Foundational Research Towards Plant Microbiome Engineering Capability

With the threat of climate change becoming more apparent in recent years, it is clear that the increased severity and regularity of extreme weather events will inevitably impact our ability to maintain agricultural productivity in the future. One relatively unexplored avenue towards increasing plant health and resiliency has also recently emerged, however, as the microbes which live in and around plant roots have been shown to influence biomass and yield, as well as resistance to both biotic and abiotic stresses. Therefore, an ability to manipulate and engineer these microbial communities, referred to as the plant microbiome, has the potential to help ensure food security amidst environmental turmoil. Unfortunately, this dream of an engineered, beneficial plant microbiome has yet to be realized. This is in large part due simply to the nascency of the field of research as a whole, with large gaps in our basic understanding still needing to be addressed. Work must be done to generate a more complete understanding of the microbes themselves and the processes by which they are regulated by plant hosts, but also towards developing more robust and efficient plant engineering capabilities in order to realize the potential real-world benefits of an engineered microbiome. The research presented in this dissertation was undertaken in an effort to address these current shortcomings, and hopefully contribute to future efforts aimed at harnessing and utilizing the plant microbiome for societal gain. First, this work investigates factors influencing the fungal microbiome assembly in a forest tree, the coast redwood Sequoia sempervirens. Because most research has been performed in model or crop species in agricultural or fully artificial conditions, investigating patterns of microbiome structure in a gymnosperm growing in a natural forest setting will allow us to assess the universality of previously reported phenomena related to the plant microbiome. We found that, as expected, soil chemistry and pH in particular is a strong determinant of root-associated fungal communities. We also demonstrated that forest continuity and heterogeneity influence the soil microbiome, which shows that principles of landscape ecology can indeed be useful in deepening our understanding of microbial ecology. Finally, we discovered that redwoods have specialized organs which function to morphologically compartmentalize symbiotic arbuscular mycorrhizal fungi, which serves to highlight the need for holistic assessment of factors influencing the plant root microbiome rather than a narrow focus on, for instance, singular -omic techniques. To build upon the theme of holistic rather than narrow microbiome investigations, this research goes on to summarize an ambitious holo-omic characterization of how sorghum and its microbiome interact with drought stress. Termed the EPICON Project, this undertaking serves as an exemplary case-study of using multiple -omic techniques, termed holo-omics, in order to better understand complex interactions governing microbiome assembly and development. Specifically, this work highlighted the correlation between a key metabolite, glycerol-3-phosphate (G3P), as well as transcriptional response to reactive oxygen stress (ROS) mitigation, with reproducible shifts in the sorghum root microbiome under drought. These findings serve as testaments to the power of holo-omic studies in progressing the field of plant microbiome research towards the ultimate goal of being able to engineer desired phenotypes relevant to world agriculture as it faces climate change-induced challenges. Finally, we used the lessons learned through holo-omic investigation of the sorghum root microbiome in conjunction with novel plant transformation techniques and the CRISPR-Cas9 gene editing system in order to provide a framework for future efforts aimed at microbiome engineering. Although significant progress was made in improving overall transformation efficiency in sorghum through the use of the morphogenic genes Babyboom (BBM) and Wuschel (WUS), the successful editing of our target genes remained elusive. Nonetheless, we hope that this work has helped lay the groundwork for future efforts towards realizing an engineered plant root microbiome.

Advisor: Coleman-Derr, Devin
Lemaux, Peggy G