Virus-microbe interactions in marine environments determined by DNA proximity linkages

Abstract

Microbial processes in the ocean drive global biogeochemical cycles and within microbial communities the most abundant entities are viruses. Viruses in the marine environment can alter microbial community composition and genomic potential when they interact with host and non-host microbes. However, because many host microbes are not yet in culture, traditional methods of culturing viruses cannot yet be undertaken for most viruses. A key component of interpreting data collected about virus presence and abundance across the world’s oceans is determining with which microbes they can interact and under what conditions. In this thesis, I apply the DNA linkage method known as Hi-C sequencing to map out virus-host interactions in three different environments. In Chapter 1, I used this method to determine the impact and interaction of viruses with hosts in both particle-associated and free-living microbial communities at a depth below the euphotic zone in a shallow coastal fjord. I inferred that infected cells on particles were likely delivered to greater depths by particle flux and that viruses moved into new environments where host cells are sparse may interact with non-host organisms. In Chapter 2, I used Hi-C sequencing to analyze viral activity within the deep chlorophyll maximum of the Eastern Tropical North Pacific. Viruses were linked across multiple phytoplankton populations. I obtained evidence of viral auxiliary metabolic genes (AMGs) within Synechococcus cells at the time of sampling. Hi-C links also provided evidence of a known Phycodnaviridae, as well as a Mimivirus infecting a Bathycoccus prasinos at the time of sampling. Furthermore, a CrAss-like phage was shown to be interacting with a Planctomycetes of the Pirellulales order, a novel host in the marine environment for the Crassvirales family. In Chapter 3, I analyzed virus-microbe interactions in an oxygen deficient zone (ODZ), in the Eastern Tropical North Pacific, from which few microbes have been cultivated. The majority of organisms at this depth are prokaryotic and live amongst a diverse and unique community of viruses that have remained difficult to characterize. Hi-C links enhanced microbial binning and resulted in 268 medium-to-high quality bins with genomic potential for a range of methane, sulfur and nitrogen cycling metabolisms in the sample examined. We associated 75 viral genomes with microbial metagenomes in one sample and identified 19 virus-host interactions with high virus per host cell values. Though some virus-host interactions were predicted with computational software, the majority of viruses linking with hosts by Hi-C were not predicted computationally and these were statistically more abundant within the metagenome. Summarily, Hi-C method applied in this thesis revealed virus-microbe activity that other tools at our disposal could not, increasing our understanding of the complex path viral DNA may travel in marine environments, suggesting unique influences on biogeochemical cycling and potential genetic diversity.