Periodic Reporting for period 4 - PhageDiff (Distinct Infection Dynamics and Ecological Success among Closely Related Marine Cyanophages: Why the Differences?) Reporting period: 2020-03-01 to 2020-08-31 Summary of the context and overall objectives of the project Viruses are extremely abundant in the oceans and impact the marine ecosystem by influencing the abundance, diversity and evolution of their hosts. However, our understanding of the differences among distinct phylogenetic lineages within a virus family are conspicuously lacking. The marine picocyanobacteria Synechococcus and Prochlorococcus are important primary producers on a global scale. They coexist with a variety of cyanophage families (viruses that infect cyanobacteria) that display phylogenetic diversity, the meaning of which has remained unclear. The main objectives of this project were: (1) to assess the physiological differences in infection properties of the two discrete lineages within the T7-like cyanophage family; (2) to investigate the manifestations of such physiological differences on their ecological distribution and infection patterns in the oceans; and (3) to elucidate the genomic underpinnings responsible for such differences. This first required the development of methods for the specific quantification of the two clades of T7-like cyanophages and the extent to which they infect their cyanobacterial hosts at the single cell level. It further required the development of a genetic manipulation system for cyanophages. The lack of these methods was impeding the progress of science in understanding the relevance of genetic diversity among environmentally important viruses such as the cyanophages. Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far Employing laboratory experiments of three pairs of clade A and clade BT7-like cyanophages infecting the same cyanobacterial host, we assessed the physiology of their infection properties. We found that one lineage of the T7-like cyanophages (clade A) is more aggressive, as it has a more rapid infection cycle, greater reproduction of viral progeny and kills more cyanobacteria per infection cycle than the second lineage of cyanophages (clade B). These findings clearly show that the separation into phylogenetic lineages is not random and likely resulted through the evolutionary process of adaptation. We next developed methods for quantification of viruses floating freely in the water column as well as the quantification of cyanobacteria infected by the different virus lineages in the marine environment, at the single cell level. Using these methods, we found that the T7-like cyanophages are very abundant in nature over seasonal cycles of changing water column conditions in the Red Sea as well as along transects of environmental change in the North Pacific Ocean. Of particular interest is the increase in the abundance of these cyanophages and in their infection to form a virus hotspot in the region between the subtropical and subpolar gyres. These results revealed that the slower and less aggressive cyanophage lineage (clade B) is the one that is more abundant in the world’s oceans under nearly all environmental conditions. In addition, the less aggressive cyanophage lineage infects more cyanobacteria than the more aggressive cyanophage lineage in nearly all waters. Therefore, it is the less virulent cyanophage lineage with the slower infection cycle and lower progeny production that is more successful in nature. Employment of a model to reconcile this apparent contradiction between infection characteristics and environmental infection and abundance patterns showed that the less aggressive cyanophage lineage maintains a more sustainable host population. Ultimately this allows for more stable host-virus coexistence and a larger population size of the less aggressive cyanophage lineage. This is directly linked to the requirement of viruses to infect their hosts to reproduce and therefore overuse of the host as a resource leads to lower population sizes in nature. These above findings raise the question as to the genetic underpinnings for the observed differences in infection properties and environmental distribution patterns between the two lineages of T7-like cyanophages. To this end, we developed a genetic inactivation system for the T7-like cyanophages. Using this method we discovered two genes that impact the speed of the infection cycle or the number of cyanophage progeny produced, one that enhances clade A infection and one that dampens clade B infection. These genes are not part of the core set of genes found in all T7-like cyanophages, but have been horizontal acquired from their cyanobacterial hosts and are specific to only one of the cyanophage lineages. These findings indicate that the acquisition of genes from the cyanobacterial host has played a major role in the differential adaptation and evolution of the two cyanophage lineages. This has influenced not only their infection physiology, but also their populations sizes, infection patterns and coexistence with their cyanobacterial hosts. This work has been presented at many national and international meetings. The methods have been published in, or submitted to, scientific journals. The findings obtained with these new methods are currently being prepared for publication. In addition, we have hosted members of the international scientific community to train them in these methods. Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far) The methods developed in this project have pushed the state of the art in the field of viral ecology forward and provide important breakthroughs. We have produced methods that quantify virus populations in a taxon-specific manner for the first time. Furthermore, these methods now allow for the direct quantification of the degree of infection of cyanobacteria in nature by different cyanophage families and lineages within those families. Lastly, the method for the inactivation of cyanophage genes will now allow the field to go beyond hypothesis building to hypothesis testing as to the function of many novel genes in cyanophage genomes, including those captured from their hosts. Importantly, these methods can be adapted to ecologically important systems other than the cyanobacteria and cyanophages. We are currently working with a number of labs for the adaptation of these methods for their systems. Modelling of lab and field results: the less aggressive cyanophage is more sustainable in nature.