The impact of spatial structure of CRISPR-phage coevolution

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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.