Lysogenized phages of methanotrophic bacteria show a broad and untapped genetic diversity

Methanotrophs are a unique class of bacteria with the ability to metabolize single-carbon compounds such as methane. They play an important role in the global methane cycle and have great potential as industrial platforms for the bioconversion of methane from industrial waste streams into valuable products, such as biofuels and bioplastics. However, many aspects of methanotroph biology have yet to be elucidated, including the prevalence and impact of lysogenized bacteriophages (phages), which can greatly affect both the ecology and the industrial performance of these bacteria. The present study investigates the presence of putative prophages in three gammaproteobacterial (Methylobacter marinus A45, Methylomicrobium album BG8, Methylomonas denitrificans FJG1) and two alphaproteobacterial (Methylosinus trichosporium OB3b, Methylocystis sp. Rockwell) methanotrophs using four programs predicting putative phage sequences (PhageBoost, PHASTER, Phigaro, and Island Viewer). Mitomycin C was used to trigger induction of prophages, which was monitored through infection dynamics. Successfully induced phages from M. marinus A45 (MirA1, MirA2), M. album BG8 (MirB1), and M. trichosporium OB3b (MirO1) were isolated and characterized using transmission electron microscopy. Subsequently, bioinformatic analyses (BLAST and phylogenetics) were performed on three induced phages to obtain a profile of their respective genetic makeup. Their broad diversity and differences from previously known phages, based on whole genome and structural gene sequences, suggest they each represent a new phage family, genus and species: “Britesideviridae Inducovirus miraone”, “Patronusviridae Enigmavirus miratwo”, and “Kainiviridae Tripudiumvirus miroone” represented by isolates MirA1, MirA2, and MirO1, respectively.

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