The ecology of prophages at the microscale

Abstract

Microbial communities shape nearly every habitat on Earth. Delineating the principles by which microbial collectives assemble, function, and evolve across systems is fundamental to transforming microbial ecology from an observational science to a predictive one. In this thesis, I argue that temperate bacteriophages – the pervasive viruses that can reproduce in either a predatory or mutualistic manner with their bacterial hosts – must be explicitly considered in order to develop a more complete framework for microbial community development. However, our understanding of the impacts of temperate phage induction and maintenance in complex communities is limited. In my first study, I investigated the ecological processes controlling community development at the microscale, which is the approximately the scale at which many microbial communities assemble in nature. Using synthetic resource particles as scaffolds for the assembly of discrete, microscale ecosystems, I characterized the complex marine microbial communities that grew on hundreds of individual particles. I found that these microscale communities diverge both taxonomically and functionally, with prophage induction, especially among founding community members, emerging as one factor significantly associated with this variability. However, the ecological modulators of lysogeny-lysis transitions in complex communities remain largely unknown. Therefore, in my second study, I explored the extent to which prophage dynamics may be influenced by chemical cues serving as proxies for the densities and identities of surrounding community members – namely, quorum sensing autoinducers. Through a large-scale genomic survey of prophages and their hosts across the bacterial domain, I estimated the extent to which prophages co-opt quorum sensing systems by encoding their components as auxiliary genes. Collectively, this work suggests that variability in community assembly at the microscale – driven, in part, by the dynamics of temperate phages – may underlie patterns in the diversity and functionality of larger-scale microbial ecosystems.