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 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.

Methane-derived carbon flow through host-virus trophic networks in soil

“…An intriguing finding was the linkage of host family-specific viruses from two different geographical regions (Scotland and Sweden) and contrasting soil types (agricultural loamy-sand and permafrost peatland soils), from this study and that of Emerson et al 9 , respectively. In the latter study, 13 of 1,907 mVCs were predicted to have a methanotroph host, of which 9 were linked specifically to the Methyocystaceae .…”

“…There was a clear difference in the prediction of category-2 (‘likely’) and category-3 (‘possible’) mVCs associated with these two clusters. While category-3 viruses are often excluded prior to analysis of soil viromes 9 , CRISPR analysis demonstrated that one-third of linked mVCs were of the lowest category of confidence. It must be recognised that a proportion of the predicted category-3 mVCs in this study will not be derived from viruses, and clusters composed exclusively of category-3 mVCs without further validation (e.g.…”

Proteomic and transcriptomic analysis ofMicroviridaeφXI74 infection reveals broad up-regulation of host membrane damage and heat shock responses

“…The ibpA/B genes have never been identified from genetic screens of hostfactors necessary for capsid morphogenesis, but sHSPs are encoded in the genomes of cyanophage infecting Synechococcus and Prochlorococcus groups (68, 69). Furthermore, a bacteriophage-encoded J-domain protein (Rki) has been identified in T4-related enterobacteriophage RB43 that interacts with E. coli J-domain interacting chaperone protein DnaK (HSP70) and stabilizes the σ 32 heat-shock response (70).…”

Tracking Double-Stranded DNA Bacteriophages and Their Hosts in a Deep Freshwater Lake by Integrating Metagenomics and The Hi-C Technique

“…As a relatively reliable computational method for detecting bacteriophage-host association signals, the CRISPR spacer-based approach has been applied in many virome studies [10,14,[26][27][28]. A total of 7,075 CRISPR spacer sequences were identi ed from 393 representative MAGs covering a total of 24 phyla (Additional File 10: Table S6).…”

“…Bacteriophages can affect the diversity and function of aquatic microbial populations through the incorporation and expression of auxiliary metabolic genes (AMGs). Currently, phage-encoded AMGs are reported to include multiple types of genes involved in not only main nutrient cycle pathways, such as carbon metabolism [12][13][14], nitrogen [15], phosphorus [16] and sulfur cycling [17,18], but also some speci c pathways, such as acetate fermentation [19], methane oxidation [14], nucleotide metabolism [20] and oxidative stress responses [21]. Taken together, these ndings imply that viral AMGs in uence most, if not all, pathways of microbial metabolism.…”