RNA Viruses in the Ocean 

In our current post-pandemic world, the term “RNA virus” has permeated headlines, conversations, and media outlets everywhere. SARS-CoV-2, the RNA virus that swept across the globe beginning in 2019, has become a sustained topic of importance and sparked numerous research efforts to understand the viral biosphere. But how much do we think about – or even know about – other types of RNA viruses, such as those that populate our oceans? Although marine RNA viruses pose little threat to human health, they may play a significant role in the progression of algal blooms – a topic of study that is only recently beginning to be explored.

The Earth’s oceans make up 70% of our planet’s surface area and are filled with microbial life that play fundamental roles in marine food webs and global elemental cycles, such as the biological carbon pump which sequesters atmospheric carbon (i.e. CO₂) into the ocean’s interior, in turn exerting a significant control on global climate. Marine viruses are especially abundant in global oceans, with millions per milliliter in surface seawater are thought to drive the mortality of 20-40% of the microbial biomass per day, thereby helping to maintain microbial community diversity and shape microbial community structure.

However, due to methodological limitations and the sheer abundance of double-stranded DNA viral particles in seawater, studies to date have primarily focused on aquatic viruses with DNA genomes, leaving marine RNA viral diversity, genomic analysis, biogeography, and ecological significance largely unexplored. While marine RNA viruses have long been recognized as infectious agents of aquatic animals — including invertebrates, fish, seabirds, and marine mammals (especially economically relevant species) —  recently emerging research has pointed at RNA viruses of unicellular micro-algal hosts being ubiquitous and abundant in global oceans. Marine RNA viral isolates confirm that these viruses infect major protist groups, including diatoms, dinoflagellates, raphidophytes, prasinophytes, and thraustochytrids, all of which are important photosynthetic plankton (i.e., phytoplankton) that play central roles in atmospheric carbon capture.

As a Wrigley Institute Graduate Fellow this summer, I have worked alongside a fellow USC graduate student, Jelani Akil Williams, as well as with a bright and hardworking undergraduate researcher, Makena Gichuru, to help shed light on the ecological effects of marine RNA viral infection on phytoplankton groups. Our team has undertaken a three-week long experiment aimed at understanding the potentially regulatory role marine RNA viruses play in the progression of algal blooms. The experiment involves stimulating an algal bloom (a period of increased growth largely due to solar and nutrient input) in a controlled setting to directly assess how marine RNA viruses may be altering phytoplankton community dynamics. To achieve this, we collected hundreds of liters of seawater (roughly 300 gallons!) from a nearby coastal site, which we used to fill 6 individual tanks, creating marine mesocosms. (A mesocosm is an outdoor experiment set up to mimic the natural world.) We placed these tanks in a larger tub filled with water and set up air bubblers in each mesocosm to help mimic the temperature and water movement typical of the natural marine environment we are attempting to replicate. Just as the soil-based plants in your home require sunlight and nutrients in order to grow, phytoplankton in seawater do as well. Therefore, to help encourage the phytoplankton in the seawater to bloom, we added nutrients – nitrate, phosphate, and silicate – to the mesocosms at two different time points.

To assess the microbial community over the course of the stimulated bloom, we collected 3 size fractions of the community daily by filtering seawater on different pore-size filters (with pores sized to capture protist, bacterial, and viral organisms). RNA and DNA from these filters will be extracted and prepared for DNA sequencing to bioinformatically characterize the phytoplankton community as well as their viral populations and how they change as the bloom progresses. Additionally, to ensure we were successful in stimulating a micro-algal bloom, we tracked how the total chlorophyll (a proxy for phytoplankton biomass) in each mesocosm changed over time. We also collected other data, such as hourly temperature and light level readings, daily nutrient concentrations of the 6 mesocosms, and prepared daily microscope slides of the microbial community in each tank for visual analysis. Ultimately, this collection of data will be used to assess relationships between putative hosts and their marine RNA viruses and help answer questions related to how (if at all) marine RNA viral infection contributes to phytoplankton bloom collapse.

While much of my time on the island has been spent setting up the mesocosms and taking daily samples of the 6 tanks, my days have also been filled with new friendships, basking in sunshine, and exploring the pristine marine environment surrounding the Wrigley Marine Science Center (WMSC). I have learned so much during my time on Catalina Island, the most recurring lesson being that things don’t always go as planned and the most valuable skill is knowing how to adapt. I have also learned how to drive and operate small boats and have obtained my California boater card while working on the island, which has been helpful not just for collecting 300 gallons of seawater for my experiment but also for finding new places to snorkel!

Through the Research Experience for Undergraduates (REU) program, this research project has also allowed me to be a mentor to Makena, which has reinforced my love for teaching and science. Makena’s attention to detail and inquisitive nature have been inspiring, and working alongside her this summer has made me a better scientist. I am beyond grateful for the Wrigley Institute Graduate Fellowship program’s support, which has granted me the opportunity to spend weeks of my summer on the island, to be surrounded by incredible people working on projects that help us better understand our oceans, to conduct the very first large-scale experiment of my PhD career, and to collect meaningful data that will allow me to contribute to the scientific understanding of marine RNA viruses.

Daria Di Blasi is supported by the Victoria J. Bertics Graduate Fellowship Fund.