Microbial community assembly along the root is interfered with the removal of the root cap

Community composition of the rhizosphere microbiota and plant gene expression levels show root zone-associated distributions. It has been suggested that the root cap represents the first selection point for rhizosphere compatible microorganisms. Here we provide experimental evidence for that by decapping the primary roots of wild type and root hair-less maize and following the zonal establishment of prokaryote and protist (Cercozoa) communities and plant gene expression. Prokaryote abundance and microbial alpha- and beta-diversity shifted along the root axis of intact roots, always showing most variation at the root tip. Co-occurrence networks showed root zone-specific correlations among microbes and between prokaryotes and protists as well as specific connections between the abundance of microbial taxa and plant gene expression levels. The zonal patterns of alpha- and beta-diversity were less distinct along decapped roots, and the Cercozoa alpha-diversity increased and its variability decreased in the root tip community by decapping. The root tips of the decapped roots showed enhanced transporter and plant secondary metabolism-related gene expression. Lack of root hairs had minor but significant effects on decapping-related changes in the zonal distribution of prokaryote and Cercozoa community composition and on root tip gene expression. The obtained data support the view that the root cap is an organizer of microbial communities and that its presence supports the further assembly process of the rhizosphere microbiome.