Coevolution in complex communities: exploring the formation, stability and the importance of microbial communities within their hosts.

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It is now clear that plants and animals, including man, harbor many more microbial cells than their own cells. The microbes living in and on a host are much more than a random assortment of bacteria that happen to colonize it. Instead, they form a complex community (the so called "microbiota") of bacteria that are interacting with one another, with the host, and also with bacteriophage viruses that infect them. What is less clear, however, is what makes a community of microbes successful within a host, and why one host's community is so different from another. It could be the result of chance colonization of some microbes on one host and others on another host. However, it could also be due to ongoing coevolution within the host, where bacteria and their phages are adapting to resist/infect one another and, in doing so, becoming more and more different from communities within other hosts.Key to understanding the role of coevolution in generating this diversity is insight to how specific phages are to their bacterial hosts. Can phages adapt to infect new bacterial types as they become common? Can the same phage type shift from one bacterial species to another? The most powerful way to address these knowledge gaps is using experimental coevolution, where microbes and phages are grown together in a test tube and sampled over time to monitor evolutionary change. This approach has offered key advances in our understanding of the evolution of bacterial resistance to phages and reciprocal adaptations of phages to overcome such resistance. However, there are many reasons that the outcome of coevolution in a test tube might not be predictive of coevolution in nature; especially within a host that is itself mounting an immune response to keep bacteria at bay. I plan to use interactions among plants, their bacteria - both harmless and harmful - and their pathogens (bacteriophages) as a model system to examine the role of the plant host immune system in shaping its microbiota, the role of the microbiota in influencing the fitness of the plant host, and the role of phages in driving dynamic changes in these microbial communities over time.To understand the importance of these coevolutionary interactions in nature, I am focusing on microbes living within the leaves of horse chestnut trees in the UK. These trees are currently under threat from an emerging bacterial pathogen, Pseudomonas syringae, that causes bleeding canker disease. Thus, understanding how their natural microbial communities and phages in the environment influence the tree's susceptibility to disease is of clear applied interest. Once I have an idea of the natural diversity of microbiota and the influence of these communities on host health, I will experimentally test the coevolutionary interactions among bacteria and their phages in the host. This will be done using experimental coevolution within tomato plant hosts, which also suffer from attack by P. syringae. Using the plant as a natural test tube, I will manipulate the number and type of bacteria the host harbors and measure coevolutionary change in real time within the host. The study of microbiota is particularly important as there is now intriguing evidence that these bacteria can act as a first line of defense against disease. This microbiota-mediated resistance could be the result of the exclusion of newly colonizing bacteria by those that are already well-adapted to the host (i.e., the microbiotia) or it could be the result of coevolution with bacteriophage viruses, as bacteria within the host are likely to have evolved increased resistance to their local pathogens while newly-arriving bacteria may still be susceptible to infection. I will use the tomato-bacteria-phage system to explicitly test the underlying mechanism of protection conferred by microbiota to their hosts and the role that phages might play in altering the establishment and progression of disease.