Evolution of virus and virophage facilitates persistence in a tripartite microbial system

Abstract

Tripartite biotic interactions are inherently complex, and the strong interdependence of species and high levels of exploitation can make these systems short-lived and vulnerable to extinction. The persistence of species depends then on the balance between exploitation and avoidance of exploitation of the resource beyond the point where sustainable exploitation is no longer possible. We used this general prediction to test the potential for long-term persistence in a recently discovered tripartite microbial system in which a eukaryotic host is preyed upon by a giant virus that is in turn 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 over time and the virophage can survive integrated into the host genome when giant viruses are scarce. Here, we grew hosts in the presence and absence of the giant virus and virophage over ~280 host generations. We found that the three players persisted, but that the beneficial effect of the virophage for the host population diminished over time. We further tested whether the level of exploitation and replication evolved in the giant virus and/or virophage population over the course of the experiment and whether the changes were such that they avoid overexploitation. We found that the giant virus evolved towards lower replication levels and the virophage towards increased replication but decreased giant virus exploitation. These changes are predicted to facilitate persistence by lowering giant virus and host exploitation and consequently reducing the protective effect of the virophage.

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

“…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).…”

Virophages, Satellite Viruses, Virophage Replication and Its Effects and Virophage Defence Mechanisms for Giant Virus Hosts and Giant Virus Defence Systems against Virophages

“…Viruses, although they do not carry out metabolic processes themselves, replicate in Eukaryota, Bacteria and Archaea and are the most abundant entities in all natural environments of the biosphere [ 1 , 2 , 3 , 4 , 5 , 6 , 7 ]. Giant viruses were included in 2003, and their ‘parasites’, the virophages, were included in 2008 and, due to their biological characteristics, have become a potential evolutionary driving force in microbiology, including and ecology [ 2 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 ]. Giant “host” viruses of virophages are classified into NCLDVs (Nucleocytoplasmic Large DNA Viruses) characterised by large virions (greater than 200 nm), and their genetic material is linear dsDNA, although, in some of them, it can also occur in a circular form [ 3 , 4 , 10 , 20 ].…”

Virophages—Known and Unknown Facts

“…Their destructive effect on giant viruses occurs through their genetic “action”, e.g., tRNA, which influences the replication and morphogenesis of giant viruses, as well as their “adaptive immunity”, making them regulators and, at the same time, defenders of giant virus hosts, which are protozoa and algal organisms that primarily condition and shape the homeostasis of the aquatic environment [ 1 , 3 , 6 , 7 , 9 , 10 ]. Virophages are membrane-less viruses, having an essentially cubic-icosahedral capsid formed from their major capsid protein (MCP).…”

“…They adopt a double-Galli fold, range in size from 34–74 nm (average 50–70 nm) with circular/linear dsDNA, and belong to the family Lavidaviridae [ 1 , 11 , 12 , 13 , 14 , 15 ]. However, there are now proposals [ 7 , 9 ] that virophages should form the class Maveriviricetes, with four orders and seven families. Like giant viruses and “classical” viruses, virophages are incapable of independent replication, and their process occurs in the viral particle factory of the giant viruses in which they parasitize.…”

“…Additionally, associated with the discovery of virophages is research into a three-part system termed CVV (cell–virus–virophage), which is formed by giant virus host cells, a giant virus, and a virophage, although an analogous relationship occurring between giant viruses, virophages, and transposons has also been described [ 1 , 9 , 18 , 19 ]. An example of such a CVV system is the giant virus, virophage, transpovirion system in amoebae ( A. polyphaga , A. castellani ) and flagellates ( Cafeteria roenbergensis —now C. burkhardei ) or the giant virus, virophage, retrotransposon system in the unicellular eukaryote Bigelovatella natans [ 8 , 12 , 18 , 20 , 21 , 22 , 23 ].…”