Our current knowledge of host–virus interactions in biofilms is limited to computational predictions based on laboratory experiments with a small number of cultured bacteria. However, natural biofilms are diverse and chiefly composed of uncultured bacteria and archaea with no viral infection patterns and lifestyle predictions described to date. Herein, we predict the first DNA sequence-based host–virus interactions in a natural biofilm. Using single-cell genomics and metagenomics applied to a hot spring mat of the Cone Pool in Mono County, California, we provide insights into virus–host range, lifestyle and distribution across different mat layers. Thirty-four out of 130 single cells contained at least one viral contig (26%), which, together with the metagenome-assembled genomes, resulted in detection of 59 viruses linked to 34 host species. Analysis of single-cell amplification kinetics revealed a lack of active viral replication on the single-cell level. These findings were further supported by mapping metagenomic reads from different mat layers to the obtained host–virus pairs, which indicated a low copy number of viral genomes compared to their hosts. Lastly, the metagenomic data revealed high layer specificity of viruses, suggesting limited diffusion to other mat layers. Taken together, these observations indicate that in low mobility environments with high microbial abundance, lysogeny is the predominant viral lifestyle, in line with the previously proposed “Piggyback-the-Winner” theory.

我们目前对生物膜中宿主-病毒相互作用的了解仅限于基于实验室实验的少量培养细菌的计算预测。然而，天然生物膜是多种多样的，主要由未培养的细菌和古细菌组成，迄今为止没有描述过病毒感染模式和生活方式预测。在这里，我们预测了天然生物膜中第一个基于 DNA 序列的宿主病毒相互作用。我们将单细胞基因组学和宏基因组学应用于加利福尼亚州莫诺县锥形池的温泉垫，提供了有关病毒宿主范围、生活方式和不同垫层分布的见解。130 个单细胞中有 34 个包含至少一个病毒重叠群（26%），与宏基因组组装的基因组一起，检测到与 34 个宿主物种相关的 59 种病毒。单细胞扩增动力学分析显示单细胞水平上缺乏活跃的病毒复制。通过将来自不同垫层的宏基因组读数映射到获得的宿主 - 病毒对，进一步支持了这些发现，这表明与宿主相比，病毒基因组的拷贝数较低。最后，宏基因组数据揭示了病毒的高层特异性，表明向其他垫层的扩散有限。总之，这些观察结果表明，在微生物丰度高的低流动性环境中，溶原性是主要的病毒生活方式，这与先前提出的“Piggyback-the-Winner”理论一致。通过将来自不同垫层的宏基因组读数映射到获得的宿主 - 病毒对，进一步支持了这些发现，这表明与宿主相比，病毒基因组的拷贝数较低。最后，宏基因组数据揭示了病毒的高层特异性，表明向其他垫层的扩散有限。总之，这些观察结果表明，在微生物丰度高的低流动性环境中，溶原性是主要的病毒生活方式，这与先前提出的“Piggyback-the-Winner”理论一致。通过将来自不同垫层的宏基因组读数映射到获得的宿主 - 病毒对，进一步支持了这些发现，这表明与宿主相比，病毒基因组的拷贝数较低。最后，宏基因组数据揭示了病毒的高层特异性，表明向其他垫层的扩散有限。总之，这些观察结果表明，在微生物丰度高的低流动性环境中，溶原性是主要的病毒生活方式，这与先前提出的“Piggyback-the-Winner”理论一致。