Les bactériophages sont les virus spécifiques des bactéries. Ils sont considérés comme les entités biologiques les plus abondantes de la biosphère (1031 au total). Une grande partie des bactériophages sont dits tempérés de part leur propriété à intégrer leur génome dans celui de leur hôte et à s'y maintenir en état de réplication passive appelé lysogénie. Les gènes de prophages apportent de nouvelles propriétés à l'hôte via la conversion lysogénique. De nombreux prophages défectifs et fonctionnels sont maintenus dans les génomes bactériens. Nous avons émis l'hypothèse que des stratégies de maintien aient été sélectionnées pour maintenir cette source de gènes, même si elle est potentiellement dangereuse car les prophages peuvent être induits dans des conditions de stress.Nos résultats suggèrent que le maintien de la lysogénie d'une catégorie de prophages, qui présente une organisation génétique atypique du module de recombinaison spécifique de site, est sous le contrôle du facteur de terminaison de la transcription Rho. Pour ces prophages, qu'ils soient défectifs ou fonctionnels, leur induction par inactivation de Rho, fait intervenir une nouvelle voie d'induction lytique indépendante de la voie classique via la réponse SOS.Ces interactions hôtes-virus reflète la coévolution de ces microorganismes, qui permet l'acquisition de gènes via le transfert horizontal tout en contrôlant l'expression des gènes délétères. Ceci permet l'acquisition de nouvelles propriétés et l'adaptation de l'hôte à différentes conditions environnementales. / Bacteriophages are the most abundant biological entities in the biosphere. A majority of them are temperate phages that are able to integrate their genome into the host and replicate passively in a lysogenic state. Hosts frequently benefit from such massive gene acquisition through lysogenic conversion. As prophages may be beneficial to their hosts, we hypothesize that hosts adapted strategies for maintaining that gene source. Since prophages integrate into and excise from the host chromosome through site-specific recombination (SSR), we investigated whether regulation of SSR at the level of gene expression could be involved in the maintenance process. Our results suggest that lysogeny maintenance of a class of prophages, which all share a same unusual genetic organization, are controlled by the transcription termination factor Rho. Rho is not only involved in horizontally acquired gene silencing but also in prophage maintenance, which can be seen as an adaptation of the host to maintain prophage genes. For these prophages, whether defective or functional, their induction by the inactivation of Rho, involves a new pathway of lysogeny escape, which is independent of the classical pathway via the SOS response. This newly characterized interaction reflects the coevolution of host and viruses, which allows the acquisition of genes, and thus new properties, via horizontal transfer, while controlling the expression of deleterious genes.

The bacteria in host-associated microbial communities influence host health through various mechanisms, such as immune stimulation or the release of metabolites. However, viruses that target bacteria, called bacteriophages (phages), may also shape the animal microbiome. Most phage lifecycles can be classified as either lytic or temperate. Lytic phages infect and directly kill bacterial hosts and can directly regulate bacterial population size. Temperate phages, in contrast, have the potential to undergo either a lytic cycle or integrate into the bacterial genome as a prophage. As a prophage, the phage may alter bacterial host phenotypes by carrying novel genes associated with auxiliary metabolic functions, virulence-enhancing toxins, or resistance to other phage infections. Lytic phages may also carry certain auxiliary metabolic genes, which are instead used to takeover bacterial host functions to better accommodate the lytic lifecycle. In either case, the ability to alter bacterial phenotypes may have important ramifications on host-associated communities. This dissertation focused on the genetic contributions that phages, and particularly prophages, provide to the bacterial members of two separate host-associated communities: the honey bee (Apis mellifera) gut microbiome and the amphibian skin microbiome. My second chapter surveyed publicly available whole genome sequences of common honey bee gut bacterial species for prophages. It revealed that prophage distribution varied by bacterial host, and that the most common auxiliary metabolic genes were associated with carbohydrate metabolism. In chapter three, this bioinformatic pipeline was applied to the amphibian skin microbiome. Prophages were identified in whole genome bacterial sequences of bacteria isolated from the skin of American bullfrogs (Lithobates catesbeianus), eastern newts (Notophthalmus viridescens), Spring peepers (Pseudacris crucifer) and American toads (Anaxyrus