Large Freshwater Phages with the Potential to Augment Aerobic Methane Oxidation

Abstract:

There is growing evidence that phages with unusually large genomes are common across various natural and human and other animal microbiomes, but little is known about their genetic inventories or potential ecosystem impacts. Here, we reconstructed large phage genomes from freshwater lakes known to contain bacteria that oxidize methane. Twenty-two manually curated genomes (18 are complete) ranging from 159 to 527 kilobases 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 show high similarity (> 90%) and affiliate phylogenetically with those of coexisting bacterial methanotrophs, and their abundance patterns correlate with the abundances of these bacteria, supporting host-phage relationships. We suggest that phage-associated PmoC has similar functions to additional copies of PmoC encoded in bacterial genomes, thus contributes to growth on methane. Transcriptomics data from one system (Lake Rotsee, Switzerland) showed that some phage-associated pmoC genes were highly expressed in situ, and interestingly, 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 powerful greenhouse gas into the environment.