Abstract
Soil microbiomes impact all natural and agro-ecosystems by regulating the terrestrial global stock of critical nutrients and promoting plant health and survival. Due to the escalating stresses of the Anthropocene, these microbiomes have become even more essential as they are able to bioremediate pollution, restore function in degraded habitats, and confer plant drought and salinity tolerances. Even though soil microbiomes harbor a quarter of earth’s biodiversity and affect the health of all organisms on the planet including humans, research on understanding healthy soil microbiome formation remains understudied. In particular, there are major knowledge gaps on how intermicrobial interactions and plant host genotype interact to shape the assembly and stability of microbiomes in the field. This dissertation investigates the interplay between intermicrobial interactions and host genotype and how these interactions impact microbiome assembly and plant disease ecology and identifies important ecological mechanisms that underpin microbiome stability and function in a variety of natural and agricultural systems. This dissertation reveals several novel findings that enhance the microbial ecology field. Specifically I showed that highly-connected central taxa within soil microbiome networks are keystone species in their natural environments (Chapter 2), discovered that the quality of the symbiotic relationship with mutualists is a strong predictor of host survival against pathogenic disease (Chapter 3), and demonstrated that woody crop microbiome assembly are not only less severely impacted by domestication than herbaceous crops but can even benefit from domestication (Chapter 4). Taken together, this dissertation helped settle a decade-long debate around the utility of co-occurrence networks for identifying significant microbes, validated fundamental principles of microbial network theory, and laid the groundwork for understanding how microbiomes form and impact plant health.