Date of Award

Spring 2023

Project Type

Dissertation

Program or Major

Molecular and Evolutionary Systems Biology

Degree Name

Doctor of Philosophy

First Advisor

Anissa Poleatewich

Second Advisor

Thomas Davis

Third Advisor

Anna Testen

Abstract

Quinoa (Chenopodium quinoa Willd.) has potential for cultivation in North America; however, abiotic stresses like high humidity and a short growing season are obstacles for production in the Northeast. Wild relatives of quinoa such as C. berlandieri and C. ficifolium thrive in New England and have the potential to serve as both genetic resources for breeding research and as sources of novel beneficial microbes for application to quinoa. Previous studies have shown that certain bacteria and fungi within the soil-root zone (or rhizosphere) microbiome can increase plant growth, aid in stress tolerance, and increase water and nutrient acquisition. It is expected that using native relatives of crops for microbial discovery can reveal novel microbes that are both environmentally adapted and genetically compatible with the crop of interest. However, the microbial community must first be characterized to identify and isolate novel beneficial microbes from the rhizosphere. This research serves as foundational work to characterize rhizosphere microbial communities associated with quinoa and its wild relatives in North America and investigate how microbial interactions at play in the rhizosphere impact plant health in the genus Chenopodium. The specific objectives of this research were to 1) determine if different Chenopodium species harbor unique rhizosphere communities (Chapter 2), 2) compare Chenopodium-associated and non-Chenopodium associated microbial communities for effects on plant growth and tolerance to stress (Chapter 3), and 3) identify Chenopodium-associated microbial taxa that provide beneficial services like phosphate solubilization and nitrogen fixation (Chapter 4). I hypothesized that the rhizosphere microbial community composition of quinoa relatives would be significantly different than that of quinoa when grown in New England and that the Chenopodium-host adapted microbiome would confer a plant health benefit to quinoa plants. To characterize the rhizosphere microbial community of Chenopodium spp. in New Hampshire, a common garden experiment was conducted at the UNH Woodman Research Farm. Bulk and rhizosphere soil was collected from 14 Chenopodium accessions representing four species. Molecular analyses showed that while bacterial community composition did not vary based on host species, fungal community composition was significantly different based on host plant evolutionary history (wild, domesticated, or hybrid species), indicating that wild Chenopodium species may form unique microbial relationships compared to domesticated quinoa (Chapter 2). To assess how microbial communities impacted Chenopodium plant growth under drought stress and non-stress conditions, controlled environment microcosm studies were performed. I evaluated the effect of microbial communities of five different origins across two separate experiments on the growth of C. quinoa and C. berlandieri var. macrocalycium. Overall, the applied microbes from these host origin treatments did not impact Chenopodium spp. growth in drought stress or non-stress conditions but C. quinoa and C. berlandieri var. macrocalycium recruited distinct microbial communities over time (Chapter 3). Rhizosphere soil was collected from drought-treated plants in the microcosm study to screen for candidate beneficial bacteria performing phosphate solubilization and nitrogen fixation. Two candidate beneficial bacterial isolates and a commercial biostimulant, Lalrise Start SC, were applied to Chenopodium spp. under abiotic stress conditions and only the commercial biostimulant had an impact on quinoa growth. Overall, this work has revealed variation in the rhizosphere microbiome among Chenopodium species as well as variation among Chenopodium spp. traits under abiotic stress (Chapter 4). While there is much more to learn about microbial interactions within the Chenopodium genus, this work provides foundational knowledge of Chenopodium microbiomes in North America, which is a critical first step in evaluating how the microbiome impacts plant health.

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