A novel uncultured marine cyanophage lineage with lysogenic potential linked to a putative marine Synechococcus ‘relic’ prophage

Abstract

Summary Marine cyanobacteria are important contributors to primary production in the ocean and their viruses (cyanophages) affect the ocean microbial communities. Despite reports of lysogeny in marine cyanobacteria, a genome sequence of such temperate cyanophages remains unknown although genomic analysis indicate potential for lysogeny in certain marine cyanophages. Using assemblies from Red Sea and Tara Oceans metagenomes, we recovered genomes of a novel uncultured marine cyanophage lineage, which contain, in addition to common cyanophage genes, a phycobilisome degradation protein NblA, an integrase and a split DNA polymerase. The DNA polymerase forms a monophyletic clade with a DNA polymerase from a genomic island in Synechococcus WH8016. The island contains a relic prophage that does not resemble any previously reported cyanophage but shares several genes with the newly identified cyanophages reported here. Metagenomic recruitment indicates that the novel cyanophages are widespread, albeit at low abundance. Here, we describe a novel potentially lysogenic cyanophage family, their abundance and distribution in the marine environment.

Genomic diversity, life strategies and ecology of marine HTVC010P-type pelagiphages

“…In contrast, our present study and previous studies suggest that many pelagiphages can proceed to lysogenize the host; likewise, integrase genes have been identified in some marine cyanophage genomes [60][61][62][63]. In addition, prophage relics were found in some marine cyanobacteria genomes [64][65][66]. Together, these results suggest that lysogenic infections also widely occur in streamlined-genome marine bacteria and play a non-negligible role in shaping bacterial genomes.…”

Comparative Genomics of Synechococcus elongatus Explains the Phenotypic Diversity of the Strains

“…Degradation of phycobilisomes and the subsequent bleaching of cells are mediated in PCC 7942 in response to nutrient limitation ( 52 ) by nonbleaching protein A (NblA). Some marine and freshwater cyanophages carry nblA genes, presumably favoring the metabolic needs of the phage during a lytic infection ( 53 – 55 ). Synpcc7942_0759 and Synpcc7942_0760 may represent a similar phage strategy of dismantling light-harvesting complexes through a pathway independent of a phage-encoded nblA .…”

Cyanophage host‐derived genes reflect contrasting selective pressures with depth in the oxic and anoxic water column of the Eastern Tropical North Pacific

“…However, T7‐like clade B cyanophages were abundant in the oxic cellular metagenomes but not in the viromes. Conversely, T7‐like clade A cyanophages and cyanophages of the unclassified clades S‐EIVI and BAC21E04 (Chenard et al ., 2015; Flores‐Uribe et al ., 2019) were abundant in the ODZ in viromes but not in the cellular metagenomes (Supporting Information Fig. S1).…”