The impact of spatial structure of CRISPR-phage coevolution

越来越清楚的是，噬菌体（噬菌体）可以在塑造微生物群落组成和功能方面发挥关键作用。该项目旨在研究最广泛的免疫机制之一CRISPR-Cas在自然环境中细菌-噬菌体相互作用的重要性。近一半的细菌编码CRISPR-Cas，因此这种免疫系统被认为在确定噬菌体在调节细菌种群动态和进化中的作用方面特别重要。面对进化出CRISPR免疫力的细菌，噬菌体的重要性将在很大程度上取决于它是否能够共同进化以克服免疫力，这可能随后导致防御和反防御的军备竞赛。尽管基于实验室的研究经常发现CRISPR抗性细菌会导致噬菌体灭绝，但对野生细菌种群的研究支持噬菌体可以与CRISPR共同进化的观点。我们假设，自然界和实验室中CRISPR-噬菌体协同进化之间的这种差异是由于基于实验室的研究缺乏生态复杂性，这可能是协同进化发生的关键。通过研究CRISPR-噬菌体在实验室介质和半自然环境中的相互作用，我们将能够确定决定CRISPR-Cas免疫机制在自然界中的重要性和共同进化后果的因素。我们的初步数据和现有数据表明，空间结构将是决定噬菌体是否可以与CRISPR共同进化的一个特别重要的因素，但潜在的机制仍不清楚。在拟议的研究中，我们将通过产生新的理论和在实验室介质和具有不同空间结构水平的灭菌土壤中进行实验测试来研究这一点。除了为我们对自然环境中CRISPR-噬菌体协同进化的基本理解做出重要贡献外，这项研究还可以为CRISPR-噬菌体相互作用在土壤微生物生态学和进化中的潜在作用提供重要见解。土壤仍然是地球上人们了解最少的生态系统，尽管据估计，土壤提供的生物服务在全球价值超过20万亿美元，对人类赖以生存的许多过程至关重要，包括食物和各种化合物的生产、水的净化、废物的处置和养分的循环。在这项研究中，我们将使用系统生物学方法，我们将生成数学模型，预测空间结构对细菌和噬菌体进化，共存和共同进化的影响。然后，我们将使用实验室进化实验来测试这些预测，在实验中，我们将在高度受控的环境中梳理空间结构对CRISPR-噬菌体相互作用的不同影响。在第三个目标中，我们将监测包含具有不同结构特性的不同土壤的土壤中的CRISPR-噬菌体协同进化，并检查不同土壤和不同混合制度下的CRISPR-噬菌体协同进化。总之，这项研究的数据将有助于了解一个简单的生态因素-空间结构-如何影响CRISPR-噬菌体协同进化，从而影响细菌和噬菌体种群动态，这可能对生态系统功能产生重要影响。我们将使用数学，分子和进化生物学以及微生物生态学的强大组合来解决CRISPR噬菌体协同进化实验和相关研究之间的重要差异。

It is becoming increasingly clear that bacteriophage (phage) can play a key role in shaping microbial community composition and function. This project aims to study the importance of one of the most widespread immune mechanisms, known as CRISPR-Cas, for bacteria-phage interactions in natural environments. Nearly half of all bacteria encode CRISPR-Cas, and this immune system is therefore thought to be particularly important in determining the role of phage in regulating bacterial populations dynamics and evolution. In the face of bacteria that evolve CRISPR immunity, the importance of phage will strongly depend on whether or not it can coevolve to overcome immunity, which could subsequently lead to an arms race of defense and counter-defense. Although lab based studies frequently find that CRISPR resistant bacteria drive phage extinct, studies on wild bacterial populations support the idea that phage can coevolve with CRISPR in nature. We hypothesize that this discrepancy between CRISPR-phage coevolution in nature and the lab is due to the lack of ecological complexity in lab-based studies, which may be critical for coevolution to occur. By studying CRISPR-phage interactions in laboratory media and semi-natural environments we will be able to identify the factors that determine the importance and coevolutionary consequences of CRISPR-Cas immune mechanisms in nature.Our preliminary data and existing suggest that spatial structure will be a particularly important factor in determining whether or not phage can coevolve with CRISPR, but the underlying mechanism remains unclear. In the proposed study, we will examine this by generating novel theory and performing experimental tests both in laboratory media and in sterilized soil with different levels of spatial structure. Apart from making an important contribution to our fundamental understanding of CRISPR-phage coevolution in natural environments, this research can also provide important insights into the potential role that CRISPR-phage interactions play in the ecology and evolution of soil microbiomes. Soils remain the most poorly understood ecosystems on Earth, even though it has been estimated that the biological services that soils provide are worth more than $20 trillion globally and are critical for many processes that humans depend on, including the production of food and various compounds, the purification of water, disposal of waste and cycling of nutrients. In this study, we will use a systems biology approach where we will generate mathematical models that predict the effects of spatial structure for bacterial and phage evolution, their coexistence and coevolution. We will then test these predictions using laboratory evolution experiments, where we will tease apart the different effects of spatial structure on CRISPR-phage interactions in highly controlled environments. In the third objective, we will monitor CRISPR-phage coevolution in soil mesocosms containing different soils with different structural properties and examine CRISPR-phage coevolution across the different soils and under different mixing regimes. Altogether, the data from this research will help to understand how a simple ecological factor - spatial structure - impacts CRISPR-phage coevolution and therefore bacterial and phage population dynamics, which can have important consequences for ecosystem functioning. We will use a powerful combination of mathematics, molecular and evolutionary biology, and microbial ecology to resolve an important discrepancy between experimental and correlational studies on CRISPR-phage coevolution.