Connecting phage genotypes to ecological function : ǂb replication protein modules reveal phage dynamics across diel and tidal cycles in Narragansett Bay
Date
2025
Authors
Journal Title
Journal ISSN
Volume Title
Publisher
University of Delaware
Abstract
Viruses are the most abundant biological entities on Earth and play critical roles in shaping microbial communities, influencing host metabolism, population dynamics, and nutrient cycling. Despite their ecological importance, the majority of viral diversity remains uncharacterized, and the connections between viral genomic features and infection phenotypes are poorly understood. Replication proteins, including Family A and B DNA polymerases (PolA, PolB), ribonucleotide reductases (RNR), and helicases, are central to viral genome replication and serve as informative markers for predicting viral infection strategies and ecological behavior. ☐ This dissertation establishes a framework for investigating the ecology of unknown viral populations across environmental gradients through replication module analysis. Aim 1 developed a reproducible workflow for identifying and quantifying viral populations in metagenomes based on co-occurring replication proteins, integrating contig assembly, functional annotation, abundance estimation, and phylogenetic placement. Aim 2 expanded detection to PolB–carrying populations, including cyanophage, by constructing a reference database and validating functional PolB proteins through active site and domain analyses. Aim 3 applied these methods to a 48-hour diel and tidal series in Narragansett Bay, Rhode Island, revealing distinct ecological patterns: temperate-associated populations (L762 PolA variants, E. coli numbering) remained stable across diel and tidal gradients, while populations encoding virulent-associated replication modules (F762/Y762 PolA, RNRs, superfamily 4 (SF4) helicases) exhibited condition-specific fluctuations linked to diel host metabolism and tidal transitions. ☐ This work demonstrates that replication module composition provides a robust approach for predicting viral infection strategy and ecological behavior, extending beyond single-protein analyses. The pipelines and PolB-focused developments enable systematic characterization of previously overlooked viral populations, linking genome content to ecological dynamics. By connecting replication machinery to viral population behavior, this research provides a scalable framework for exploring viral ecology across spatial and temporal gradients and lays the foundation for predictive bioinformatic approaches to infer infection strategies in uncultivated viral communities.
Description
Keywords
Metagenomics, Phylogenetics, Viral ecology, Ribonucleotide reductases, DNA