The plant microbiome is composed of diverse bacterial, archaeal, and fungal species that support the health of the plant in various plant compartments, including the root and surrounding soil, leaf surfaces, and internal tissues. These microbial species play an important role in plant health such as protecting the plant from pathogenic species and assisting with water and nutrient assimilation. With the ongoing climate crisis, it is important to understand how repeated seasons of stress, such as drought, are impacting the plant microbiome of agricultural crops, particularly staple food crops like common bean (dry beans). Work is being done to improve the resilience of common bean to environmental stress, including utilizing beneficial microbiome members to support the plant. However, the effect of drought on the common bean plant microbiome is not well understood, and it is important to select microbial inoculants that are also resistant to abiotic stress in the environment. Chapter 2 describes a multigenerational experiment conducted to study the impact of repeated drought exposure to common bean over two plant generations and in two common bean genotypes, Red Hawk and Flavert. We identified more significant effects of the drought treatments and legacy effects in the microbiome of the Flavert plants, while the microbiome of Red Hawk was more stable. Additionally, we identified bacterial orders that are consistently associated with the drought treatment across generations and genotypes, particularly Xanthomonadales and Rhizobiales, which may contain target bacterial inocula for microbiome modification under drought stress. In Chapter 3 the seeds of the Red Hawk plants in the multigenerational experiment were investigated, with an additional treatment condition of increased fertilizer concentration. The aim of this study was to identify vertically transmitted taxa in common bean seeds under abiotic treatment conditions. The stress treatments had a negligible effect on the resulting seed microbiomes, but we identified a significant impact of parental plant line and a signature of stable transmission of 22 prevalent seed microbiome members. These prevalent taxa included previously identified core taxa for common bean, and could be a valuable point of interest for the development of beneficial bacteria applications in agriculture. Chapter 4 investigates the development of the rhizoplane and rhizosphere microbiome in common bean roots across plant growth stages. An innovative experiment utilizing a growth delay in common bean plants allowed the influence of plant growth stage and time across the common bean lifecycle to be investigated separately. We identified closely aligned bacterial communities in the rhizoplane of common bean based on growth stage in plants, despite differing growth rates. Indicator taxa associated with plant growth stages were identified and found to be under a selective pressure by the plant, and included known beneficial plant microbiome taxa. This work provides important knowledge in understanding the impacts of repeated seasons of drought on plant microbiomes, exposes the importance of parental line in seed microbiome studies and the maintenance of the plant microbiome across generations, and provides insight into beneficial bacteria and the assembly processes of the plant microbiome. The need for sustainable solutions to support agricultural crops continues to rise, and this thesis contributes to our understanding of the processes shaping the beneficial plant microbiome that could be utilized in agricultural applications.
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