Using methyl halides as a reporter in a model soil consortium and for intercellular signaling
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Over the past decades, there has been an increasing understanding of the important and diverse role played by the soil microbiome in maintaining soil health, plant productivity, and biogeochemical cycles. Understanding the precise nature and contribution of these roles can allow us to harness soil microbial communities for agriculture, environmental engineering, and bioremediation. While -omics approaches and other bulk measurements have provided insights into soil microbial communities and their composition, these attempts can be confounded by a lack of suitable tools for understanding the perception and responses of individual microbes to different events and community members in soil. In this thesis, I review applications of synthetic biology to address some of the aforementioned challenges in researching and applying soil microbial communities. Then, I describe my work in evaluating and expanding the use of gas-output microbial biosensors in individual soil bacterial species and in a soil bacterial consortium via a gas-mediated cell-cell signaling relay. Additionally, I describe the construction of safe soil habitats for synthetic biology that allow us to evaluate intercellular microbial interactions and gas-output biosensor applications at centimeter- and meter-length scales. I also describe my efforts at constructing novel biosensor inputs for gas-output microbial biosensors and characterizing these new biosensors in liquid and soil environments. Finally, I discuss avenues for expanding on my work by applying gas-output microbial biosensors in more realistic soil conditions to answer fundamental soil science questions.
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Lu, Li Chieh. "Using methyl halides as a reporter in a model soil consortium and for intercellular signaling." (2023) Diss., Rice University. https://hdl.handle.net/1911/115273.