Root-associated bacterial communities as an extended phenotype of the plant

Abstract

Land plants associate with a root microbiota distinct from the complex microbial community present in surrounding soil. The microbiota colonizing the rhizosphere (immediately surrounding the root) and the endophytic compartment (within the root) contribute to plant growth, productivity, carbon sequestration and phytoremediation. In my research I primarily wanted to test the hypothesis that plants that evolved to live in environments with different challenges also evolved the ability to associate with a unique microbiota as one means of overcoming these challenges. Despite great agronomic interest, genetic principles governing the derivation of host-specific endophyte communities from soil communities are poorly-understood. I first used extensive sequencing of ribosomal 16S rRNA genes to characterize bacterial populations from hundreds of roots of different genotypes of the model plant Arabidopsis thaliana grown in two wild (non-native) soils from North Carolina. These results demonstrated that soil type is the major determinant of the membership of the bacterial community in the rhizosphere and the community living inside roots, and that the developmental stage of the plant as well and the plant genotype actually have relatively minor effects on the colonization behavior of major bacterial taxonomies. Because in wild microbial communities bacteria with different genomic content may share a similar 16S rRNA gene, and because of limitations in the 16S sequencing technology, we were limited to statements about bacterial families, and could not say with confidence to which Arabidopsis genotypes individual strains of bacteria associated. This was a major limitation, because the presence or absence of specific bacterial genes may be a strong determinant of potential host genotypes for a given symbiont. Therefore, I developed technological improvements to increase the accuracy and depth of sequencing, while meanwhile culturing individual strains of bacteria from roots and creating a gnotobiotic system for growing plants in direct association with mixtures of cultured strains. Initial results from this system demonstrate that we can culture a wide diversity of root-associated bacteria and can successfully recolonize plants with complex but defined cocktails of bacteria. Experiments to explore microbe-by genotype association in this gnotobiotic system are underway.

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