Bacteria and their viruses, bacteriophages (or phages), are arguably the most representative biological organisms on planet Earth. Apart from being amongst the most ancient entities, they are unparalleled in sheer numbers, biomass, and diversity. Ubiquitous in nature, their interactions profoundly affect their environments and, consequently, humans. This thesis offers a study into the ecosystems of this host-parasite pair, focusing on population dynamics.
Laboratory studies of phage-bacteria dynamics predominantly operate under optimal conditions. However, in nature, phages and bacteria often face suboptimal conditions, ranging from limited resources to intense pressure from competition or predation. This thesis delves into phagebacteria ecosystems under such challenging conditions, employing a spectrum of scientific methodologies. These methodologies range from data-driven theoretical analysis and collaborative work with experimentalists to purely experimental research.
Chapter 1 introduces the foundational terms and ideas necessary for a reader to navigate this work. Chapter 2 dives deep into the dynamics between phages and bacteria in the ocean’s upper layers. Through a theoretical modeling approach, it elucidates mechanisms that can sustain diversity under intense competition for resources. Additionally, this chapter deciphers the underlying dynamics of infection patterns observed in previous field studies. Our research reveals patterns of network self-organization that promote specialization, thereby reducing competition between strains. Notably, even slight deviations from perfect specialization can profoundly benefit slower-growing bacteria. These bacteria, although growing at a reduced rate, can outcompete and potentially eliminate even the fastest-growing strains, through shared phage interactions. Our results challenge the notion of using growth rate as a definitive metric for fitness, hinting instead at an evolutionary process that proceeds in waves.
Chapter 3 delves into the phenomenon of bacterial dormancy, particularly under suboptimal conditions for growth and pressure from viruses. This work combines both experimental and theoretical methods to study sporulation in Bacillus Subtilis, which serves as a model for dormancy in Gram-positive bacteria. Apart from the widely accepted starvation-trigger for sporulation, this chapter reveals that the presence of viruses can also induce sporulation. Our findings suggest that susceptible cells can turn into dormant as a response to a molecular signal released upon cell lysis. In spatial environments, this leads to a collective defense in Bacillus Subtilis communities, which helps contain the spread of the viruses. This work is the first to document virally induced sporulation in Bacillus Subtilis and its significant role in offering protection at the population level by restricting the spread of viral infections.
Chapter 4 is devoted to a purely experimental study of how a host’s metabolic state affects phage infection. Initial results resonate with previous findings, suggesting that phages might be selective, choosing not to infect Escherichia coli cells in a low metabolic state—an often characteristic state of cells facing challenging environmental conditions in nature. The primary goal of this research is to assess the prevalence of this behavior across various phage-bacteria systems.
In summary, this thesis underscores that suboptimal conditions commonly found in natural systems can profoundly influence phage-bacteria dynamics.