Taxonomies, Functions, and Applications of Rice-Associated Microbiome
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Taxonomies, Functions, and Applications of Rice-Associated Microbiome


Plant-associated microbes form complex interactions within their microbial community as well as with the host, affecting processes such as nutrient and carbon cycling, abiotic stress protection, and disease resistance. Understanding the interactions of the host and host-associated microbiomes could potentially aid plant health in a variety of ways and is therefore of interest to the plant science community. Rice is a unique system to study plant-microbe interactions because of flooded conditions in which it is cultivated. This anoxic environment leads to a host of anaerobic microbial taxa associating with the rice host which harbor functions dependent on the anoxic conditions, including methanogenesis. In this thesis, I describe three studies where we profile the taxonomies and functions of rice-associated microbiomes and demonstrate how the knowledge gained from these methods can be applied in discovering microbial isolates that are beneficial to the plant host.In the first chapter, I present a study that characterizes the microbiomes of a high- and a low-methane-emitting rice cultivar throughout the growing season. We found that the high methane emitting cultivar had a higher relative abundance of methanogenic archaea in the rhizosphere, and additionally had a greater abundance of taxa associated with fermentation, which could be responsible for producing methanogenic precursor molecules. In the second chapter, I present a study that characterizes the effects of drought and recovery on the microbiome. We found that a Streptomyces taxa became the most abundant member of the endosphere community during and after drought, and that this member was prevalent in rice samples from various locations. We cultured a corresponding isolate and demonstrated that it had similar qualities to the Streptomyces from the study (it was endophytic and increased in relative abundance under drought stress) and promoted root growth, demonstrating the enrichment of this microbe under drought could potentially mitigate drought effects. In the third chapter, I present a study demonstrating the effects of nitrogen on the microbiome in three different soils by profiling both the taxonomies and functions through genome-resolved metagenomics. We found that the response of rice-associated microbiomes to the nitrogen fertilizer was largely soil specific, though there were general increases in Gammaproteobacteria and decreases in Actinobacteria in response to nitrogen. Profiling the metagenome demonstrated that nitrogen fertilizer increased the abundance of genes related to aromatic compound degradation, fermentation, and methanogenesis. We also recovered 60 metagenome assembled genomes, which to our knowledge is the first such dataset of its kind in rice, and can be a valuable resource to further understanding the dynamics of microbes associating with rice.

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