Polinton-like virus diversity in aquatic ecosystems

Viruses are often thought of as a human problem, however they are the most abundant biological entities on the planet. There are millions of viruses in every drop of river, lake or seawater, they are found everywhere there is life and probably infect all living organisms. Most are completely harmless to humans and infect microscopic animals, plants and bacteria, which they hijack and reprogram to produce new virus particles. Every day, viruses destroy a huge number of microorganisms in the environment, which changes the flow of energy in food webs on global scales. Recently, we discovered a new group of viruses in the high mountain lake, Gossenköllesee, Tyrol, which are called `Polinton-like viruses`. We found they are also present in rivers and lakes around the world, however, we have little information on who they infect and how they may be interacting with their hosts. This project will investigate Polinton-like virus diversity in many lakes across Tyrol. We will use a technique called metagenomics to sequence large amounts of DNA from the water. We aim to decode new virus genomes to reveal which microbial organisms they infect, and how this infection may influence host populations of algae and other single celled microorganisms. Hence uncover previously overlooked controls on the microbial community in freshwater ecosystems. For the second phase of the project, we will also be working in collaboration with scientists from the University of Minnesota and the Nebraska centre for virology to examine the wider diversity of these new viruses across the continental USA and beyond.

Summary of Findings from the POLVIRIDAE Project The POLVIRIDAE project set out to understand a little-known group of viruses called Polinton-like viruses (PLVs) and to uncover their role in the defence and evolution of single-celled eukaryotic organisms. PLVs are unusual because they sit at the boundary between classic viruses and mobile pieces of DNA. Some PLVs exist as DNA segments integrated within their host genomes, while others are known to form virus particles and are therefore fully functional viruses. Notably, several PLVs are now known to co-infect their hosts with more harmful giant viruses (they are virophages), often inhibiting giant virus replication and promoting host survival. This makes PLVs central to understanding virus-driven defence systems and virus evolution. A major breakthrough of the POLVIRIDAE project was the discovery that PLVs are widespread in the genomes of single-celled eukaryotic organisms, including plankton, symbiotic algae in corals, and even human and plant pathogens. By developing new tools to detect PLVs in eukaryotic DNA, the project identified thousands of previously unrecognised viral sequences embedded in host genomes, demonstrating that PLVs have repeatedly infected eukaryotes over long evolutionary timescales. Importantly, however, they are not simply genetic fossils. They are closely related to known, active PLVs and virophages and show the potential for reactivation. This work, published in Proceedings of the National Academy of Sciences (PNAS), revealed that PLVs have played a persistent role in shaping eukaryotic genomes and potentially in eukaryotic evolution. Building on this discovery, the POLVIRIDAE project uncovered the full scale of PLV diversity in natural environments. By searching for viruses in alpine lakes and combining these findings with thousands of publicly available genome datasets, the project assembled a collection of over 50,000 previously unrecognised virus genomes. This dataset revealed dozens of entirely new virus groups and enabled the proposal of a new evolutionary framework for these viruses (in review at the time of writing). PLVs are not a single virus group; they represent multiple virus families which can be divided across three major viral classes. Crucially, several of these new virus groups form evolutionary links between PLVs and giant viruses (the most complex virus genomes known), supporting the hypothesis that giant viruses evolved from PLV-like ancestors. These findings highlight an evolutionary network connecting mobile genetic elements, PLVs, and giant viruses. To support future research, the project produced an open-access reference dataset and a software tool that allows researchers worldwide to detect and classify PLVs. Together, these results show that Polinton-like viruses are abundant, diverse, and likely important in the evolution and defence of single-celled eukaryotic organisms.