A new family of "megaphages" 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 megaphages. Genomic analysis showed Mar_Mega_1 shares relatively few homologues with its closest relatives, but, as with other megaphages Mar_Mega_1 contained a variety of auxiliary metabolic genes responsible for carbon metabolism and nucleotide biosynthesis, including a NADP-dependent isocitrate dehydrogenase [Idh] and nicotinamide-nucleotide amidohydrolase [PncC], which have not previously been identified in megaphages. Mar_Mega_1 was abundant in a marine virome sample and related phages are widely prevalent in the oceans.

Fig. 1. Phylogeny of megaphages.

A Phylogenetic analysis of selected phages and  all megaphages (including incomplete megaphage genomes) based on the amino acid sequence of the terminase large subunit. Protein sequences were aligned with MAFFT and trees constructed with IQ-TREE, based on the LG + R7 model of evolution with 1000 bootstrap replicates. Mar_Mega_1 is marked in red, Lak phages in yellow and other megaphages in green. Filled circles denote bootstrap values >70%, with the size of the circle proportional to the bootstrap value. Some clades have been collapsed for clarity. B Subtree containing Mar_Mega_1.

Fig. 2. Abundance and distribution of Mar_Mega_1 -like phages.

A Relative abundance of vOTUs associated with known phages in the Plymouth Sound virome. Abundance is represented by counts per million. Each black dot represents a viral contig that could be associated with a known phage based on mash similarity, or clusters in the same group as a known phage using vContact2. Host information was extracted from known phages. Mar_Mega_1 is represented by a red dot (unknown host). The median relative abundance of all 269 vOTUs with similarity to known phages is denoted by a blue horizontal line. B The distribution of Mar_Mega_1-like phages. Reads from GOS and GOV2.0 were mapped against Mar_Mega_1 and 9 TARA vOTUs carrying a TerL that clustered with Mar_Mega_1. Stations are marked where read coverage was >1x across 70% of the genome. Blue dots denote where Mar_Mega_1-like phages were detected and red where Mar_Mega_1 was detected.