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Plants host diverse, multi-kingdom microbial communities in aboveground and belowground organs, referred to as phyllosphere and rhizosphere microbiota. The interactions of respective microbes with their host plants range from parasitic to mutualistic. Traditionally, plant pathogens (parasitic interactions) have received larger attention within the scientific community. Pathogenic microbes are recognized by genetically encoded receptors located either at the cell surface or intracellularly. In a first part of the seminar, I will present my recent work on the architecture of immune signaling networks in the solanaceous plant Nicotiana benthamiana (wild tobacco). However, in particular many rhizosphere microbiota position on the opposite end of the parasitism-mutualism continuum, and provide important services to their hosts. In agreement, plants deposit large, but variable, fractions of the photosynthetically-fixed carbon into the rhizosphere to nurture and structure the rhizosphere microbiome. In a second part, I want to present envisaged approaches to identify genetic determinants controlling carbon deposition and structuring of root microbiota, which remain to date largely elusive.