Despite important ecological roles posited for virocells (i.e., cells infected with viruses), studying individual cells in situ is technically challenging. We introduce here a novel correlative microscopic approach to study the ecophysiology of virocells. By conducting concerted virusFISH, 16S rRNA FISH, and scanning electron microscopy interrogations of uncultivated archaea, we linked morphologies of various altiarchaeal cells to corresponding phylogenetic signals and indigenous virus infections. While uninfected cells exhibited moderate separation between fluorescence signals of ribosomes and DNA, virocells displayed complete cellular segregation of chromosomal DNA from viral DNA, the latter co-localizing with host ribosome signals. A similar spatial separation was observed in dividing cells, with viral signals congregating near ribosomes at the septum. These observations suggest that replication of these uncultivated viruses occurs alongside host ribosomes, which are used to generate the required proteins for virion assembly. Heavily infected cells sometimes displayed virus-like particles attached to their surface, which agree with virus structures in cells observed via transmission electron microscopy. Consequently, this approach is the first to link genomes of uncultivated viruses to their respective structures and host cells. Our findings shed new light on the complex ecophysiology of archaeal virocells in deep subsurface biofilms and provide a solid framework for future in situ studies of virocells.

尽管病毒细胞（即感染病毒的细胞）具有重要的生态作用，但原位研究单个细胞在技术上具有挑战性。我们在这里介绍一种新的相关微观方法来研究病毒细胞的生态生理学。通过对未培养的古菌进行协同病毒 FISH、16S rRNA FISH 和扫描电子显微镜检查，我们将各种古菌细胞的形态与相应的系统发育信号和本土病毒感染联系起来。虽然未感染的细胞在核糖体和 DNA 的荧光信号之间表现出适度的分离，但病毒细胞表现出染色体 DNA 与病毒 DNA 的完全细胞分离，后者与宿主核糖体信号共定位。在分裂细胞中观察到类似的空间分离，病毒信号聚集在隔膜处的核糖体附近。这些观察结果表明，这些未培养的病毒的复制与宿主核糖体一起发生，宿主核糖体用于生成病毒粒子组装所需的蛋白质。严重感染的细胞有时会显示出附着在其表面的病毒样颗粒，这与通过透射电子显微镜观察到的细胞中的病毒结构一致。因此，这种方法是第一个将未培养病毒的基因组与其各自的结构和宿主细胞联系起来的方法。我们的研究结果为了解深层地下生物膜中古细菌病毒细胞的复杂生态生理学提供了新的线索，并为未来病毒细胞的原位研究提供了坚实的框架。