Microbiome Assembly Processes in Arabidopsis thaliana

Plants are colonized by a diverse community of bacteria, fungi, and other microorganisms. This community, or microbiome, impacts numerous plant traits including growth rate, reproductive yield, abiotic stress tolerance, and disease resistance. Disentangling the processes that govern plant microbiome assembly will provide insight into plant-microbe interactions and reveal strategies to effectively engineer microbiomes to achieve ecological or agricultural goals. In this dissertation, I explored microbiome assembly processes in Arabidopsis thaliana from several angles, First, I evaluated if plant pattern recognition receptors, one arm of the plant immune system, affect plant microbiome structure in the field. These receptors detect microbe-associated molecular patterns (MAMPs), which are prevalent across diverse microbial taxa and trigger a broad-spectrum antimicrobial response that regulates microbial growth in single microbe infections. I found that the loss of MAMP-detecting pattern recognition receptors had little effect on the structure of bacterial and fungal communities residing within the tissues of A. thaliana, despite evaluating several tissue types over four developmental stages. Next, I tested if disease induced by two native bacterial pathogens, Pseudomonas syringae NP29.1a and Pseudomonas viridiflava RMX3.1b, altered resistance phenotypes in future generations of A. thaliana. In contrast to previous work that used high intensity infections, I found no evidence that these native pathogens triggered transgenerational induced resistance; bacterial growth and disease symptoms were not significantly different between plants derived from lineages with or without historic pathogen exposure. Finally, I explored how microbial dispersal affects plant and soil microbiome assembly. Using a synthetic bacterial community in a closed, peat-based microcosm, I found that variation in bacterial through-soil dispersal rates significantly affected microbiome structure in both plants and soil for more than five weeks. Bacterial dispersal patterns generated pervasive, long-lasting priority effects over time and spatial scales highly relevant to plants in the field. Together, this dissertation provides a deeper understanding of plant-microbe interactions and the forces that influence microbiome assembly. This work demonstrates the challenges of predicting plant interactions with complex microbial communities and/or native pathogens using results obtained from high-intensity, single-microbe infections. Thus, to understand plant microbiome assembly and function, experiments in the field, or experimental designs that mimic conditions in the field, are required. Additionally, I found that bacterial dispersal has a substantial impact on plant and soil microbiome assembly, illustrating that microbial dispersal dynamics warrant increased consideration in microbiome studies.