Endophytic Bacteria From Roots of High-Performing Tepary Bean (Phaseolus acutifolius A. Gray): Functional Traits, Genomics, and Influence on Seedling Growth and Development

Abstract

Common bean (Phaseolus vulgaris) is a globally consumed protein source that is vulnerable to increasing drought under climate change. An alternative protein source is the closely related tepary bean (P. acutifolius). It has gained attention for being a high protein source, with genetic traits that confer resilience to the increased drought and heat predicted to affect agriculture under our changing climate. Over its evolution in arid regions, tepary bean has established beneficial relationships with symbiotic microbes that may be important in enhancing their stress resilience, especially when grown in native soils. In this thesis, I aimed to characterize root endophytes from field grown tepary bean under water-limited and standard-irrigated conditions, to investigate the potential plant-growth promoting traits and genomic features of those microbes, and to evaluate their potential to alter tepary bean seedling phenotypes and microbiomes under field conditions. Focal bacteria from high-performing tepary bean had a variety of plant-growth-promoting traits and genomes with evidence of biosynthetic potential. We did not find evidence that seed inoculation altered root endophytic microbiomes or seedling traits, but longer-term impacts on plants or yield were not measured and thus remain for further study. Overall, this thesis highlights the common bacteria affiliated with roots of tepary bean in a field setting in Arizona, examines their traits in vitro, reveals aspects of their genomes and secondary metabolite repertoires, and demonstrates a method for inoculating seeds for field cultivation, while providing a basis for future studies of plant responses to inoculation under arid land conditions. Together, the lines of inquiry presented in this work are important for advancing our understanding of microbiomes of plants and how they may contribute to addressing global food security as we seek sustainable approaches for producing nutritious foods in a changing world.