Graduate Defense: Adedotun Arogundade

Thesis Information

Title: Exploring Sagebrush Microbial Metagenomes From Deep, Host-Derived Sequencing

Program: Master of Science in Biology

Advisor: Dr. Leonora Bittleston, Biological Sciences

Committee Members: Dr. Sven Buerki, Biological Sciences and Dr. Kevin Feris, Biological Sciences

Abstract

Advanced sequencing technologies and improvements in bioinformatics have provided a new way to study plant-associated microbial communities, including the use of host genomic sequencing. Our study focuses on the leaf microbiome of big sagebrush (Artemisia tridentata subsp. tridentata), an important shrub that dominates the western United States. We used host-derived Illumina shotgun sequences of sagebrush from three different sources to explore metagenomes of leaf-associated microbes that were sequenced along with their host. We aimed to profile the leaf microbiome across different sample sources, reconstruct metagenome-assembled genomes (MAGs) where possible, and study some relevant functions of the resulting MAGs. To achieve this, Illumina shotgun sequence reads (containing both host and associated microbial reads) from plants were mapped to the reference genome of Artemisia tridentata, A. annua, and the human hg38 reference genome to remove host-associated sequences. Host-cleaned reads were then analyzed using microbial metagenomics techniques. Taxonomic profiling revealed that Phyllobacterium and Sphigomonas were the most abundant microbial genera in greenhouse-grown plants, with very little variation among the samples. Wild, field-collected samples were much more variable and were dominated by Klebsiella and Aureobasidium species. From the co-assembly of greenhouse samples, we reconstructed two high-quality MAGs (a Phyllobacterium species and a Sphingomonas species) with >98% completion and <1% contamination. Functional annotation of these MAGs uncovered genes associated with the degradation and metabolism of camphor, and other essential oils such as pinene, geraniol, and limonene which are part of sagebrush leaf chemistry. This study showed that metagenome-assembled genomes can be recovered from plant host-derived sequence data, providing a new way to explore the identity and functional capabilities of difficult-to-culture microbes.