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"Ubiquitous but unseen: Making sense of global free-living and plant-associated biological nitrogen fixation and exploring how host plants and endophyte communities influence nitrogenase enzyme activity"


James P. Kupihea Jr.
Environmental Systems

University of California, Merced



Nitrogen (N) is essential to life and tends to be the most limiting nutrient to terrestrial net primary production (NPP). Specialized bacteria and archaea called diazotrophs can perform biological nitrogen fixation (BNF), converting atmospheric N2 into bioavailable ammonia (NH3) using the enzyme nitrogenase. However, we have a poor understanding of how climate interacts with the BNF globally, how host plant growth and development influence rates of nitrogenase enzyme activity (NA), and how diversity in the endophyte community potentially shapes NA. Chapter 1 uses a meta-analytical approach to data acquisition combined with structural equation modeling to identify potential climate drivers of global free-living and plant-associated BNF. We also highlight the challenge/incongruency of relating satellite imagery and unstandardized plot-level observations of BNF. Chapter 2 focuses on a field study conducted in Yosemite National Park, CA, USA, from 2016-2019. We assessed the nitrogenase activity in the foliage of Sierra lodgepole pine across multiple developmental stages; seedlings, saplings, sub-canopy trees, and canopy-forming trees. We show higher NA rates in seedlings relative to older/larger trees. Chapter 3 is a greenhouse study examining the endophyte community’s role in determining the NA rate in the foliage of Sierra lodgepole pine seedlings. We cultivated Sierra lodgepole pine seedlings and used foliar applications of antibiotics and plant and soil-based inoculum to modify endophyte communities in seedlings and record differences in NA.


James Kupihea was born in Glendale, Arizona, in 1987. As a child, he developed a passion for the outdoors, fishing, hiking, and camping. By age six, he was often found analyzing the stomata of his father’s garden vegetables with a flea market microscope, raising tadpoles and fish, and sneaking his mother's mason jars under his bed to keep ant
farms. Decades later, he still loves to talk about stomata, the scientific value of vegetable gardens, and his undying love for the outdoors. At UC Merced, he met his wife, adopted a dog, became a father, learned from an incredible community, and developed an affection for the often-overlooked natural areas of the California central valley.

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