Award: OCE-1829640
Award Title: Collaborative Research: Inferring Cellular Lysis and Regeneration of Organic Matter by Marine Viruses
Outcomes Report
The oceans cover two-thirds of our planet. Beyond hosting coral reefs, fisheries, whales and dolphins, the oceans also play critical roles for the Earth System. For example, microbes in the oceans produce half of the oxygen we breath and the oceans themselves soak up about one-third of the carbon dioxide that humans have pushed into the atmosphere. At the foundation of oceanic food webs sits the microbial loop that is populated by tiny organisms like algae and bacteria. Even smaller, viruses can alter the flow of nutrients within the microbial loop by infecting marine microbes and lysing them, altering their genetic makeup, and/or completely reprogramming them during infection. Through these direct and indirect effects, viruses can drastically alter oceanic food webs and ecosystem functioning in ways that are likely important components of the generation of long-lived dissolved organic carbon in the oceans. Problematically, the high variability of these community-level interactions has so far prevented accurate quantification of virus-bacteria interactions. In fact, the ability to infer virus-bacteria cross-infection represents one of the foremost challenges in viral ecology. Ultimately, generating such data is critical to model - and ultimately better predict - the fate of elements and nutrients in the marine environment that is so critically helping buffer us against climate change. In this project, we first aimed to develop a mathematical model to better predict virus-bacteria interactions using data from a closely monitored, time-series experiment of a synthetic community composed of multiple phage-bacteria host pairs. Across the expertise of three laboratory teams, we used a combination of network theory (to analyze virus-host relationships), informatics, and laboratory-grown virus-host experiments to gather and analyze data that would drive our model. Our second aim was to develop new laboratory methods to determine novel virus-host interactions, but doing so at scale. This is important to give researcher a method to empirically determine which virus infects which bacterium in a natural, mixed community and indeed strong advances were made in developing ID-PCR, a novel measurement capability that links viruses to their host(s). Our last aim was to examine natural communities from the Atlantic ocean, and analyze their ecological patterns to see if our model could be useful in real-world data. To this end, we produced a time series dataset on a research criuse in the Sargasso Sea and leveraging the Bermuda Atlantic Time Series that has been long studied. Across the three team collaboration, we examined the ecogenomics of bacteria and viruses across time, ocean depth, and day cycles. In our lab, we identified nearly ~50,000 marine virus populations (~species-level taxa) over a 100 hour time course, and used these data to demonstrate virtually no community-level differences through time, but significant population-level abundance shifts at both surface (5-50 meters) and deep chlorophyll maximum (100-120 meters) waters. Deeper population-level analyses revealed the subset of viruses that demonstrated diel periodicity, and function-related and selection-based explanations. It is an ideal example, not shown anywhere yet for viruses, of how community-aggregated measures can miss the dominant signal in time series datasets and that these signals can be recovered at the finer-scale population level. Beyond the science, this project also had strong training and broader impacts. Internally, cross-disciplinary training benefited researchers from microbiology, oceanography, and physics, across three laboratories. On the public-facing side, extensive video, photo, and timelapse content from the sampling cruises were generated, and involved a communication specialist for enhanced dissemination. An associated Twitter campaign gathered 17,800 views. Lastly, all the datasets generated by the multiple cruises are publicly accessible and will benefit many scientific disciplines including oceanography, microbial- and virus ecology. Last Modified: 03/11/2024 Submitted by: MatthewSullivan