Role of Phages in Structuring Bacterial Communities: Ciona Intestinalis as a Model Organism

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The animal gut hosts a complex community of specially-adapted bacteria that interface directly with the host epithelial cells and fundamentally affect host health and nutrition. Because gut bacteria play such vital roles in host health, a detailed understanding of how bacteria colonize the gut and how biological and biophysical factors affect the stability and longevity of their symbiotic existence with the host is of enormous significance. One often overlooked factor that may play a significant role in structuring gut-associated bacterial communities is the presence of viruses, specifically phages (viruses that infect bacteria). The investigators have developed a simple marine invertebrate model system (the sea squirt Ciona intestinalis) that affords the opportunity to dissect numerous aspects of host:bacteria symbiosis, such as initial colonization, effects of feeding and digestion, and interactions with the host immune system. In this project, they will test the hypothesis that phages serve important roles in shaping overall bacterial community structure through their ability to break apart specific hosts, thereby releasing dissolved organics and facilitating gene transfer among hosts, and driving microbial evolution. By carefully examining phage-bacteria interactions both in vitro and within the gut of the sea squirt, they will gain unprecedented insight into the effects of phages on bacterial communities living within animal guts. This research will benefit society by exploring the promise of phages for remodeling complex microbial communities, which has important implications for human health, bioremediation, and ecosystem restoration projects. The investigators will develop an outreach program that encourages high school students to undertake mentored science fair projects encompassing microbial ecology concepts and provide hands-on training in molecular microbiology techniques. To reach a distinct target audience, they will also run microbial ecology modules for Girl Scouts, Girls Incorporated, and the University of South Florida's Oceanography Camp for Girls.To examine the roles of phages in shaping the overall structure and function of bacterial communities, the investigators will accomplish three specific research objectives: 1) characterize phage diversity in the Ciona gut using culture-based and culture independent methods, 2) dissect phage-bacteria interactions in vitro and determine if phages can modify bacterial community (microbiome) structure in experimentally colonized Ciona, and 3) culture Ciona in both the presence and absence of phages in the water to determine the effects of phage presence on gut microbiomes and host physiology. As a filter-feeding sessile organism, Ciona directly interfaces with the marine environment and encounters a continuous stream of microbes that can potentially colonize or influence its gut flora. Previous work with adult, field-harvested, Ciona indicated that a consistent, "core" microbiome dominates their gut. Additionally, they have successfully cultured various members of the core gut microbiome, isolated phages for some of these bacteria, and are studying the process of extracellular biofilm formation by these bacteria on artificially constructed matrices that resemble the surface of the gut epithelium in the presence and absence of phages. Ciona is a highly tractable experimental system that can be grown under predominantly sterile conditions, allowing experimental control of of nearly every aspect of the symbiotic conversation between host, bacteria, and phages. The results of this work have the transformative potential of redefining our understanding of the factors that shape the establishment and maintenance of stable, host-associated, bacterial communities and in turn affect the physiology of the host itself.