Recent advances in sequencing technologies have shown that there are a few hundred species of microorganisms associated with plants both below and above ground, with the roots being a major staging ground for the strongest functional interactions. Plants interact closely with their endophytes and with microorganisms growing on the root surface and in the rhizosphere. This plant microbiome constitutes a complementary genome in service of the plant and there is growing evidence that it can be manipulated to benefit plant growth and productivity. The most effective form of manipulation has been to use beneficial microorganisms, either singly or in combination to improve the yield by what is generally termed growth promotion or as biocontrol agents that eliminate or reduce the deleterious effects of pathogens. Until recently the ability to study the influence of the added inoculant on the other microorganisms was limited to a few members of cultured species whereas after the explosive development of sequencing technologies and bioinformatic tools there can be a more comprehensive coverage of the effects on the microbiome. This chapter discusses these developments and the emergence of analytical tools to study networks of members of microbiomes as well as mechanisms to manipulate and engineer microbiomes.

Plant roots have both direct and indirect effects on nutrient availabilities and fluxes in rhizosphere soil. Direct effects include impacts that are a consequence of root growth, water/nutrient uptake and secretion of compounds that promote solubility of poorly available elements such as phosphorus and iron. Indirect effects are largely a consequence of plant–microbe interactions, mediated by the release of organic compounds from roots that both shape rhizosphere microbial community structure and promote microbial nutrient cycling activity. In recent years, significant advances have been made in the quantification of root-mediated impacts on soil biogeochemical processes, demonstrating the importance of these interactions for nutrient cycling to support plant productivity and as a critical control point for the response of soils to environmental change. This is now supplemented with an appreciation that there is a strong element of regulation, both plant and microbial, in how the underlying interactions are established and maintained. This raises the exciting possibility that management of root–microbiota interactions could be a realistic means of improving plant health and productivity, while potentially also mitigating environmental impacts. This chapter discusses progress in quantifying root impacts on soil processes and parallel advances in characterising the specificity of the plant-driven selection of associated microbiota. A clear opportunity for future research is to combine these approaches, functional -omics technologies and bioinformatics to guide next-generation crop breeding that targets both the plant and its associated microbiota (i.e. the holobiont), for productivity and resilience in sustainable agricultural systems.

Plant roots are the primary source of organic materials that become stabilized in soil. While most root carbon is decomposed into carbon dioxide (CO₂), the remainder typically undergoes multiple microbial transformations before it forms longer-term associations with soil minerals. However, the mechanisms by which roots affect microbial utilization of organic materials and subsequent mineral stabilization processes are poorly understood. It is well known that living roots increase the biomass of nearby microbial communities, and shape their population dynamics, diversity, and interactions. Community assembly and metabolic potential of these rhizosphere-enriched microorganisms are strongly influenced by the chemical composition of the exudates released by the host plant. The root exudate pools of plants undergo compositional changes as they grow, reproduce, and senesce. In the well-studied annual grasses Avena barbata and Avena fatua, this changing rhizosphere substrate pool and the “bloom” of organisms that respond are phylogenetically coherent; Acidobacteria and Actinobacteria are consistently depleted, whereas Alpha and Betaproteobacteria and Bacteroidetes are reliably enriched. When compared to non-root-influenced bulk soils, the responsive community is predictably less taxon-rich, yet forms more complex networks. These rhizosphere dynamics have significant downstream effects on the colonization of nearby soil minerals, degradation of prior season’s root litters, and the balance of stabilized versus lost soil carbon.