Date Available


Year of Publication


Degree Name

Doctor of Philosophy (PhD)

Document Type

Doctoral Dissertation


Agriculture, Food and Environment


Plant and Soil Sciences

First Advisor

Dr. Luke A. Moe

Second Advisor

Dr. Elisa M. D’Angelo


Plants modify the soil environment through their root system, changing its physical properties and exuding compounds that promote or inhibit the growth of certain microorganisms. Therefore the structure of the soil microbial community is different in the rhizosphere than in the bulk soil. This dissertation introduces three research projects that investigated the effects of specific root exudate compounds on the soil microbial community structure, and plant cultivar specific differences in the rhizosphere microbiota.

The progenitor of maize is Balsas teosinte (Zea mays subsp. parviglumis). In a greenhouse experiment we compared the structure and function of its bacterial and fungal rhizosphere community with that of domesticated corn cultivars sweet corn and popping corn by terminal restriction fragment length polymorphism, fatty acid methyl ester analysis, and soil enzyme assays. The results allude to functional and structural differences in the rhizosphere microbial communities of the corn varieties that could lead to useful discoveries on how corn domestication has altered rhizosphere processes.

To study how root exudate flavonoids 7,4′-dihydroxyflavone and naringenin influence the soil bacterial community structure we constructed model systems to approximate the flavonoid exudation of Medicago sativa roots. Soil samples from the model systems were subjected to ATP assays and 16S rRNA gene amplicon sequencing. Our results suggest that 7,4′-dihydroxyflavone can interact with a diverse range of soil bacteria, including members of Acidobacteria subdivision 4, Gaiellales, Nocardioidaceae, and Thermomonosporaceae and may have other functions in the rhizosphere in addition to nod-gene induction in the legume–rhizobia symbiosis.

Hydroxyproline is the most common amino acid in plant cell wall proteins and serves as an important carbon and nitrogen source for soil bacteria. We treated soil with the L or the D enantiomer of hydroxyproline and collected samples for 16S rRNA gene amplicon sequencing three and seven days after the treatment. The L- and D-hydroxyproline treatments induced very similar responses in the bacterial community structure, but there were several differentially abundant groups. Our results inform about the role of hydroxyproline in shaping the soil microbial community in the rhizosphere and about the catabolism of its enantiomers in the soil.

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