Visualization of plant-microbe interactions

Abstract

Plants form complex mosaics of different microhabitats, each of them colonized by adapted microorganisms ranging from beneficials to pathogens. Since only a minor fraction of environmental microbes can be cultivated in the laboratory, molecular methods are usually employed to characterize the whole microbiome. However, spatial information at micro-scale, which is fundamental to understand the dynamics of host-microbe interactions, is usually lost during the sample processing. Therefore, it is useful to complement the indirect molecular techniques with direct visualization methods. Confocal laser scanning microscopy (CLSM) allows the exploration of microbial habitats at a spatial resolution level unattainable with molecular methods. In this chapter, we will show how CLSM played a fundamental role in understanding plant-microbe interactions and their significance. Moreover, this chapter is expected to be an inspiration for integrating microscopy with molecular methods in research on plant microbiology.