Investigating Rhizobium Leguminosarum Metabolism and Rhizosphere Colonization Using High-Throughput Genomics and Erythritol Enrichments
Mullock, Kevina Renee
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The demand for sustainable agriculture practices is increasing as conditions related to climate change intensify, and plant-based diets gain in popularity. Rhizobia bacteria are used as inoculants to increase the yield of legume crops by fixing nitrogen in nodules on legume roots; this reduces the use of costly and environmentally harmful nitrogen fertilizers. Erythritol is exudated from legume roots, and is catabolized by Rhizobiaceae genera. The goal of the thesis is to explore how erythritol influences community composition, and to discover novel genes influenced by erythritol catabolism in Rhizobium leguminosarum 3841. Microbial communities from bulk soil, and roots, and nodules of pea plants prepared in the bulk soils were enriched on general and erythritol media. Colony morphology assays and high throughput sequencing of the microbial communities reveal that erythritol metabolism is strongly correlated with nodulating Rhizobia strains on the roots of pea plants. High throughput analyses were also employed to explore the functional genes involved in catabolizing erythritol. RNA sequencing results reveal that genes previously reported to be involved with erythritol uptake and catabolism were expressed in higher abundances in cells grown in erythritol. As well, new genes were identified whose transcription is regulated by the presence of erythritol, suggesting a larger gene network involved in erythritol metabolism than previously thought; including stress mitigation, sugar transport, and rhizosphere quorum sensing. The results suggest that erythritol may act as a chemical signal that triggers a specialized response in R. leguminosarum 3841 to out-compete other soil bacteria in colonizing the rhizosphere, thereby nodulating legume roots. Overall, these results provide direction for developing inoculant strains that are more competitive in pea rhizospheres.