UC Riverside

This dissertation describes two agricultural disease microbiomes and the novel utilization of a Universal Assay primer to sequence all three domains of life. Chapter 1 reviews the current literature on Replant Disease, a multi-kingdom agricultural plant disease with no proven causal agents. In Chapter 2, the first fungal ITS sequencing of Coffee Potato Taste Defect disease highlights the importance of multiple domains of life in identifying causal agents in agricultural microbiome diseases. Coffee beans with varying levels of Potato Taste Defect were sequenced. This project identified four fungi as putative causal agents: Aspergillus versicolor, Penicillium cinnamopurpureum, Talaromyces radicus, and Thermomyces lanuginosus. Two putatively beneficial fungi were also identified: Clavispora lusitaniae and Kazachstania humilis. Chapter 3 introduces a novel Illumina amplicon assay designed to characterize organisms across all three domains of life: Archaea, Bacteria, and Eukarya. Samples from commonly studied microbiomes are used to illustrate the value of a single Illumina assay as a first look at complex microbiome questions. Environmental samples that are rich in some or all microbial kingdoms were chosen, including animal gut, plant roots, soil, and ocean water. Chapter 4 focuses on Walnut Replant Disease. Through the Universal Assay and qPCR, this chapter identifies the nematode Pratylenchus vulnus as a putative causal organism. A single Mucoromycota fungal ASV along with numerous bacteria are also significantly correlated to the disease.