Degree Type


Date of Award


Degree Name

Doctor of Philosophy


Ecology, Evolution, and Organismal Biology



First Advisor

Kirsten S. Hofmockel

Second Advisor

Brian Wilsey


Microbial communities are initiators, controllers, and mediators of biogeochemical processes, and nutrient and carbon cycling within terrestrial environments. Soil health is also maintained by microbial communities, including water retention, organic matter build-up, and aggregation of soil particles. All of these factors combined, create an enormous impact on terrestrial ecosystems, disproportionate to the microbial cell size, influencing everything from plant productivity and diversity, soil habitat maintenance, and the balance between carbon lost to respiration and carbon maintained within soil as organic matter.

Inclusion of microbial communities into management decisions is necessary to fully improve sustainability efforts and productivity. This research investigates the interaction of the aboveground management’s impact on microbial community diversity, function, and resiliency. Specifically, the impact of cropping system and nitrogen application on the soil fungal and bacterial community were explored. In addition, local interactions between plants and fungal communities are examined to determine how trait-based approaches can be applied to microbial ecology. Soil itself is examined as a determinant of microbial community diversity, and is demonstrated to have a strong impact on both fungal and bacterial community structure. In compliment, a novel technique utilizing fluorescently labeled cellulose nanocrystals allows us to address ecosystem scale questions regarding cellulose degradation and utilization within a reductionist and tractable approach.


Copyright Owner

Racheal Nichole Upton(Erb)



File Format


File Size

184 pages

Included in

Microbiology Commons