Investigations in plasmid biology at the levels of the gene, community, and ecosystem

Abstract

Bacteria are diverse microorganisms that interact with and impact human life in myriad ways. Their genomes are typically comprised of a single chromosome on which core genes are encoded, and additional genetic structures that carry additional, accessory loci. Plasmids are one type of accessory genetic element that have a capacity to jump horizontally between bacteria, and in doing so, provide genes and associated functions to new hosts. Plasmids have established impacts on bacterial physiology and evolution, but many ques- tions remain about how plasmids persist, spread, and change in nature. Furthermore, since plas- mids evade standard sequencing and assembly approaches, scientists have uncovered only a frac- tion of total plasmid diversity in nature. In this thesis I describe my efforts to investigate plasmids at the levels of gene, commu- nity, and ecosystem. I used computer-based methodology to analyze existing plasmid sequences, took traditional microbiological approaches to test plasmid traits in the lab, and worked toward sequencing plasmids from an ecologically important natural environment. By analyzing the distribution of a conserved protein on public plasmid sequences, I dis- covered a long-term association between the locus and a specific backbone. I used bioinformatic methodology to investigate and predict roles that the protein might fulfill and related these to the plasmid’s immense success across several bacterial genera. This investigation furthered our understanding of plasmid biology at the level of a single gene. Then, I used further computer-based methodology to chart a population of unique and pervasive plasmid sequences. I described sev- eral lineages within this population and related these to bacterial hosts in which they are found, then identified one group that appears to have mobilized between several hosts in recent history. This study centred upon a population of plasmids and how they might interact with bacterial communities. Taking my investigations on plasmids to the lab, I used molecular techniques to create an experimental system to track the mobility of a Salmonella plasmid. I found that the plasmid is more frequently transferred between bacteria when it encodes a toxin-antitoxin sys- tem. This analysis further related to plasmids in bacterial communities as it identified a modula- tor of plasmid transmission. Finally, I made efforts to sequence plasmids from freshwater agri- cultural ponds in Saskatchewan, Canada. Although I did not characterize complete plasmid se- quences, I took steps toward reliably sequencing environmental plasmids from an important eco- system. Together, these research projects contribute to an enhanced understanding of the evolu- tionary success strategies and natural diversity of bacterial plasmids. My work highlights that re- search in the field of plasmid biology is essential and exciting.