Theoretical and Experimental Studies of the Population and Evolutionary Dynamics of Bacteria and Bacteriophage.

摘要 细菌和古细菌的病毒，噬菌体，被吹捧为地球上最丰富的生物体， 关于它们的分子生物学、结构和复制机制，我们知道很多。然而 关于种群生物学仍然存在基本的未回答或未完全回答的问题， 生态作用和这些病毒的进化。在这次调查中，我们将解决并提供答案， 这些基本问题中的三个：1-什么是生态，遗传和进化条件， 裂解（毒性）噬菌体保持和调节细菌种群的密度？2-下 什么样的条件有利于温和的噬菌体复制而不是单纯的裂解性噬菌体复制， 传输？3-在什么条件下，裂解性噬菌体和温和性噬菌体的选择有利于进化 和维持CRISPR-Cas介导的适应性免疫，而不是包膜或其他组成性免疫， 抵抗机制？为了解决这些问题，我们将使用数学和计算机模拟 模型，其属性将进行数值分析，参数估计在 实验系统，将用于人口动态和进化实验。我们 将测试我们对这些模型的分析所产生的预测（假设）， 细菌和噬菌体保持在液体、表面和半固体培养物中。根据这些结果， 实验中，我们将修改我们的模型，使其更加逼真。实验将在 大肠杆菌、铜绿假单胞菌、铜绿假单胞菌和金黄色葡萄球菌及其组合。 裂解性和/或温和性噬菌体。除了对学术生态学的重要性，人口和 进化生物学，这项基础科学研究的结果很可能有实际用途。这 调查将提供一个经验支持的理论，可用于促进设计和 利用噬菌体治疗人类和家庭细菌感染项目的评价 动物，并控制农作物中病原菌的爆发。 !

ABSTRACT The viruses of bacteria and archaea, phage, are touted to be the most abundant organisms on Earth, and a great deal is known about their molecular biology, structure, and mechanisms of replication. Nevertheless there remain fundamental unanswered or incompletely answered questions about the population biology, ecological role, and evolution of these viruses. In this investigation we will address and provide answers to three of these fundamental questions: 1- What are the ecological, genetic and evolutionary conditions for lytic (virulent) phage to be maintained in and regulate the densities of bacterial populations? 2- Under what conditions will selection favor a temperate rather than a purely lytic mode of phage replication and transmission? 3- Under what conditions will selection by lytic and temperate phage favor the evolution and maintenance of CRISPR-Cas mediated adaptive immunity, rather than envelope or other constitutive resistance mechanisms? To address these questions, we will use mathematical and computer simulation models, the properties of which will be analyzed numerically with parameters estimated in the experimental systems that will be employed for population dynamic and evolutionary experiments. We will test the predictions (hypotheses) generated from our analysis of these models in populations of bacteria and phage maintained in liquid, surface, and semisolid culture. Based on the results of these experiments, we will modify our models to make them more realistic. The experiments will be done with Escherichia coli, Pseudomonas aeruginosa, Pseudomonas syringae, and Staphylococcus aureus and their lytic and/or temperate phage. In addition to their importance to academic ecology, population and evolutionary biology, the results of this basic science study may well have practical utility. This investigation will provide an empirically supported theory that could be used to facilitate the design and evaluation of programs to use phage for the treatment of bacterial infections in humans and domestic animals, and to control outbreaks of pathogenic bacteria in crops. !