Identification of a new family of “megaphages” that are abundant in the marine environment

Abstract

Megaphages - bacteriophages harbouring extremely large genomes - have recently been found to be ubiquitous, being described from a variety of microbiomes ranging from the animal gut to soil and freshwater systems. However, no complete marine megaphage has been identified to date. Here, using both short and long read sequencing, we assembled >900 high-quality draft viral genomes from water in the English Channel. One of these genomes included a novel megaphage, Mar_Mega_1 at >650 Kb, making it one of the largest phage genomes assembled to date. Utilising phylogenetic and network approaches, we found this phage represents a new family of bacteriophages. Genomic analysis showed Mar_Mega_1 shares relatively few homologues with its closest relatives, but, as with other mega-phages Mar_Mega_1 contained a variety of auxiliary metabolic genes responsible for carbon metabolism and nucleotide biosynthesis, including isocitrate dehydrogenase [NADP] and nicotinamide-nucleotide amidohydrolase [PncC] which have not previously been identified in megaphages. The results of this study indicate that phages containing extremely large genomes can be found in abundance in the marine environment and augment host metabolism by mechanisms not previously described.

Infection strategy and biogeography distinguish cosmopolitan groups of marine jumbo bacteriophages

“…PGC_A was the largest of the PGCs with 469 phages in total, including 134 marine jumbo phages (63 bins from this study). This genome cluster contained the largest jumbo phages, such as Bacillus phage G (498 kb) and the marine megaphage Mar_Mega_1 (656 kb) recently recovered from the English Channel [38]. Unlike other PGCs, PGC_A contained mostly metagenomic phages (401, 85%, Figure 2b,c).…”

“…85 bins were retained for downstream analyses. Bins were clustered into populations with a compiled set of jumbo bacteriophages (RefSeq phages over 200 kilobases, phage sequences over 200 kilobases from the INPHARED database [36], Iyer et al 2021 [6], Al-Shayeb et al 2020 [4] jumbo phage genomes, GOV 2.0 [25], ALOHA 2.0 [37], and a megaphage assembled from the English Channel [38]) based on nucleotide sequences of genes (predicted with prodigal -d flag) aligned with BLASTn [59] (>95% average nucleotide identity, >80% genes) [23]. See Supplemental Methods for details.…”

“…To assess global diversity patterns of jumbo bacteriophage we combined these jumbo phage bins together with a compiled database of previously-identified jumbo phages that included all complete jumbo Caudovirales genomes on RefSeq (downloaded July 5th, 2020), the INPHARED database [36], the Iyer et al 2021 study [6], the Al-Shayeb et al 2020 study [4], and marine jumbo phage contigs from metagenomic surveys of GOV 2.0 [25] (60 jumbo phages), ALOHA 2.0 [37] (8 jumbo phages), and one megaphage MAG recovered from datasets of the English Channel [38]. Ultimately, we arrived at a set of 223 jumbo phages present in at least one Tara Oceans sample that we analyzed further in this study and refer to as marine jumbo phages.…”

Infection strategy and biogeography distinguish cosmopolitan groups of marine jumbo bacteriophages

“…To assess global diversity patterns of jumbo bacteriophages, we combined these jumbo phage bins together with a compiled database of previously-identified jumbo phages that included all complete jumbo Caudovirales genomes on RefSeq (downloaded July 5th, 2020), the INPHARED database [ 14 ], a recent survey of cultivated jumbo phages [ 6 ], the Al-Shayeb et al study [ 4 ], and marine jumbo phage contigs from metagenomic surveys of GOV 2.0 [ 26 ] (60 jumbo phages), ALOHA 2.0 [ 38 ] (8 jumbo phages), and one megaphage MAG recovered from datasets of the English Channel [ 39 ]. Ultimately, we arrived at a set of 244 jumbo phages, including the 85 bins, that were present in at least one Tara Oceans sample (min.…”

“…The largest of the phage genome clusters, PGC_A, contained 469 phages, including 135 marine jumbo phages (63 bins from this study). This genome cluster contained the largest jumbo phages, such as Bacillus phage G (498 kb) and the marine megaphage Mar_Mega_1 (656 kb) recently recovered from the English Channel [ 39 ]. Unlike other PGCs, PGC_A contained mostly metagenomic phages (401, 85%, Fig.…”