The Impacts of Genotype-by-Environment Interactions on Switchgrass Rhizosphere Microbiome Composition and Insights for Breeding in Sustainable Agriculture

Open Access
- Author:
- Sutherland, Jeremy
- Graduate Program:
- Bioinformatics and Genomics (PhD)
- Degree:
- Doctor of Philosophy
- Document Type:
- Dissertation
- Date of Defense:
- May 01, 2023
- Committee Members:
- Jia Li, Outside Unit & Field Member
Terrence Bell, Co-Chair & Dissertation Advisor
Jesse Lasky, Co-Chair & Dissertation Advisor
Emily Davenport, Major Field Member
George Perry, Program Head/Chair - Keywords:
- switchgrass
microbiome
genotype-by-environment interactions
microbial heritability - Abstract:
- As a survival strategy, plants often host microorganisms on and within their tissues to facilitate and aid in resource acquisition and host defense. While host-microbiota relationships are widely hypothesized to benefit plants, the ecological and evolutionary importance of such relationships, and many of the underlying genetic mechanisms, remain elusive. Our understanding of this relationship is complicated by several abiotic and biotic factors simultaneously. For instance, not all microbiota deliver benefits to plants and the availability of certain microorganisms varies between environment. Additionally, the strength of host genetic influence on associated microbiomes often varies by plant species, age, tissue type, and other host factors, and plant phenotypic expression can differ between environments. The independent abiotic influences on plants and microbiomes, separately, also complicate our understanding of the host-microbiome relationship. Lastly, plant-associated microbiomes are made up of autonomous organisms with complex ecologies entirely separate from their host. Nevertheless, it remains widely observed that host genetic variation can influence the diversity and composition of plant-associated microbiomes, which then may also impact host traits. However, a critical knowledge gap remains regarding how these relationships change between different environments and how they might impact plant phenotypes in ways that are desirable to humans. Switchgrass (Panicum virgatum) is a highly outcrossing, perennial grass species with substantial locally-adaptive genotypic and phenotypic diversity across its native North American range. Due to this, switchgrass offers a useful biological model to study the complex interactions between host genotypes, the environment, and associated microbiomes. From an applied research perspective, there is also considerable interest in advancing switchgrass as a cellulosic biofuel feedstock to replace corn-based ethanol production, since switchgrass offers numerous ecological benefits over corn and does not directly compete with food prices. The viability of this venture, however, may depend on influencing host-associated microbiomes to supplement costly agricultural soil inputs (e.g., synthetic fertilizers and pesticides). Yet, little is known regarding the switchgrass microbiome, specifically in the northeast U.S. climate, and even less regarding its effects on host performance. Therefore, the objectives of this study were to (1) examine the relationships between switchgrass-genetic influence on rhizosphere microbiome composition and how those relationships may correspond to host traits, and (2) understand how host genetic influence on its rhizosphere microbiome changes between environments and between bacterial and fungal taxonomic levels. To achieve this, we employed four common garden experiments, combined with host genetic mapping, rhizosphere microbiome sequence analysis, statistical modeling, and associative analyses to disentangle the host genetic impacts on microbiome composition and diversity from environmental impacts. Switchgrass hosts were sourced from 68 diverse populations, capturing much of the phenotypic and genotypic diversity within the United States, and planted between, ultimately, four common gardens (an original common garden used in Chapter 2 and three subsequent cloned transplanted common gardens used in Chapters 3 and 4). By propagating cloned plant material into new environments, we captured a diversity of environmental factors that could influence host phenotype and microbiome composition. From the perspective of switchgrass producers, uncovering the genetic basis for larger, disease-resistant plants using minimal agricultural inputs is desirable. The research presented here accomplishes that goal by investigating the switchgrass rhizosphere microbiome assembly and its relationship to host phenotypes in different environments. We studied primarily two plant phenotypes: Biomass Yield and Anthracnose Disease Resistance – a common fungal pathogen in the region that can reduce yield. In Chapter 2, we hypothesized that the composition and diversity of rhizosphere bacterial assemblages in the original common garden would differentiate due to genotypic differences between hosts. Those findings establish that switchgrass genomic and life-history variation influences bacterial composition in the rhizosphere, potentially due to host adaptation to local environments. In Chapters 3 and 4, we sought to address two additional questions: How does host genetic influence on associated rhizosphere microbiome change between different environments? And, if the microbial response to host traits and the abiotic environment are phylogenetically conserved, how might host genetic influence change at different microbial taxonomic levels in response? Our findings support that host genetic influence on the rhizosphere microbiome in switchgrass varies across both microbial taxonomic level and local environmental conditions, and the abundance of select microorganisms under host genetic influence correlate with desirable traits relevant to the U.S. bioenergy market. Overall, this study shows that genotype-by-environment interactions impact the strength of switchgrass genetic influence on rhizosphere microbiome composition and differentiates along bacterial and fungal taxonomic levels. This research offers host genetic insights into the associative interactions that may influence microbiome composition in ways that are important to the sustainable production of switchgrass as a biofuel feedstock.