AbstractIntroductionPlant microbiomes contribute directly to plant health and productivity, but mechanisms that underpin plant microbiome assembly in different compartments (e.g., root, leaf) are not fully understood. Identifying environmental and management factors that affect plant microbiome assembly is important to advance understanding of fundamental ecological processes, and to harness microbiome for improved primary productivity and environmental sustainability. Irrigation and fertilization are two common management practices in Australian tree plantations, but little is known about the effects of these treatments on soil, plant host and their microbiome. Here, we investigated the impact of decade‐long irrigation, fertilization and their combined application on soil, plant traits and microbiome of a Eucalyptus saligna plantation.Materials and MethodsMicrobial profiling of bulk soil, rhizosphere, root and leaves was performed using amplicon sequencing 16S ribosomal DNA and internal transcribed spacer (ITS) markers for bacteria and fungi, respectively, along with measurements of soil properties and plant traits.ResultsThe results indicated that both management practices significantly affected soil properties and soil and root microbiomes. Irrigation increased but fertilizer treatment reduced microbial alpha diversity. However, neither irrigation nor fertilizer treatment impacted the leaf microbiome. Our findings suggest that management practices impact soil edaphic factors, which in turn influence the below‐ground microbiome (soil and root), but the leaf microbiome remains unaffected. In addition, the leaf microbiome was distinct from soil and root microbiomes, and a source tracker analysis suggested that root and bulk soils only contributed to 53% and 10% operational taxonomic units of the leaf bacterial community, suggesting strong and sequential host selection of the leaf microbiome. In addition, management practices had a limited impact on leaf traits and, consequently, the leaf microbiome maintained its distinct composition.ConclusionThese findings provide mechanistic evidence for ecological processes that drive plant microbiome assembly and indicate that host selection plays a more important role than management practices in the leaf microbiome assembly.