Assembly patterns of the rhizosphere microbiome along the longitudinal root axis of maize (Zea mays L.)

This study was conducted within the framework of the DFG project SPP2089 “Rhizosphere Spatiotemporal Organization – a Key to Rhizosphere Functions”.

Different plant species select for individual subsets of bulk soil microbial communities within root systems. The fast variability of root environments implies that roots constitute highly dynamic habitats. Rapid root elongation, combined with widely varying quality and quantity of rhizodeposition between different root regions, lead to continuously changing conditions for colonizing microorganisms. As the microbiome concept implies a rather static outcome of the microbial assembly, it raises the question as to where and how the dynamic transition of a microbial bulk soil community into a plant species-specific rhizosphere microbiome is taking place.

To investigate the assembly of communities of prokaryotes and their microbial predators (Cercozoa, Rhizaria; protists) along the longitudinal root axis of maize (Zea mays L.), plants were grown in an agricultural loamy soil. Rhizosphere soil was sampled at distinct locations along roots. Diversity and co-occurrence of rhizosphere microbiota along the root axis were tracked by high-throughput sequencing, diversity measures and network analyses.

High variation in beta diversity at root tips and the root hair zone indicated substantial randomness of community assembly. Deterministic processes of community assembly were revealed by low variability of beta diversity, changes in network topology, and the appearance of regular phylogenetic co-occurrence patterns in bipartite networks between prokaryotes and their microbial predators. Deterministic processes were most robust in regions with fully developed lateral roots, suggesting that a consistent rhizosphere microbiome finally assembled. For the targeted improvement of microbiome function, such knowledge on the processes of microbiome assembly on roots and its temporal and spatial variability is of crucial importance.