More than the sum of their parts: Building a framework for understanding host-microbe interactions in Medicago sativa

This dissertation seeks to understand plant-microbe interactions in the agriculturally relevant plant Medicago sativa from three distinct vantage points within microbiology. Within the plant microbiome, we examine how primer usage and the application of peptide nucleic acids impacts 16S and 18S rRNA gene sequencing. In doing so, we design a novel peptide nucleic acid, PNA, and test its impact using multiple primers and sequencing protocols. Once microbial sequencing methodology is established, we generate a synthetic consortium of bacterial isolates from M. sativa leaves and modulate nitrogen levels to better understand microbial structure. Drop out communities, where we remove one member at a time, elucidate what community members colonize to high levels, and how they change the microbial community when present. Using this approach, we uncover how, and which microbes can consistently colonize plants across nutrient conditions. Further, we examine multiple genetic approaches to investigate potential genetic mechanisms behind plant colonization, such as high throughput sequencing techniques such as randomly barcoded transposon sequencing (RB-TnSeq) and traditional transposon mutagenesis. By using a variety of approaches within biology, we elucidate plant-microbe interactions in alfalfa.