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

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.

The scientific output of the work will be disseminated to the academic community through publication in scientific journals and presentation at both national and international conferences. Both of the plant-bacteria-phage systems being examined are highly topical given the current outbreak of bleeding canker disease in horse chestnut populations across the UK and the continued need to control bacterial pathogens on crop species. Thus, the results from this research can be easily tailored for coverage by the popular press. A dedicated website is in progress to link current basic and applied research being carried out on bacteriophage control of bacterial pathogens. The website will describe the progress of my work, catalogue the strains of bacteria and phages available for users from approved laboratories, and discuss new work on microbial diversity and its importance to human and agricultural health. This will act as a resource for researchers and agencies involved in the control of emerging tree diseases.

Phage therapy is an exciting and novel control method for many important diseases. It does, however, involve the introduction into the environment of live viruses. As such, there is bound to be a public concern as to the safety of the approach. Previous public relations disasters around GM crops, for example, have emphasized the need for scientists to accurately inform the public of ongoing research. Using my NERC fellow platform, I will continue to be an active voice in the debate, informing the public of the potential benefits of biocontrol and allaying fears of the risk.

I have also designed and implemented a number of simulation-based learning activities with which to demonstrate the evolutionary theories taught in the University classroom. I am now working with professional game developers and graphic designers to create an interactive online game demonstrating the power of experimental evolution in understanding fundamental topics in biology. I am combining my conceptual understanding of population genetics and ability to model population-level responses to selection to generate a series of simulations in which the effects of biotic and abiotic factors on microbial diversity can be tested. As a NERC fellow and a STEM ambassador, I will develop a complementary lab module that explicitly links the concepts and aims of the game to those in the curriculum. I will work with teachers to implement both the game module and a hand-on laboratory module in which students quantify microbial diversity found in the schoolyard.