Healthy plants in nature are colonized by multi-kingdom microbial communities including bacteria and fungi, termed the plant microbiota, which promote plant growth and health. Our work focuses on the root microbiota and aims at a deeper understanding of the mechanisms underlying the establishment of root-associated microbial communities and their beneficial functions for the host. We have established systematic culture collections of the root microbiota of the crucifer Arabidopsis thaliana and the legume Lotus japonicus, allowing us to culture the majority of bacterial and fungal taxa associated with healthy roots of these two plant hosts 1,2. We then compose defined consortia, called synthetic communities (SynComs), from the isolated root commensals and reconstitute the root microbiota in co-cultivation experiments with germ-free plants to study microbial community functions for the host in laboratory environments 1, 2. This enabled us to demonstrate that the bacterial root microbiota is crucial for the survival of the host in natural soil by protecting the plant against harmful fungal root endophytes 2. Our experiments also show that suppression of chronic Arabidopsis immune responses is a widespread but typically strain-specific trait across the major bacterial taxa of the plant microbiota 3, 4. We have identified two immunomodulatory mechanisms acting in parallel within a core lineage of the bacterial root microbiota and demonstrate that cross-talk with the plant immune system is needed for plant-microbe homeostasis.