Host-mediated microbiome engineering (HMME) of drought tolerance in the wheat rhizosphere

Host-mediated microbiome engineering (HMME) is a strategy that utilizes the host phenotype to indirectly select microbiomes though cyclic differentiation and propagation. In this experiment, the host phenotype of delayed onset of seedling water deficit stress symptoms was used to infer beneficial microbiome-host interactions over multiple generations. By utilizing a host-centric selection approach, microbiota are selected at a community level, therein using artificial selection to alter microbiomes through both ecological and evolutionary processes. After six rounds of artificial selection using host-mediated microbiome engineering (HMME), a microbial community was selected that mediated a 5-day delay in the onset of drought symptoms in wheat seedlings. Seedlings grown in potting medium inoculated with the engineered rhizosphere from the 6th round of HMME produced significantly more biomass and root system length, dry weight, and surface area than plants grown in medium similarly mixed with autoclaved inoculum (negative control). The effect on plant water stress tolerance conferred by the inoculum was transferable at subsequent 10-fold and 100-fold dilutions in fresh non-autoclaved medium but was lost at 1000-fold dilution and was completely abolished by autoclaving, indicating the plant phenotype is mediated by microbial population dynamics. The results from 16S rRNA amplicon sequencing of the rhizosphere microbiomes at rounds 0, 3, and 6 revealed taxonomic increases in proteobacteria at the phylum level and betaproteobacteria at the class level. There were significant decreases in alpha diversity in round 6, divergence in speciation with beta diversity between round 0 and 6, and changes in overall community composition. This study demonstrates the potential of using the host as a selective marker to engineer microbiomes that mediate changes in the rhizosphere environment that improve plant adaptation to drought stress.