Harvesting the Root Microbiome of Grasses Toward Sustainable Increase Crop Production

The major and global increased demand for food commodities and energy supply highlight the necessity to further improve crop productivity.  A variety of plant functions and traits are co-dependent on the microbial communities that exist within and around them. Characterizing, manipulating and /or mimicking the plant microbiota provide a promising path toward increasing crop production. Microbiota at the surface of the root (rhizosphere) and within the root (endophytic compartment) are of particular importance because of their potential influences on nutrient uptake.

The extent to which the host selects its root microbial community remains poorly understood, especially across vastly divergent species. Grasses constitute our main source of food, feed, and bioenergy, but how their microbiomes relate to or may differ from other plant microbiomes remain unclear. We are comparing the well-studied root microbiome of Arabidopsis thaliana Col-0, with those of two grass species model Brachypodium distachyon Bd21 and Setaria viridis A10-1. All plant species were grown in the same wild soil. Both bacterial and fungal microbiota were defined using high-throughput bacterial 16S rDNA, and fungal internal transcribed spacer 2 profiling, respectively. We are establishing the nature of a core, species-specific and potential grass-specific root microbiomes.

Whether the core microbiome may also present functional conservation across species remain to be assessed. We have isolated ~600 bacterial strains from the rhizoplane and endophytic compartments of Arabidopsis thaliana and evaluated the effect of these isolates on plant health under various nutrient starvation stresses. This bacterial collection is currently being tested on Setaria viridis focusing on the identification of isolates that rescue phosphate starvation stress. We are in parallel establishing a collection of bacterial strains isolated from the root of Setaria viridis to help refine the design of bacterial biocontrol agents specifically targeting crops.