Efficient Evolution of Growth-Promoting Bacterial Rhizosphere Communities through Plant-Microbiome Co-Propagation

Beneficial rhizosphere bacteria can enhance growth and health of plants, for example by solubilizing nutrients or secreting protective antibiotics.  To elucidate functions of hyperdiverse communities of rhizosphere bacteria, we developed an efficient method of plant-bacterial-community co-propagation that enhances plant growth by selecting indirectly on root-associated bacterial communities while selecting directly on shoot biomass of Brachypodium distachyon.  We adapted engineering principles observed in natural host-microbiome co-propagation regimes to select artificially on beneficial bacterial rhizosphere-microbiomes of B. distachyon, keeping plant genotype constant between generations (cycles of selection on bacterial microbiomes).  Metagenomic surveys confirm that bacterial communities rapidly evolve differences between replicated selection-lines that are selected for either growth-enhancing effects ("high-lines") vs growth-attenuating effects ("low-lines") on plants.  We isolated bacterial strains that differed most prominently in abundance between high- and low-lines, then tested these candidate growth-promoting bacteria for improved plant growth when inoculating seeds with single bacterial strains.