Developing and applying mass spectrometry-based omics to study plant-microbiome interactions in Populus spp. using a reductionist approach

Microbes are ubiquitously associated with plants and play a crucial role in plant’s health and fitness. Due to their pivotal roles in plant health, it is important to understand how the microbiomes assemble and establish themselves in various plant niches. Of the various plant niches, the rhizosphere serves as a reservoir of beneficial microbes which are selectively recruited by the plant. The molecular mechanisms that facilitate these associations between the plant and microbes are not fully known. Studying plant-microbe interactions in nature is challenging due to the complexity and technical limitations. However, reductionist approaches using constructed microbial communities and laboratory-controlled experiments have proven to be valuable in advancing our knowledge of plant-microbe interactions as they simplify the complexity of natural systems and thereby allowing us to focus on specific interactions. High-throughput omics technologies provide invaluable information in studying these complex and dynamic plant microbiomes. Metaproteomics can identify and quantify thousands of proteins and provide insights into microbiome composition and functions of individual members of the microbiome. Metabolomics helps in studying the chemicals released by plants and microbes that serve as nutrients and/or chemical signals to establish interactions with each other. In this dissertation, liquid chromatography coupled with mass spectrometry-based metaproteomics and metabolomics approaches have been used to advance our understanding of interactions between the Populus spp. and its rhizosphere microbiome. The research presented here describes (1) application of metaproteomics in understanding microbial functions in a constructed microbial community and assembly of stable microbiomes, (2) methodological advancements to achieve spatially resolved metaproteomes along plant root axis, (3) understanding microbial functions and responses to plant root chemicals using metaproteomics, (4) application of untargeted metabolomics to characterize root and exudate metabolite profiles of Populus trichocarpa. In summary, this dissertation has contributed significantly to understanding the responses of rhizosphere bacterial species associated with Populus spp., development of novel methods with new capabilities and experimental platforms that can be easily applied to other plant-microbe studies.