americanus). Prophages were additionally identified in publicly available genomes of non-amphibian isolates of Janthinobacterium lividum, a bacteria found both on amphibian skin and broadly in the environment. In addition to a diverse set of predicted prophages across amphibian bacterial isolates, several Janthinobacterium lividum prophages from both amphibian and environmental isolates appear to encode a chitinase-like gene undergoing strong purifying selection within the bacterial host. While identifying the specific function of this gene would require in vitro isolation and testing, its high homology to chitinase and endolysins suggest it may be involved in the breakdown of either fungal or bacterial cellular wall components. Finally, my fourth chapter revisits the honey bee gut system by investigating the role of geographic distance in bacteriophage community similarity. A total of 12 apiaries across a transect of the United States, from Virginia to Washington, were sampled and honey bee viromes were sequenced, focusing on the lytic and actively lysing temperate community of phages. Although each apiary possessed many unique bacteriophages, apiaries that were closer together did have more similar communities. Each bacteriophage community also carried auxiliary carbohydrate genes, especially those associated with sucrose degradation, and antimicrobial resistance genes. Combined, the results of these three studies suggest that bacteriophages, and particularly prophages, may be contributing to the genetic diversity of the bacterial community through nuanced relationships with their bacterial hosts. / Doctor of Philosophy / The microbial communities of animals, called "microbiomes", play important roles in the health of animals. The bacteria in these microbiomes can help strengthen the immune system, provide resistance to dangerous pathogens, and break down nutrients. However, bacteria are not alone in the microbiome; viruses are also present. Surprisingly, the vast majority of the world's viruses, even those living inside animals, infect bacteria. These viruses, called "bacteriophages" or "phages", can impact the bacterial communities in a microbiome. Phages can be grouped in to two broad categories based on lifecycle. Lytic phages kill the bacterial host directly after infection. Temperate phages, on the other hand, can either immediately kill the host like lytic phages or alternatively, become a part of the bacterial genome and live as prophages. Phages with both lifecycles can sometimes carry genes that, although not essential to the phage, may change the traits of the bacteria during infection. For example, some phages carry toxin genes, which bacteria use to cause disease in animals. Other phages might carry genes that provide antibiotic resistance or alter the metabolism of the infected bacteria. If a phage gene benefits the infected bacteria, the bacteria may begin interacting with its environment in a new way or may even become more abundant. Alternatively, phages that directly kill infected bacteria may have a negative effect on bacterial population sizes. To begin unraveling how phages influence bacterial species in microbiomes, I investigated two different animal systems: the Western honey bee (Apis mellifera) gut microbiome and the amphibian skin microbiome. I first identified prophages of several common bacterial species that reside in the honey bee gut (Chapter 2). Prophages were more common in certain bacterial species than others, and some possessed genes associated with the breakdown of sugars or pollen, suggesting they help honey bees process their food. Using similar techniques, I then identified prophages in bacteria isolated from the skin microbiomes of several amphibian species common in the eastern United States (American bullfrogs, Eastern newts, Spring peepers, and American toads) (Chapter 3). Most notably, the bacteria Janthinobacterium lividum may benefit from prophages that carry genes for potentially antifungal chitinase enzymes that destroy the fungal cell wall. Finally, I returned to the honey bee gut microbiome system by investigating how honey bee bacteriophage communities change over large geographic distances (Chapter 4). This study, which examined honey bees from 12 apiaries sampled from the east to west coast of the United States, looks primarily at lytic phage and temperate phage that are not integrated as prophage, but are instead seeking a bacterial host to infect. I found that nearby apiaries tended to have more similar communities of bacteriophages, compared to apiaries far away. Additionally, most bacteriophage communities carry genes associated with the breakdown of sugars like sucrose. Overall, these three studies show that phages, and especially prophages, contribute to the genetic landscape of the microbiome by broadly providing bacterial hosts with access to a diverse set of genes.

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