The continental subsurface houses a major portion of life’s abundance and diversity, yet little is known about viruses infecting microbes that reside there. Here, we use a combination of metagenomics and virus-targeted direct-geneFISH (virusFISH) to show that highly abundant carbon-fixing organisms of the uncultivated genus Candidatus Altiarchaeum are frequent targets of previously unrecognized viruses in the deep subsurface. Analysis of CRISPR spacer matches display resistances of Ca. Altiarchaea against eight predicted viral clades, which show genomic relatedness across continents but little similarity to previously identified viruses. Based on metagenomic information, we tag and image a putatively viral genome rich in protospacers using fluorescence microscopy. VirusFISH reveals a lytic lifestyle of the respective virus and challenges previous predictions that lysogeny prevails as the dominant viral lifestyle in the subsurface. CRISPR development over time and imaging of 18 samples from one subsurface ecosystem suggest a sophisticated interplay of viral diversification and adapting CRISPR-mediated resistances of Ca. Altiarchaeum. We conclude that infections of primary producers with lytic viruses followed by cell lysis potentially jump-start heterotrophic carbon cycling in these subsurface ecosystems.

大陆地下拥有生命丰富和多样性的主要部分，但对感染居住在那里的微生物的病毒知之甚少。在这里，我们使用宏基因组学和病毒靶向的直接基因鱼 (virusFISH) 的组合来表明未培养的Candidatus Altiarchaeum属的高度丰富的固碳生物是深部地下以前未被识别的病毒的常见目标。CRISPR 间隔物的分析与Ca 的显示电阻匹配. Altiarchaea 针对 8 个预测的病毒进化枝，这些进化枝显示出跨大陆的基因组相关性，但与先前确定的病毒几乎没有相似性。基于宏基因组信息，我们使用荧光显微镜标记和成像一个假定的病毒基因组富含原始间隔区。VirusFISH 揭示了相应病毒的裂解生活方式，并挑战了先前的预测，即溶原性在地下占主导地位的病毒生活方式。随着时间的推移 CRISPR 的发展和来自一个地下生态系统的 18 个样本的成像表明病毒多样化和适应 CRISPR 介导的Ca抗性之间存在复杂的相互作用. 土古菌。我们得出结论，初级生产者感染裂解病毒，随后细胞裂解可能会在这些地下生态系统中启动异养碳循环。