Date of Award
Fall 2023
Document Type
Dissertation
Degree Name
Doctor of Philosophy (PhD)
Department
Ecology and Evolutionary Biology
First Advisor
Turner, Paul
Abstract
Chapter I:Characterization of microbial growth is of both fundamental and applied interest. Modern platforms can automate collection of high-throughput microbial growth curves, necessitating the development of computational tools to handle and analyze these data to produce insights. However, existing tools are limited. Many use parametric analyses that require mathematical assumptions about the microbial growth characteristics. Those that use non-parametric or model-free analyses often can only quantify a few traits of interest, and none are capable of importing and reshaping all known growth curve data formats. To address this gap, here I present a newly-developed R package: gcplyr. gcplyr can flexibly import growth curve data in every known format, and reshape it under a flexible and extendable framework so that users can design custom analyses or plot data with popular visualization packages. gcplyr can also incorporate metadata and generate or import experimental designs to merge with data. Finally, gcplyr carries out model-free and non-parametric analyses, extracting a broad range of clinically and ecologically important traits, including initial density, lag time, growth rate and doubling time, carrying capacity, diauxie, area under the curve, extinction time, and more. In sum, gcplyr makes scripted analysis of growth curve data in R straightforward, streamlines common data wrangling and analysis steps, and easily integrates with common visualization and statistical analyses. Chapter II: Bacteria-infecting viruses, bacteriophages, are the most abundant biological entities on the planet, frequently serving as model systems in basic research and increasingly relevant for medical applications such as phage therapy. A common need is to quantify the infectivity of a phage to a given bacterial host (or the resistance of a host to a phage). However, current methods to quantify infectivity suffer from low-throughput or low-precision. One method that has the potential for high-throughput and high-precision quantification of phage-bacteria interactions is growth curves, where bacterial density is measured over time in the presence and absence of phages. Recent work has proposed several approaches to quantify these curves into a metric of phage infectivity. However, little is known about how these metrics relate to one another or to underlying phage and bacterial traits. To address this gap, we apply ecological modeling of phage and bacterial populations to simulate growth curves across a wide range of trait values. Our findings show that many growth curve metrics provide parallel measures of phage infectivity. Informative metrics include the peak and decline portions of bacterial growth curves, are driven by the interactions between underlying phage and bacterial traits, and correlate with conventional measures of phage fitness. Moreover, we show how intrapopulation trait variation can alter growth curve dynamics. Finally, we test the sensitivity of growth curve metrics to inoculum densities, and assess techniques to compare growth curves across different bacterial hosts. In all, our findings support the use of growth curves for precise high-throughput quantification of phage-bacteria interactions across the microbial sciences. Chapter III: Bacteria-phage symbioses are ubiquitous in nature and serve as valuable biological models. Historically, the ecology and evolution of bacteria-phage systems have been studied in either very simple or very complex communities. Although both approaches provide insight, their shortcomings limit our understanding of bacteria and phages in multispecies contexts. To address this gap, here we synthesize the emerging body of bacteria-phage experiments in medium-complexity communities, specifically those that manipulate bacterial community presence. Generally, community presence suppresses both focal bacterial (phage host) and phage densities, while sometimes altering bacteria-phage ecological interactions in diverse ways. Simultaneously, community presence can have an array of evolutionary effects. Sometimes community presence has no effect on the coevolutionary dynamics of bacteria and their associated phages, whereas other times the presence of additional bacterial species constrains bacteria-phage coevolution. At the same time, community context can alter mechanisms of adaptation and interact with the pleiotropic consequences of (co)evolution. Ultimately, these experiments show that community context can have important ecological and evolutionary effects on bacteria-phage systems, but many questions still remain unanswered and ripe for additional investigation. Chapter IV: Organisms face ubiquitous threats from parasites in the natural world. This pressure can drive strong reciprocal coevolution between hosts and their parasites, and can potentially lead to the extinction of one antagonistic partner. However, host-parasite interactions do not occur in isolation: hosts and parasites are embedded in a complex network of interspecies interactions. Despite this, our understanding of how other species alter host-parasite coevolution and coexistence is limited. This is especially true in the microbial world, where the coevolution and coexistence of bacteria and their viral parasites, phages, is well understood in isolation but poorly understood in a multispecies context. To address this gap, here we used experimental evolution to test how the presence of nonhost bacterial species alters the coevolution and coexistence of a phage and its bacterial host. We found that bacterial diversity favored the persistence of the phage, which frequently tended towards extinction in treatments with only the host bacteria. However, surprisingly, we did not observe a clear effect of bacterial diversity on coevolutionary dynamics: bacteria evolved high levels of resistance to phage infection regardless of treatment. Future work will sample our evolved populations more deeply, resolving the mechanisms driving the observation that diversity facilitated host-parasite coexistence in our experimental communities.
Recommended Citation
Blazanin, Michael, "Methods and Complexity in Phage-Bacteria Ecology and Evolution" (2023). Yale Graduate School of Arts and Sciences Dissertations. 1110.
https://elischolar.library.yale.edu/gsas_dissertations/1110
