Degree Type


Date of Award


Degree Name

Master of Science


Plant Pathology and Microbiology



First Advisor

Larry Halverson


Agricultural nitrogen (N) waste is a serious problem that causes many environmental issues. Plant roots and microorganisms work in synchrony; roots exude carbon which fuels the metabolism of microorganisms, and microbes in turn increase N availability near the root that both plants and microbes can use. There is mounting interest in taking advantage of this interaction to better couple N availability with crop demand. This thesis explores questions regarding how plant roots and agricultural management interact to affect the root microbiome, with implications for soil N retention. We compared two cropping systems at the Marsden experimental farm: conventional (two-year rotation, inorganic fertilization) and diversified (four-year rotation, manure inputs). Chapter 2 investigates how maize development and agricultural management interact to shape the root-associated community. We used next-generation amplicon sequencing to assess the prokaryotic and fungal communities at four points in maize development corresponding to high or low predicted plant N demand in both cropping systems. We found that prokaryotic and fungal communities follow different patterns of assembly in relation to maize development. Additionally, roots in the diversified system hosted a bacterial community better suited to complex C decomposition at a period of high predicted N demand, implicating better coupling of N mineralization in the soil to plant demand. Chapter 3 examines competition between arbuscular mycorrhizal fungi (AMF), symbionts that help roots absorb nutrients from the soil, and ammonia-oxidizing (AO) bacteria and archaea (AOB, AOA), which mediate ammonium conversion to nitrate. Competition between these groups for ammonium may reduce AO abundance and hence nitrate leaching from soil. We used quantitative PCR to assess the abundances of AOB and AOA in the bulk and rhizosphere soils of the conventional and diversified systems, planted with AMF deficient or AMF proficient maize genotypes. We found that the impact of AMF on the population sizes of AOB and AOA in N-rich agricultural soils is limited and that the rhizosphere and fertilization have a greater influence instead. Overall, these studies bring us closer to understanding the complex interactions between plant roots, soil management, and microorganisms that may help us build more sustainable agroecosystems with less N waste.

Copyright Owner

Cassandra Wattenburger



File Format


File Size

97 pages

Included in

Microbiology Commons