Abstract
Nutrients are essential elements for the sustenance of microorganisms. Microbes and their surrounding environment have an intricate relationship, and it hinges significantly on nutrient availability. The responses of microorganisms to nutrients are highly diverse, each harboring distinct nutrient preferences. This phenomenon is of particular significance in the field of biomanufacturing, a sustainable technology facilitated by microorganisms. Thus, I aimed to delve into biocomponents for nutrient management, utilization, and generation in various biomanufacturing fields, while contributing to a sustainable environment. The primary objective is nutrient utilization to facilitate sustainable biomanufacturing beyond Earth by in-situ resource utilization (ISRU). As humans embark on the lifelong goal of alternative habitation, biomanufacturing can play a pivotal role in achieving this goal, using microbes as remote laborers. I developed an alternative feedstock utilizing in-situ biomanufacturing platform. Deconstructed plastic utilizing Rhodococuss jostii strain served as the host. Lunar and Martian regolith (simulants) served as micronutrients, discarded plastics from space missions served as carbon sources, and human fecal waste served as a replacement for macronutrient sources. This effort demonstrated the feasibility of sustainable space biomanufacturing, significantly reducing space mission costs and paving the way for sustainable microbiology in extraterrestrial environments. The second objective is to understand cyanobacterial behavior and develop a process model to predict nutrient control and utilization. The aim was to establish a solid understanding of how nutrients affect the harmful algal bloom problem, offering a promising solution to address this issue. The model forecasts nutrient consumption and related algal growth. A comprehensive understanding of microcystin production from Microcystis aeruginosa in aquatic systems under different nitrogen and phosphorus conditions, along with coculturing with another cyanobacterium, Synechocystis elongatus, was achieved. Based on these findings, a kinetic model for aquatic environmental safety was developed, providing a useful tool for predicting algal blooms. The last objective is genetic engineering to produce nitrogen compounds, such as guanidine, from cyanobacteria used as biofertilizers. Synechocystis sp. PCC 6803 served as a host for gene modification. A functional module leveraging the potentially guanidine-producing enzyme called Din11 was introduced to catalyze guanidine synthesis from arginine. Additionally, AI-assisted and database-based screening of protein candidates for cyanobacterial guanidine production uncovered new enzymes with underexplored capabilities. Improving the cell factory by secreting nitrogen products through the insertion of a guanidine exporter was achieved using the Design-Build-Train-Learning (DBTL) cycle. To understand the nitrogen metabolism uncharacterized when these heterologous enzymes are introduced, 15N metabolomics was performed. A significant increase in nitrogen flux in the Din11 strain with an exporter was confirmed. This study demonstrated that sequestering atmospheric gas and optimizing nutrient use via enzymatic reactions is a less energy-intensive and more profitable approach. These engineered cyanobacteria have the potential to revolutionize green biomanufacturing by producing biofertilizers. In summary, this doctoral research offers a detailed investigation of how microbes respond to different nutrients, focusing on optimizing nutrient use, understanding microbial behavior under various conditions, and developing strains for nutrient production. The study primarily aimed to promote sustainability from a microbiological viewpoint as an environmental engineer. In an era when technological advancement must be balanced with environmental responsibility, this integrated approach reflects the philosophy of environmental microbiology and biomanufacturing.
Committee Chair
Yinjie Tang
Committee Members
Himadri Pakrasi; Jianping Yu; Kimberly Parker; Zhen He
Degree
Doctor of Philosophy (PhD)
Author's Department
Energy, Environmental & Chemical Engineering
Document Type
Dissertation
Date of Award
4-29-2026
Language
English (en)
DOI
https://doi.org/10.7936/z6dg-a430
Recommended Citation
Lee, Hakyung, "Microbial Resource Engineering for Sustainable Biomanufacturing" (2026). McKelvey School of Engineering Graduate Student Theses & Dissertations. 1370.
The definitive version is available at https://doi.org/10.7936/z6dg-a430