Date of Award


Document Type

Open Access Thesis

Degree Name

Doctor of Philosophy (PhD)


Biology/Molecular, Cellular, and Organismal Biology

First Advisor

Rick Kesseli

Second Advisor

Douglas Woodhams

Third Advisor

Michael Shiaris, Karen Ricciardi


The microbiome's role in shaping host phenotypes is a critical area of investigation, with implications for ecology, evolution, and host health. Dynamic plant-microbe interactions are influenced by factors like soil type, environment, and genotype. Understanding their impact on microbial communities is key for tailored plant benefits. An artificial ecosystem selection experiment was done for eight generations with Arabidopsis thaliana Ler and Cvi. This revealed distinct microbial communities shaped by genotypes and biomass treatments. Initially, environment dominated, but over time, genotype and biomass gained influence, explaining ~40% of the variation. Moreover, genotype-specific rhizobacterial associations were observed, enhancing understanding of community dynamics and genetics, with potential for agricultural applications. Plant genes interact with microorganisms, fostering beneficial or antagonistic relationships. This control affects microbe abundance, aiding nutrient uptake, disease defense, and stress tolerance. Despite a century of research, our understanding of these genetic mechanisms remains limited. Our study focused on using near-isogenic lines (NILs) obtained from crossing Arabidopsis thaliana Ler and Cvi to narrow down a plant genomic region previously identified in the lab. This region spans approximately 3.75 Mbp on chromosome 1 and houses around 995 genes. Employing fine-mapping with near-isogenic lines and metagenomic data, we confirm a small yet significant genotype impact on microbial community structure, identifying genotype-specific microbial taxa abundance. Our work reduces the candidate region to 418 genes, advancing insight into the genetic control imposed by Arabidopsis thaliana on the microbiome.


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