Abstract
Austrovenus stutchburyi, or the New Zealand cockle, is of cultural, economic and ecological significance. As filter-feeders, they can be utilised as ecosystem indicators, capturing the health of their surroundings, including the microbial communities present. However, almost nothing is known about the microbial communities, particularly the diversity of viruses, that is harboured within this species and their potential to cause disease, threatening intertidal ecosystem health. Moreover, previous investigations into whole viromes in aquatic hosts and environments have focused on a cross-sectional timeline, highlighting the virus taxa present at only a single point in time. This leaves a knowledge gap of how virus diversity changes over time in response to external factors, especially given the highly fluctuating aquatic environment. Filling this knowledge gap is crucial in order to understand how the virome adapts over time and how environmental parameters can influence these dynamics, especially with predicted changing parameters in light of global climate change. In this thesis, I used a meta-transcriptomic approach, along with key aquatic abiotic data, to identify the RNA virome of New Zealand cockles over a 12-month period and determine how abiotic parameters might influence their diversity. This longitudinal sampling unveiled a highly diverse RNA virome, with viruses belonging to 16 taxonomic orders within the Orthornavirae kingdom. Phylogenetic analysis based on conserved genes revealed 358 viruses across 213 viral species, of which 199 were considered novel. We found no viruses that were genetically related to known human or aquatic pathogens. Perhaps surprisingly, we found no clear seasonal patterns on the total virome scale. However, within individual viral orders, correlations between abiotic parameters and viral order abundance were identified for several viruses within the Picornavirales, Wolframvirales, Bunyavirales and Sobelivirales. Overall, the seasonal dynamics of viruses within the aquatic intertidal ecosystem appeared complex. While there are limitations for any molecular-based virome investigation, this thesis has discovered novel and highly abundant viruses, opening a new line of enquiry for further monitoring of viromes in New Zealand cockle populations.