Host selection has a stronger impact on leaf microbiome assembly compared to land‐management practices

Abstract

Introduction: Plant 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 Methods: Microbial 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. Results:The 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. Conclusion:These 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.

Plants and endophytes interaction: a “secret wedlock” for sustainable biosynthesis of pharmaceutically important secondary metabolites

“…The composition, richness, and population of endophytic microbial communities differ based on factors such as plant species, the specific plant compartments (e.g. roots, stems and leaves), plant age, and surrounding environmental conditions [ 1 , 41 , 42 ]. Evidence suggests that endophytes are acquired vertically (via seed) and horizontally from the plants soils where plant grow.…”

“…However, such approaches have their own set of limitations and have been discussed in detail in agricultural contexts [ 139 , 222 ]. Recently, approaches to overcome such limitations were proposed, including explicit consideration of theoretical framework in inoculant testing and in situ microbiome manipulations/engineering [ 42 , 222 ]. In this regard, modulating the plant holobiont through microbiome engineering is an emerging biotechnological approach for increasing crop yields, resilience and secondary metabolite biosynthesis in plants [ 223 , 224 ].…”