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

现在很清楚，植物和动物，包括人类，体内的微生物细胞比它们自身的细胞多得多。生活在宿主体内和宿主表面的微生物远不止是碰巧在宿主体内定居的随机细菌组合。相反，它们形成了一个复杂的细菌群落（所谓的“微生物群”），这些细菌相互作用，与宿主相互作用，也与感染它们的噬菌体病毒相互作用。然而，不太清楚的是，是什么使宿主内的微生物群落成功，以及为什么一个宿主的微生物群落与另一个宿主的微生物群落如此不同。这可能是一些微生物在一个宿主上偶然定植，而另一些微生物在另一个宿主上偶然定植的结果。然而，这也可能是由于宿主内正在进行的共同进化，细菌及其噬菌体正在适应相互抵抗/感染，并且在此过程中，与其他宿主内的群落越来越不同。理解共同进化在产生这种多样性中的作用的关键是洞察噬菌体对其细菌宿主的特异性。噬菌体能否适应感染越来越常见的新细菌类型？相同的噬菌体类型能从一种细菌转移到另一种细菌吗？解决这些知识差距的最有效方法是使用实验共同进化，在试管中微生物和噬菌体一起生长，并随时间采样以监测进化变化。这种方法在我们理解细菌对噬菌体的抗性进化和噬菌体克服这种抗性的相互适应方面取得了关键进展。然而，试管中共同进化的结果可能无法预测自然界的共同进化，这有很多原因；尤其是在宿主体内，宿主本身也在进行免疫反应，以防止细菌入侵。我计划利用植物、它们的细菌（无害的和有害的）和它们的病原体（噬菌体）之间的相互作用作为一个模型系统来研究植物宿主免疫系统在塑造其微生物群中的作用，微生物群在影响植物宿主适应性中的作用，以及噬菌体在驱动这些微生物群落动态变化中的作用。为了理解自然界中这些共同进化相互作用的重要性，我专注于生活在英国七叶树叶子内的微生物。这些树木目前正受到一种新出现的细菌病原体——丁香假单胞菌的威胁，这种细菌会导致出血性溃疡病。因此，了解环境中的天然微生物群落和噬菌体如何影响树木对疾病的易感性具有明确的应用兴趣。一旦我了解了微生物群的自然多样性以及这些群落对宿主健康的影响，我将通过实验测试宿主体内细菌及其噬菌体之间的共同进化相互作用。这将通过番茄植株宿主的实验共同进化来完成，这些宿主也遭受丁香假单胞菌的攻击。将植物作为天然试管，我将操纵宿主所携带细菌的数量和类型，并实时测量宿主体内的共同进化变化。微生物群的研究尤其重要，因为现在有有趣的证据表明，这些细菌可以作为抵御疾病的第一道防线。这种微生物群介导的耐药性可能是那些已经很好地适应宿主的细菌（即微生物群）将新定植的细菌排除在外的结果，也可能是与噬菌体病毒共同进化的结果，因为宿主内的细菌可能已经进化出对当地病原体的抵抗力增强，而新到达的细菌可能仍然容易受到感染。我将使用番茄-细菌-噬菌体系统来明确测试微生物群对宿主的潜在保护机制，以及噬菌体在改变疾病的建立和进展中可能发挥的作用。

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.