PhD defence by Peter Erdmann Dougherty

Life on the Spectrum: Phage Lifestyle Diversity and its Impacts on the Wheat Phyllosphere Microbiome

Microbial communities are essential to all Earth’s ecosystems and play crucial roles in almost every biogeochemical cycle. Although our knowledge of microbial community composition has advanced greatly in recent years, we still have a very limited understanding of how these communities assemble and interact, limiting our ability to manipulate and control our microbes.

One microbial ecosystem of particular importance to us are those that colonize the crops we eat. In this thesis, I aim to improve our understanding of the microbes that colonize the above-ground part of plants, known as the phyllosphere microbiome. In particular, I focus on the bacteriophages, viruses that infect and kill bacteria.

Phages are sometimes thought of as simple “bacteria-eaters” who only predate their bacterial hosts, but the reality is far more complicated. In six manuscripts, this thesis explores the diversity of phage lifestyles including virulent bacteria-eaters, temperate prophages weaponized for bacterial warfare, and phage satellites that predate other phages. I find both novel phages and functions, such as satellites encoding predicted host beneficial genes such as xanthorhodopsin, a proton pump that can harvest light energy. I also examine evidence of phages that slip through the cracks of traditional classification systems and argue that phage lifestyles should be thought of as a spectrum rather than discrete categories. Throughout this thesis, I link phage biology to the phyllosphere microbiome, emphasizing its role in intraspecies bacterial warfare, horizontal gene transfer, and bacterial predation. In conclusion, this thesis argues that phages are influential components of the wheat phyllosphere and shape their communities through underappreciated mechanisms.