Integrated analysis of plant gene expression and bacterial and protozoan community composition reveals changes related to root zonation, root cap and root hair formation

This study was conducted within the framework of the DFG project SPP2089 “Rhizosphere Spatiotemporal Organization – a Key to Rhizosphere Functions” (project number 403641192).

As plant roots grow into the soil, the formation of biological gradients occurs at different spatial scales. It has been shown that plants recruit specific subsets of the soil bacterial community at their roots through excretion of mucilage at root tips and exudates at the sites of root hair formation. The promotion of or defense against certain bacterial taxa is also reflected in the composition of the protist communities that feed on bacteria.

Using high-throughput sequencing methods, we investigated emerging patterns in root gene expression in relation to bacterial and protozoan community structures. We found highly distinct root region specific patterns relating to differential root gene expression relating to growth, defense and transporter activity, as well as bacterial and protist (cercozoan) diversity. Root cap removal led to differently composed microbial communities, as well as a regulation of root genes relating to stress and defense. The lack of root hairs was only reflected in the amount of microbial carbon in soil and a small number of differentially expressed genes involved in cell wall processes.

We could show that the rhizosphere microbiome, is as dynamic as its environment. Root regions differentially affect microbial communities, which is also reflected in the expression of plant genes of categories relating to defense, immunity and stress. Our findings will further enhance our understanding of microbial root interactions at single root scale.