Department of Biology, University of Waterloo, Waterloo, ON, Canada.
Sci Rep. 2023 Apr 5;13(1):5611. doi: 10.1038/s41598-023-32078-6.
Viruses are the most abundant microbial guild on the planet, impacting microbial community structure and ecosystem services. Viruses are specifically understudied in engineered environments, including examinations of their host interactions. We examined host-virus interactions via host CRISPR spacer to viral protospacer mapping in a municipal landfill across two years. Viruses comprised ~ 4% of both the unassembled reads and assembled basepairs. A total of 458 unique virus-host connections captured hyper-targeted viral populations and host CRISPR array adaptation over time. Four viruses were predicted to infect across multiple phyla, suggesting that some viruses are far less host-specific than is currently understood. We detected 161 viral elements that encode CRISPR arrays, including one with 187 spacers, the longest virally-encoded CRISPR array described to date. Virally-encoded CRISPR arrays targeted other viral elements in interviral conflicts. CRISPR-encoding proviruses integrated into host chromosomes were latent examples of CRISPR-immunity-based superinfection exclusion. The bulk of the observed virus-host interactions fit the one-virus-one-host paradigm, but with limited geographic specificity. Our networks highlight rare and previously undescribed complex interactions influencing the ecology of this dynamic engineered system. Our observations indicate landfills, as heterogeneous contaminated sites with unique selective pressures, are key locations for atypical virus-host dynamics.
病毒是地球上最丰富的微生物类群，影响着微生物群落结构和生态系统服务。在工程环境中，病毒的研究特别不足，包括对其宿主相互作用的研究。我们通过城市垃圾填埋场两年间的宿主 CRISPR 间隔区到病毒原间隔区的映射，研究了宿主-病毒相互作用。病毒约占未组装读数和组装碱基对的 4%。总共捕获了 458 个独特的病毒-宿主连接，随着时间的推移，这些连接记录了高度靶向的病毒种群和宿主 CRISPR 阵列的适应性。有 4 种病毒被预测可以感染多个门，这表明有些病毒的宿主特异性远低于目前的理解。我们检测到 161 个编码 CRISPR 阵列的病毒元件，其中一个含有 187 个间隔区，这是迄今为止描述的最长的病毒编码 CRISPR 阵列。病毒编码的 CRISPR 阵列在病毒间冲突中靶向其他病毒元件。整合到宿主染色体上的病毒编码 CRISPR 前病毒是基于 CRISPR 免疫的超感染排斥的潜伏例子。观察到的大多数病毒-宿主相互作用符合一病毒-一宿主模式，但地理特异性有限。我们的网络突出了影响这个动态工程系统生态的罕见和以前未描述的复杂相互作用。我们的观察表明，垃圾填埋场作为具有独特选择压力的异质污染场所，是研究非典型病毒-宿主动态的关键地点。
