Plants interact with a plethora of soil microbes that help them to acquire nutritional resources, to be protected against pathogens, and to face challenging and fluctuating external conditions. Understanding how the microbiota of roots and rhizospheres is shaped and conserved by host plants, and how it changes in response to genetic and environmental pressures, is crucial for the preservation of natural ecosystems and to harness its potential for the development of novel strategies in agroecosystems. This Research Topic presents a series of articles that summarizes the latest research updates on the impact of the plant microbiota and its specific symbionts [i.e., arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) fungi, nitrogen-fixing rhizobia, and plant growth-promoting rhizobacteria (PGPR)] on plant performance and resilience, and the external factors that influence plant microbiota assembly. Novel next generation sequencing technologies and analytical platforms provide us with more insights into the plant microbiome. In this Research Topic, Ma et al. discussed the development and potential use of single-cell RNA-sequencing technology in the area of plant microbiomes. Although still challenging to apply routinely, it opens the way toward the discovery of very specific and localized functions of bacterial communities in plant microbiota. Multiple studies have shown that the microbiome composition differs among cultivars of a given plant species, such as corn (Walters et al., 2018), cotton (Wei et al., 2019), or grape (Mezzasalma et al., 2018). Using three switchgrass cultivars grown under various conditions (i.e., monoculture, intraspecific, or interspecific mixtures), Revillini et al. showed that plant diversity influences the structure of AM fungal and bacterial communities in the root rhizosphere, but that nitrogen fertilization only affects the composition of the AM community but not of the rhizobacterial community. These findings highlight the importance of adapted cultivar and management practices in agricultural settings to maintain optimal microbiomes. Although it is described that herbivores can also influence the leaf microbiota composition (Humphrey and Whiteman, 2020), their impact on root microbiota assembly, and particularly on AM fungi, is still unclear. In this Research Topic, Wilkinson et al. demonstrated that the inoculation with aphids does not alter the AMcolonization and community composition in barley, but that the formation of fungal vesicles and the relative abundance of some fungal species in these communities is affected.