A War of Tiny Giants - Do viruses impact Pelagibacterales genotype dynamics in the Western English Channel

One often hears that the rainforests are the 'lungs of the Earth', producing the oxygen that we breathe through photosynthesis and drawing down atmospheric carbon dioxide. However, perhaps less well-known is the fact that the oceans, and in particular coastal regions, are responsible for about half of all global photosynthesis as marine bacteria and algae (known as phototrophs) capture sunlight to produce metabolites for growth. Through cell death and the leaky nature of cell walls, products of photosynthesis find their way into the water, where they are consumed by other bacteria (known as heterotrophs), releasing the captured carbon dioxide back to the atmosphere. Perhaps the most important group of heterotrophs is the Pelagibacterales. These tiny cells dominate global oceans (up to 500,000 in every mL of seawater) and are responsible for converting up to 40% of marine photosynthetic products back to atmospheric CO2. As a result, they have a major impact on global carbon cycling and can be considered global bioengineers. For over a decade we have been studying how nutrient availability in the oceans drive Pelagibacterales ecology and evolution, in a bid to build better models of future global carbon cycling under the influences of climate change. As oceans warm and nutrients become less available, Pelagibacterales abundance, and their importance in carbon cycling, is set to increase further. However, not every member of the Pelagibacterales is equal - they differentiate into distinct ecological niches (known as 'ecotypes') with different capacities to take up resources and release important climate-changing gases such as methane and dimethylsulfide. Therefore, understanding which conditions favour which type of Pelagibacterales is of major importance for climate modelling.

Perhaps the only organisms on Earth more important to global carbon cycles than the Pelagibacterales are the viruses that infect them. Based on their extraordinary abundance and diversity, J.B.S. Haldane once quipped that 'The Creator would appear as endowed with a passion for stars, on the one hand, and for beetles on the other'. In comparison, the Creator's zeal for viruses would make stars and beetles appear to be a side-project performed with perfunctory indifference. Virus numbers are staggering - they are by far the most abundant and diverse organisms on Earth. If one assumes that there are 10 trillion galaxies in the universe and each one is similar to our Milky Way and contains 100 billion stars, then the oceans are populated with a million viruses for every star in the universe. Of these, the vast majority are viruses that infect and kill bacteria (known as 'phages'), and of these, around a quarter are thought to infect Pelagibacterales. Yet, until 2013, the existence of viruses that infect Pelagibacterales was entirely unknown! Similar to interactions between lions and wildebeest in the Serengeti, predation is rather unfortunate for the host, but provides benefits to the scavengers of the ecosystem. Phage-induced cell death releases the contents of the host cell into the water column and this soup of dissolved organic matter provides nutrients to surviving cells. Furthermore, like the arms-race between lions and wildebeest (bigger claws, horns etc.), bacteria and viruses co-evolve to produce resistance and counter-resistance mechanisms. In some cases, this co-evolution can lead to the emergence of new types of host, resistant to viruses and capable of thriving despite high viral abundance. Therefore, both nutrients and viral predation can influence the abundance and diversity of marine bacteria. This project is the first attempt to evaluate the impact of the viruses infecting Pelagibacterales on their diversity and abundance over seasonal timescales. The findings will enable us to build better models of future carbon biogeochemistry by accurately incorporating viral predation of the Pelagibacterales in global carbon cycling.

Over the last two decades, models of ecosystem function have matured into sound scientific tools for operational forecasting systems to inform policy and management on issues critical to society including climate change and food security. Interactions between microbes and abiotic factors are the first level in a complex strophic web and thus underpin community function. Much of the work in developing these models, such as the European Regional Seas Ecosystem Model (ERSEM), include parameters for capturing microbial interactions, but the role of viruses in these systems has, to date, been largely ignored. A recent study into how ecosystems differ with and without viruses showed that viral interactions promote community productivity, increasing primary production and reducing the amount of carbon transferred to higher trophic levels. Yet, understanding of how viruses should be incorporated into models such as ERSEM remains unknown. Understanding how host-virus interactions differ across evolutionary scales will determine the evolutionary scale at which we need to incorporate viruses into future models. If host-range is broad and impact of viral predation across is uniform, then parameterisation may be reduced to simple terms such as total viral abundance. However, if host-range and infection efficiency differ widely across evolutionary and/or temporal scales, then parameterisation will need to be more nuanced. The focus of this proposal, the Pelagibacterales and its viruses, are the most abundant organisms on Earth. The amount of carbon encapsulated within members of the Pelagibacterales is similar to that of all marine fish, and it is responsible for converting up to 20% of global primary production back to atmospheric carbon dioxide. As oceans warm and become more stratified, further limiting nutrient availability, the dominance of Pelagibacterales is set to increase further. Similarly, there is as much carbon within pelagiphages as 45 million blue whales, but as yet, we are ignorant as to whether interactions between these groups are significant in situ. Thus, it is difficult to imagine an organism for study that would that would have greater impact on the accuracy of our models. Therefore, we can say with confidence that this research is of significant societal important to the broadest range of international stakeholders, including the general public, academics and policy makers. These benefits will be provided over the longest timescales as incorporation of data from this proposal improves model accuracy.

Furthermore, development of novel methods to measure viral host range in situ in complex communities will be of significant benefit to those both directly and indirectly involved in developing phage therapy as an alternative means of controlling infection in the face of increasing antimicrobial resistance. The disease burden and economic costs of infectious diseases continue to increase, even in developed countries such as the UK, and the lack of new antibiotics to combat emerging resistance and the threat of a post-antibiotic world is well publicised and a major focus of targeted funding. Phage therapy is most effective when the phages used are broad host range phages, to limit the emergence of counter resistance by the bacterial pathogen. The development of epicPCR approaches as part of this proposal will facilitate identification of broad-host range viruses for use in phage therapy, as well as enable monitoring of coevolution over time so that we can better understand long-term effectiveness of phage therapy.

The Pathways to Impact section details some of the avenues that will be used to engage with the general public to promote the benefits of this work.