Articles on CRISPR commonly open with some variant of the phrase “these short palindromic repeats and their associated endonucleases (Cas) are an adaptive immune system that exists to protect bacteria and archaea from viruses and infections with other mobile genetic elements.” There is an abundance of genomic data consistent with the hypothesis that CRISPR plays this role in natural populations of bacteria and archaea, and experimental demonstrations with a few species of bacteria and their phage and plasmids show that CRISPR-Cas systems can play this role in vitro. Not at all clear are the ubiquity, magnitude, and nature of the contribution of CRISPR-Cas systems to the ecology and evolution of natural populations of microbes and the strength of selection mediated by different types of phage and plasmids to the evolution and maintenance of CRISPR-Cas systems. In this perspective, with the aid of heuristic mathematical–computer simulation models, we explore the a priori conditions under which exposure to lytic and temperate phage and conjugative plasmids will select for and maintain CRISPR-Cas systems in populations of bacteria and archaea. We review the existing literature addressing these ecological and evolutionary questions and highlight the experimental and other evidence needed to fully understand the conditions responsible for the evolution and maintenance of CRISPR-Cas systems and the contribution of these systems to the ecology and evolution of bacteria, archaea, and the mobile genetic elements that infect them.

CRISPR上的文章通常以短语的变体开头：“这些短回文重复序列及其相关的核酸内切酶（Cas）是一种适应性免疫系统，其存在是为了保护细菌和古细菌免受病毒和其他移动遗传元件的感染。” 大量的基因组数据与CRISPR在细菌和古细菌的自然种群中发挥这种作用这一假设相一致，并且对几种细菌及其噬菌体和质粒的实验证明表明CRISPR-Cas系统可以在体外发挥这种作用。普遍性，程度，CRISPR-Cas系统对微生物自然种群的生态学和进化的贡献的性质，性质以及由不同类型的噬菌体和质粒介导的选择强度对CRISPR-Cas系统的进化和维持的影响。从这个角度出发，借助启发式数学计算机仿真模型，我们探索了先验条件，在这些条件下，裂解菌和温带噬菌体以及结合质粒的暴露将为细菌和古细菌种群选择并维持CRISPR-Cas系统。