Diversity, Activity, and Adaptations of Phage Communities in Anoxic Hydrocarbon-Rich Marine Sediments

Citation

Narayanan, Aditi Kalpagam (2025) Diversity, Activity, and Adaptations of Phage Communities in Anoxic Hydrocarbon-Rich Marine Sediments. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/v5x8-7447. https://resolver.caltech.edu/CaltechTHESIS:05272025-172840679

Abstract

The viruses of the global ocean, especially those infecting prokaryotic taxa, are known to play an important role in maintaining the genetic and taxonomic diversity of their host communities and in the cycling of atmospheric carbon and key nutrients like nitrogen and iron. However, the vast majority of these conclusions are drawn from the surface ocean and upper water column, while the sediments, which constitute one of the largest biomes on earth, are understudied in comparison. Of special interest are areas on the ocean floor where methane and other hydrocarbons are produced and released by geological activity and oxidized by a consortium of archaea and bacteria. Using direct genomic sequencing of the viruses from a variety of simplified sediment-free enrichments of hydrocarbon oxidizers, I compare viral communities sampled from different locations and incubated under a range of temperatures to understand the role these parameters might play in shaping distribution and community structure. I then present the most comprehensive picture thus far of viral diversity and distribution from a methane cold seep and discuss whether the viral assemblages are influenced by the steep geochemical gradients that characterize seep sediments. From these datasets, I propose that viral communities in methane-oxidizing sediments are tailored specifically to the physical constraints of the sediment matrix rather than to the dominant members of the cellular community or to other physicochemical parameters such as temperature, sampling location, or depth below the seafloor. I then outline the development of two methods, stable-isotope probing coupled to nanoSIMS and biorthogonal non-canonical amino acid tagging, to work in heterogenous sediment virus samples rather than the liquid pure cultures on which they had previously relied. Implementation of these methods, which allow us to temporally constrain viral production and virus-influenced nutrient flow, resulted in the hypothesis that viral production likely responds to shifts in the major metabolic processes within an ecosystem and may influence cellular community composition.

Thesis Files