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Clades of huge phage from across Earth’s ecosystems
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Edité par CCSD ; Nature Publishing Group -
International audience. Phage typically have small genomes and depend on their bacterial hosts for replication. DNA sequenced from many diverse ecosystems revealed hundreds of huge phage genomes, between 200 kbp and 716 kbp in length. Thirtyfour genomes were manually curated to completion, including the largest phage genomes yet reported. Expanded genetic repertoires include diverse and new CRISPRCas systems, tRNAs, tRNA synthetases, tRNA modification enzymes, translation initiation and elongation factors, and ribosomal proteins. Phage CRISPRCas systems have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phageencoded functions. In addition, some phage may repurpose bacterial CRISPRCas systems to eliminate competing phage. We phylogenetically define major clades of huge phage from human and other animal microbiomes, oceans, lakes, sediments, soils and the built environment. We conclude that their large gene inventories reflect a conserved biological strategy, observed over a broad bacterial host range and across Earth's ecosystems. Bacteriophage (phage), viruses of bacteria, are considered distinct from cellular life due to their inability to conduct most biological processes required for reproduction. They are agents of ecosystem change because they prey upon specific bacterial host populations, mediate lateral gene transfer, alter host metabolisms, and redistribute bacteriallyderived compounds via cell lysis (Rascovan et al. , 2016; Breitbart et al. , 2018; Emerson et al. , 2018) . They spread antibiotic resistance (Balcazar, 2014) and disperse pathogenicity factors that cause disease in humans and animals (Penadés et al. , 2015; BrownJaque et al. , 2018) . Most knowledge about phage is based on laboratorystudied examples, the vast majority of which have genomes a few 10s of kbp in length. Widely used isolationbased methods select against large phage particles, and they can be excluded from phage concentrates obtained by passage through 100 nm or 200 nm filters (Yuan and Gao, 2017) . In 2017, only 93 isolated phage with genomes of >200 kbp in length had been published (Yuan and Gao, 2017) . This motivates cultivationindependent approaches to evaluate the existence and biology of phage with huge genomes. Only with this information on hand will
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