RNA Viral Diversity and Dynamics Along the Antarctic Peninsula

Abstract

Marine viruses are capable of driving species succession during plankton blooms and greatly influencing biogeochemical cycling and food web dynamics through cell lysis. Most of our knowledge has come from studies in temperate and sub-tropical waters, but whether they play a major role in eukaryotic phytoplankton blooms in polar waters has not been investigated. RNA viruses in particular have been shown to contribute up to half of the total virioplankton and are known to predominantly infect eukaryotes. The goals of this dissertation were to provide the first description of RNA viruses in the Antarctic, determine their relative and absolute abundances, and investigate the diversity and dynamics of these viruses to better understand how they contribute to the ecology of eukaryotic plankton. A temporal analysis of RNA viral metagenomes collected throughout the summer bloom in the Western Antarctic Peninsula (WAP) revealed an abundant and diverse community of positive-sense, single-stranded (+ss) RNA viruses within the order Picornavirales. RNA viral metagenomes from the Eastern Antarctic Peninsula were analyzed to investigate spatial diversity, and revealed a similar dominance of +ssRNA viruses in the order Picornavirales, but a much lower diversity than the WAP metagenomes. Novel RNA virus genomes were assembled and primers were designed to target the RNA-dependent RNA polymerase gene to track individual phylotypes throughout the season in the WAP. In order to determine the absolute abundance of these RNA viruses, two methods were evaluated and optimized. First, a method for extraction of viral nucleic acids from plankton harvested on nanoporous anodic aluminum oxide filters was improved and validated. Second, a reverse transcription quantitative PCR (RT-qPCR) assay was developed to accurately quantify specific RNA viruses in nucleic acid extracts. Both methods were applied to provide the first estimates of abundance of specific RNA virus phylotypes in the ocean, revealing three distinct patterns of abundance from four unique virus phylotypes. The results of this dissertation not only suggest the pervasiveness and ecological significance of RNA viruses in polar waters, but also present molecular techniques that should be of interest to virologists, oceanographers, and microbial ecologists.