Functional rhizosphere microbiomes and effects on plant-host growth, development, and abiotic stress toleranc

The rhizosphere microbiome is the community of microorganisms on and surrounding plant roots. This community is important for both above and below ground ecosystem functioning as well as plant growth and development. The depth and complexity of microbe-microbe and plant-microbe interactions within the rhizosphere remain largely uncharacterized. In this dissertation, I explore the rhizosphere system from three directions. First, I propose multiple levels of selection upon extracellular enzyme production and soil organic matter depolymerization as a conceptual framework for explaining the evolution of cooperative rhizospheres. Second, I demonstrate the ability to apply ecosystem-level selection to rhizosphere microcosms to assemble functional microbiomes capable of altering plant flowering phenology and biomass partitioning. I also test the ability of the assembled flowering microbiomes, and sub-communities cultivated from them, to reproduce their function in novel and familiar plant hosts. Flowering microbiomes were able to reproduce their function in several novel Arabidopsis thaliana genotypes and Brassica rapa, a family-level relative. Cultivated sub-communities displayed variability in their effects on host plant growth and development depending on the composition of the cultivation media. Two of the four cultivation media reproduced the flowering effects of the early-flowering whole microbiome from which they were cultivated. These two sub-communities also increased plant biomass in contrast to the decrease in plant biomass associated with the whole microbiome. Third, I investigate the rhizosphere microbiome of 116 closely-related tall fescue varieties under drought stress to assess the role of the rhizosphere microbiome in genotype-specific variations in abiotic stress tolerance. Differences in drought tolerance were primarily associated with shifts in microbial extracellular enzyme production and fungal endophyte infection rates over differences in bacterial community composition. This work adds to the growing understanding of the complex network of interactions within the rhizosphere and presents ecosystem selection and cultivation as a means of enhancing and characterizing microbiomemediated effects on plant growth and development. Furthermore, the parallel investigation of rhizosphere microbiome function between plant genotypes and the response of the microbiome to selective pressure begins to uncover the potential of microbial components in traditional plant breeding programs.