Model Communities to Study Mechanisms of Plant-Microbiome Function

The microbiome of plants is comprised of thousands of taxonomically and functionally diverse microbiota, the majority of which are uncultivable. Current methods for studying how the genetics of community members contribute to microbiome function include shotgun metagenome sequencing and microbiome replacement studies. In this work we present the design and analysis of a model community of cultivable, genome-sequenced representatives of taxa in the microbiome of Populus plants, a second generation biofuel feedstock. Results from one-on-one studies show that individually, strains induce diverse changes in root architecture and have unique metabolic capabilities; and as a community lead to increased root growth in Populus hosts. Across 20 plants from two host genotypes the community is dominated by two taxa, with Burkholderia and Pantoea isolates representing 99% of detected organisms. Within the remaining 1%, the Streptomyces and Rhizobium representatives are the most abundant, followed by Sphingobium and Duganella isolates. These abundance results suggest structuring of the community, rather than dominance by a single taxon. We also observe positive and negative correlations in abundance between community members, emergent properties that are not predicted from community design. This work demonstrates the feasibility and analysis of model communities to study microbiome function in plant systems.