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Kehila, Dan

University of British Columbia

This thesis combines experimental data and mathematical modeling to study microbial metabolic enzymes in a social evolutionary context. Microbial enzymes degrade organic polymers, inactivate antibiotics, or metabolize synthetic chemicals like plastics or pesticides ("xenobiotics"). These modify the environment and thereby affect not only the microbe possessing the enzyme, but neighboring microbes as well. Consequently, the evolution of these enzymes is shaped by social interactions. Using case studies from natural habitats and laboratory microcosms, I investigate how social interactions influence metabolic innovation and maintenance. I also develop methods and tools to test hypotheses about enzyme effects on microbial growth and interactions in the lab. Chapter 1 introduces the topic. Chapters 2 and 3 propose mathematical models (in collaboration with Alireza G. Tafreshi) to explain two natural microbial systems with unique social and metabolic features. Chapter 2 explains the stable maintenance of microbial consortia collectively harboring multi-genic metabolic pathways, allowing them to degrade xenobiotics cooperatively, as observed in laboratory enrichments experiments from half a century ago. Chapter 3 examines structural features in oceans that can sustain the high observed levels of cooperative hydrolysis of organic debris, despite the well-mixed nature of the habitat. The remaining two chapters study interactions between engineered microbial strains in the laboratory. Chapter 4 introduces a real-time measurement method to track the simultaneous growth of multiple microbes labeled with distinct fluorescent reporters. This method is used to answer a broad range questions relevant to microbiology and genetics. Chapter 5 uses the system described above to study how ecological interactions can select for microbes with highly efficient antibiotic-inactivating enzymes. I show that such enzymes are advantageous due not only to the high levels of antibiotic resistance they confer to the microbe, but also because they allow to withstand ecological pressures from other species. In all cases, social interactions provide key insights into the evolution and maintenance of microbial enzymes.

Text

2024-11-29

Attribution-NonCommercial-NoDerivatives 4.0 International

http://hdl.handle.net/2429/89765

Genome Science and Technology

University of British Columbia

UBCV

http://creativecommons.org/licenses/by-nc-nd/4.0/