Doctoral Dissertations

Date of Award


Degree Type


Degree Name

Doctor of Philosophy


Energy Science and Engineering

Major Professor

Scott Retterer

Committee Members

Jennifer Morrell-Falvey, Sara Lebeis, Jason Fowlkes


The interactions amongst plants and microorganisms within the rhizosphere have a profound influence on global biogeochemical cycles, and a better understanding of these interactions will benefit society through improved climate change prediction, increased food security, and enhanced bioenergy production. However, the rhizosphere is one of the most complex and bio-diverse ecosystems on earth, making it difficult to parse apart specific interactions between species. This difficulty is compounded by the inability to directly visualize rhizosphere interactions through the soil. Additionally, conventional laboratory techniques do not offer real-time, high-resolution visualization or the proper environmental control to isolate and probe these interactions. A knowledge gap persists in how to design appropriate culturing platforms that allow researchers to collect spatially and temporally sensitive information about physical and chemical interactions in the rhizosphere. This dissertation addresses that gap by demonstrating the design and use of several custom-engineered micro-habitats in characterizing plant-microbe interactions. Specifically this thesis introduces novel protocols for culturing plants and microorganisms together in microfluidic platforms, pairing platforms to multi-modal imaging techniques with organelle scale resolution, and recreating the structural complexity of the rhizosphere in a microfluidic habitat. Not only does this thesis introduce novel engineered systems, but the work contained herein also goes beyond proof-of-concept experiments and demonstrates the ability of these platforms to generate hypotheses and answer outstanding biological questions.


Portions of this document were previously published in Advanced Biosystems, JoVE, and bioRxiv.

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