There is growing evidence that phages with unusually large genomes are common across various microbiomes, but little is known about their genetic inventories or potential ecosystem impacts. In the present study, we reconstructed large phage genomes from freshwater lakes known to contain bacteria that oxidize methane. Of manually curated genomes, 22 (18 are complete), ranging from 159 kilobase (kb) to 527 kb in length, were found to encode the pmoC gene, an enzymatically critical subunit of the particulate methane monooxygenase, the predominant methane oxidation catalyst in nature. The phage-associated PmoC sequences show high similarity to (>90%), and affiliate phylogenetically with, those of coexisting bacterial methanotrophs, including members of Methyloparacoccus, Methylocystis and Methylobacter spp. In addition, pmoC-phage abundance patterns correlate with those of the coexisting bacterial methanotrophs, supporting host–phage relationships. Future work is needed to determine whether phage-associated PmoC has similar functions to additional copies of PmoC encoded in bacterial genomes, thus contributing to growth on methane. Transcriptomics data from Lake Rotsee (Switzerland) showed that some phage-associated pmoC genes were highly expressed in situ and, of interest, that the most rapidly growing methanotroph was infected by three pmoC-phages. Thus, augmentation of bacterial methane oxidation by pmoC-phages during infection could modulate the efflux of this potent greenhouse gas into the environment.

越来越多的证据表明，具有异常大基因组的噬菌体在各种微生物组中很常见，但人们对其遗传库存或潜在的生态系统影响知之甚少。在本研究中，我们从已知含有氧化甲烷的细菌的淡水湖中重建了大型噬菌体基因组。在人工整理的基因组中，有 22 个（18 个完整），长度从 159 kb 到 527 kb 不等，被发现编码pmoC基因，这是颗粒甲烷单加氧酶的酶促关键亚基，是自然界中主要的甲烷氧化催化剂. 噬菌体相关的 PmoC 序列与共存的细菌甲烷氧化菌（包括甲基副球菌属）的序列显示出高度相似性（>90%），并且在系统发育上与它们有关联，Methylocystis和Methylobacter spp。此外，pmoC-噬菌体丰度模式与共存细菌甲烷氧化菌的丰度模式相关，支持宿主-噬菌体关系。未来的工作需要确定噬菌体相关的 PmoC 是否具有与细菌基因组中编码的额外 PmoC 拷贝相似的功能，从而有助于甲烷的生长。Rotsee 湖（瑞士）的转录组学数据表明，一些与噬菌体相关的pmoC基因在原位高度表达，有趣的是，生长最快的甲烷氧化菌被三个 pmoC 噬菌体感染。因此，在感染期间 pmoC 噬菌体增强细菌甲烷氧化可以调节这种强效温室气体向环境中的流出。