Genomic and experimental insights into the ecology and evolution of transferable genetic elements

Abstract

Bacteria have dynamic genomes that allow them to adapt and survive almost anywhere on Earth. This genetic flexibility is facilitated by mobile DNA elements, which can transfer within or between genomes independently of cell lineages and drive bacterial evolution. Mobile genetic elements influence many aspects of bacterial life by encoding and transferring antimicrobial resistance genes, pathogenicity factors, and toxin-antitoxin modules. Plasmids, integrons, and genomic islands are several types of mobile DNA elements that can carry beneficial genes which help host cells adapt to new environments or provide new ecological functions. However, much is still unknown about how mobile genetic elements persist in the environment, how they mediate cell survival, and how they impact interactions in bacterial communities. In this thesis, genomic and experimental techniques were used to investigate the ecology and evolution of mobile genetic elements at three different scales: genes, species, and ecosystems. At the gene level, I performed a literature review to determine how the main processes of horizontal gene transfer (conjugation, transduction, and natural transformation) impact antimicrobial resistance gene transmission in clinical environments. Conjugation of antimicrobial resistance gene-encoding plasmids does occur within clinics and patients, but there is less evidence for transduction and transformation. This may be due to low transfer rates or difficulty detecting the transfer of core genes with key mutations that provide resistance. In another project, I used comparative genomics to assess the evolutionary history of the Salmonella pathogenicity island SPI-1, which encodes a type three secretion system for invasion of mammalian intestinal cells and is remarkably conserved across the Salmonella genus. I defined the multiple genomic islands that comprise the mosaic structure of SPI-1, with some islands having arrived in the Salmonella clade earlier than others. Related pathogenicity islands possess homologs to SPI- 1 transcriptional regulator hilA, but are missing homologs to hilD and hilC; the high nucleotide identity between hilD and hilC suggests they may be paralogs. To assess how mobile genetic elements impact communities at the species level, I designed a synthetic multi-species community wherein only Escherichia coli can access a carbon source and Salmonella enterica must rely on cross-feeding to survive while simultaneously killing the E. coli with a plasmid-encoded colicin toxin. Despite relying on cross-feeding to survive, S. enterica consistently emerged as the dominant community member. Experimental results and mathematical modeling confirmed that the colicin liberates nutrients through cell lysis and benefits the colicin-producing population, which had not been previously described for this type of toxin. At the ecosystem level, I attempted to isolate all of the plasmids (“plasmidome”) from surface water of agricultural ponds (dugouts) to determine how the gene content changes over time using long-read DNA sequencing. However, ongoing technical difficulties caused by environmental contaminants resulted in limited DNA sequencing data and interference in enzymatic reactions during library preparation. Nevertheless, additional insights into these ecosystems were possible through 16S rRNA bacterial community profiling and qPCR of select antimicrobial resistance genes and mobile elements. Antimicrobial resistance genes are detectable and persist over time in dugouts, and regression modeling demonstrated that their abundance was explained by the abundance of the mobile integrin integrase intI1 and cattle presence. Altogether, these diverse projects have contributed new knowledge on the transmission, persistence, and ecological impact of mobile genetic elements at multiple scales (gene, species, ecosystem) by using experimental techniques and high-throughput sequencing technologies.