Advancing Polycyclic Aromatic Hydrocarbon Bioremediation using Genetic Bioaugmentation in Soil Microbial Communities

Polycyclic aromatic hydrocarbons (PAHs) are introduced into the environment through forest fires, fossil fuel combustion, and crude oil spills, posing significant health and ecological risks. These compounds are carcinogenic and disrupt soil microbial processes essential for ecosystem functions. Bioremediation, which uses microorganisms to degrade pollutants, can be applied to ameliorate contaminated environments. However, biodegradative functions are often limited because exogenous bacteria cannot compete with native microbes. Genetic bioaugmentation offers a promising solution by equipping native microbes with biodegradative capabilities encoded and delivered via mobile genetic elements such as plasmids. This approach leverages the adaptability and ecology of native microbial communities. I hypothesize that delivering catabolic genes on plasmids to native microbes enhances PAH removal by engaging a diverse, well-adapted bacterial community rather than relying on a single species. Previous research on genetic bioaugmentation has inadequately addressed the fitness impacts of plasmids on recipient bacteria, the range of plasmid recipients, and their effect on biodegradation rates. This thesis investigates these factors by engineering plasmids with the bphC dioxygenase gene and conjugating them to soil bacteria. Results revealed that plasmid fitness effects significantly influenced conjugation rates, community structure, and PAH biotransformation. Moreover, plasmid transfer rates were strongly associated with recipient bacterial abundance in synthetic communities. To track plasmid persistence, the pKJK5 plasmid was modified with a genetic memory biosensor. This plasmid persisted in soil microbial communities for 10 days without selective pressure and showed enhanced stability and biodegradation efficiency in the presence of a model PAH. These findings highlight the critical role of plasmid fitness effects in shaping microbial community dynamics and biodegradation efficiency. By addressing the activity and longevity of biodegradative functions at the community level, this research advances the design of effective genetic bioaugmentation strategies for PAH-contaminated environments.

Name thesis:degree_name

Doctor of Philosophy

Level thesis:degree_level

Doctoral

Discipline thesis:degree_discipline

Engineering

Grantor

Rice University

Year dc:date.issued

2025

Author dc:creator

• Crosby, Tessa Marie

Advisor dc:contributor.advisor

• Stadler, Lauren

• genetic bioaugmentation
• conjugation
• polycyclic aromatic hydrocarbons
• bioremediation
• dioxygenase

Statement dc:rights

• Copyright is held by the author, unless otherwise indicated. Permission to reuse, publish, or reproduce the work beyond the bounds of fair use or other exemptions to copyright law must be obtained from the copyright holder.

Language dc:language.iso

eng

Handle dc:identifier.uri

https://hdl.handle.net/1911/118384

OAI identifier oai:identifier

oai:repository.rice.edu:1911/118384