Bacterial and Viral Predator-Prey Dynamics within Bacterial Biofilms at Cellular Resolution

PROJECT SUMMARY The Nadell lab studies the spatial mechanics and community dynamics of bacterial biofilms, using Vibrio cholerae, V. parahaemolyticus, Escherichia coli, and their respective bacterial and viral predators as model systems. While some marine Vibrio species cause human disease, with cholera being the most historically important, my lab does not study virulence mechanisms or bacterial pathogenesis. Rather, we use these species to understand the architectural and community dynamics of live biofilms at cellular resolution. Most bacteria produce surface-bound biofilm communities in nature, but we have strikingly little understanding of how cell-cell interactions lead to their higher order composition, architecture, and community dynamics. Since biofilm structure and composition can contribute to their role in acute and chronic infection, understanding the mechanisms controlling their structure and composition, and in particular how predatory viruses and bacteria attack biofilm- dwelling cells, may lead to novel approaches to fight clinical infections. Over the next five years we will focus on two major frontiers that have received minimal attention using cellular resolution imaging in the biofilm field thus far. First, no work thus far has examined how temperate phages interact with biofilms at high resolution; temperate phages can amplify and kill susceptible bacteria, but they can also integrate into the bacterial genome and amplify passively along with the host bacterial cell. This phage life history is widely important in nature and in host microbiota, and indeed often affects bacterial virulence. We will study in detail where and when within biofilms these temperate phages infect and kill target bacteria, and where they integrate into the host genome. Further, we will rigorously compare the propagation dynamics of temperate phages and lytic phages within biofilms to understand how these fundamentally distinct life history strategies influence phage and bacterial fitness in realistic environments. Second, the vast majority of high-resolution biofilm research has focused on biofilms grown on glass under flow of nutrient media. Many realistic environments, including those of marine Vibrio bacteria, are not this simple, with biofilms growing on topographically complex substrates, and with nutrients derived directly from the underlying surface rather than the surrounding liquid media. We will explore the consequences of these complex topographical environments by cultivating multispecies biofilms of V. cholerae and V. parahaemolyticus growing on and consuming particles of shrimp shell chitin. This system will permit us to study how growth in a multispecies context on naturalistic substrates influences community architecture and dynamics. Lastly, we will rigorously test how the realistic chitin environment influences the ability of a ubiquitous bacterial predator, Bdellovibrio bacteriovorus, is able to attack and kill Vibrio prey within single and multispecies biofilms. Our research will expand along two important new frontiers, both of which will yield insight into how predatory viral and bacterial species kill prey bacteria dwelling in otherwise protected biofilms.