Viral mortality in a marine diazotroph: characterizing the diversity and ecology of a novel phage-plasmid lineage which infects the keystone N2-fixing cyanobacterium Trichodesmium

Bacteria, like other organisms, are infected by viruses, which are called phages. Phage infection can influence the abundance, distribution, genome content, and physiology of their hosts. Thus, understanding phage diversity and ecology is a critical area of study. Photosynthetic cyanobacteria are at the base of the marine food web and are infected by a distinct and poorly described subset of phages that can act as mobile genetic elements and are thus called phage-plasmids. They can be transmitted as host cells grow and divide (like a plasmid) but can also produce virions that infect and kill host cells (like a phage). The ability of these phage-plasmids to integrate into the host genome is distinct from traditional phage and their effects on host populations is a major knowledge gap with important implications for marine bacterial populations. This project will investigate the global diversity, ecology, and evolution of T.NPSG, a newly described lineage of phage-plasmids that infect the marine nitrogen-fixing cyanobacterium Trichodesmium. Phage-plasmid genome analysis will provide critical new insight into the diversity of the phage-plasmids related to T.NPSG and their potential role in Trichodesmium biology. Additionally, this research will support the development and application of informatic workflows and machine learning (ML) models by creating an expanded bioinformatics research infrastructure to advance understanding of phage-plasmids in marine microbes. The identification of a phage-plasmid lineage (T.NPSG) which infects the cyanobacterial diazotroph Trichodesmium provides a new source of mortality for this keystone genus. T.NPSG is both the first genome of a virus infecting Trichodesmium and the first phage-plasmid genome from the oligotrophic open ocean. Trichodesmium forms colonies, which may impose unique eco-evolutionary forces on T.NPSG-like phage-plasmids. Currently, genome-based analysis of how host and phage-plasmid lifestyle simultaneously drive evolutionary processes is limited by the availability of complete T.NPSG-like phage-plasmid genomes This project will increase the geographic and temporal distribution of complete genome sequences of T.NPSG-like phage-plasmids using a combination of short- and long-read metagenomic sequencing methods. Newly sequenced samples and publicly available metagenomes in which T.NPSG has previously been detected will be assembled using strain-aware tools. The assembled genomes will illuminate the ecological factors shaping diversification of the T.NPSG-like phage-plasmid lineage. By determining the impact of sampled colony abundance on phage-plasmid microdiversity, this work will establish the role of Trichodesmium colonies as either a source of evolutionary bottlenecks or a hotspot for recombination and gene transfer. Analysis of the primary source of variation between T.NPSG-like genomes (i.e. gene content or mutations) will resolve evolutionary mechanisms driving this novel lineage. This project will resolve the ecological factors shaping diversification of the T.NPSG-like phage-plasmid lineage by producing the first analysis of intra- and inter-population variation for a Trichodesmium-infecting marine phage-plasmid, laying the necessary foundation for future work on marine phage-plasmids, and the role the T.NPSG lineage plays in Trichodesmium physiological ecology. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.