaging to Functional Traits in Interactions Between Roots and Microbes

The microbes in the rhizosphere constitute very complex communities, in which some are beneficial, others are pathogenic, but the vast majority of microbes are neutral commensals. Methods to unravel the interactions between roots and rhizospheric microbes have involved genetic approaches to determine the molecular bases of plant-microbe recognition and specific adaptive programs for either symbiosis or defense. In addition, imaging techniques have become particularly important to describe and understand the processes that occur within the spatially highly complex environments in and around the roots. Recently developed imaging techniques, in conjunction with appropriate labeling procedures, allow to address functional questions involving tissue-specific gene expression and elemental fluxes in the interactions between roots and rhizospheric microbes. Here, we discuss several imaging techniques from in situ hybridization, that allows the visualization of plant and microbial transcripts, to surface analytical imaging methods that can visualize chemical elements and molecules with micrometer resolution. These spectrometric techniques reveal the distribution of nutrient elements or toxic substances and allow, in combination with stable isotope labeling, to study nutrient fluxes within and between plants and microbes. Finally, we give an example of live-tissue imaging with fluorescent proteins to understand in more detail the process of root colonization through novel transcellular apoplastic compartments. All these techniques have virtually unlimited potential in their applications to other research questions in rhizosphere research.