The protist microbiota of maize and their functional roles for the self-organization of the rhizosphere bacterial microbiome

Abstract

Plants interact closely with their belowground environment. The rhizosphere is a dynamic habitat where biotic and abiotic factors, along with the plant itself, shape the microbial community. This study, conducted within the DFG Priority Program “Rhizosphere Spatiotemporal Organisation” (SPP 2089), aimed to investigate the spatiotemporal organization of microbial communities in the rhizosphere of Zea mays (maize), with a particular focus on the role of protists as bacterial predators. Using high-throughput amplicon sequencing, we analyzed microbial compositions and co-occurrence patterns along the root axis. Microbial community structures varied markedly between developmental zones, with stochastic processes dominating in young root regions and deterministic processes, such as selective protistan predation, prevailing in more mature zones. Targeted manipulations revealed that the root cap significantly influences microbial assembly. Network and plant gene expression analyses indicated active, plant-mediated modulation of microbial communities. Additionally, we showed that both the composition and concentration of root exudates substantially impact microbial metabolism. Experiments with varying soil textures highlighted the strong influence of abiotic factors on root development and microbial community structure. A protist diversity experiment demonstrated that increasing protist diversity altered bacterial community composition and enhanced bacterial diversity, although this did not improve plant nitrogen uptake. Overall, our findings underscore the role of protists as active regulators within microbial networks and contribute to a deeper understanding of self-organizing processes in the rhizosphere