Evolution of exploitation and replication of giant viruses and virophages

Abstract

Tripartite biotic interactions are inherently complex, and the strong interdependence of species and often one-sided exploitation can make these systems vulnerable to extinction. The persistence of species depends then on the balance between exploitation and avoidance of exploitation beyond the point where sustainable resource use is no longer possible. We used this general prediction to test the potential role of trait evolution for persistence in a tripartite microbial system consisting of a marine heterotrophic flagellate preyed upon by a giant virus, which in turn is parasitized by a virophage. Host and virophage may benefit from this interaction because the virophage reduces the harmful effects of the giant virus on the host population and the virophage can persist integrated into the host genome when giant viruses are scarce. We grew hosts and virus in the presence and absence of the virophage over ∼280 host generations and tested whether levels of exploitation and replication in the giant virus and/or virophage population evolved over the course of the experiment, and whether the changes were such that they could avoid overexploitation and extinction. We found that the giant virus evolved toward lower levels of replication and the virophage evolved toward increased replication but decreased exploitation of the giant virus. These changes reduced overall host exploitation by the virus and virus exploitation by the virophage and are predicted to facilitate persistence.

Virophage replication mode determines ecological and evolutionary changes in a host-virus-virophage system

“…This is because reactivation of integrated virophages leads to virus production and thus, on average, higher virus densities, whereas co-infection only leads to virophage production and thus lower virus densities. Since previous work has shown that increased reproduction and reduced virus exploitation by the virophage evolve together (del Arco et al 2024), we further predict that virophage reproduction will either not evolve or evolve with a smaller increase.…”

“…Host densities were quantified from life samples using a hemacytometer and light microscopy. Virus and virophage samples were frozen for later DNA extraction (DNeasy 96 Blood & Tissue Kit, Qiagen, Hilden, Germany) and quantification by digital ddPCR (del Arco et al 2023(del Arco et al , 2024. All ddPCR results were analyzed using QUANTASOFT 1.7.4 The detailed methods and quality requirements for the data are described in the reference (del Arco et al 2022).…”

“…During co-infection, the virophage also exploits the virus factory of the virus for its own replication, allowing for horizontal transmission. While the importance of virophages for host and virus dynamics has been demonstrated in a few studies (Wodarz 2013; Taylor et al 2014; Yau et al 2016; Fischer and Hackl 2016; del Arco et al 2024), the ecological consequences of this viral exploitation by the virophage for the microbial community remain largely unknown.…”

“…In addition, traits underlying virus and virophage replication and host exploitation may evolve rapidly. For example, previous work with the Cafeteria-CroV-Mavirus system has shown that the high degree of exploitation and interdependence in this tripartite system leads to the rapid evolution of reduced replication of the virus (CroV) and increased virophage (Mavirus) replication, but reduced exploitation of the virus by the virophage (del Arco et al 2024). These observations together suggest that the virophage replication mode is not constant over time and that the relative contribution of the two modes to virophage and virus reproduction may continuously change.…”

“…The long-term persistence of such a tripartite system should favor virophage traits that allow adaptations for sufficient exploitation of the virus without compromising the abundance of its viral host as a resource (Morozov et al 2007; Heilmann et al 2010). This can be achieved if the virophage evolves higher levels of replication and lower levels of exploitation of the virus (del Arco et al 2024), as high levels of exploitation would result in low virus densities over time and thus few opportunities for the virophage to parasitize the virus. With more integrated virophages per host, we predict that selection for reduced exploitation will be weaker compared to hosts with fewer integrated virophages.…”