Biological context modulates virus-host dynamics and diversification

Virus-bacterial interactions are fundamental to microbial ecology and evolution, but they have been studied mostly under simplified laboratory conditions. To better understand how ecological complexity shapes these dynamics, we examined the extreme halophilic bacterium Salinibacter ruber strain M1 and the EM1 virus in the presence of additional Sal. ruber strains and viruses. In the short term, the presence of other strains delayed lysis and reduced EM1 virus production, indicating that community composition directly affects viral replication. In the long term, both Sal. ruber M1 and the EM1 virus persisted across all experimental conditions, but their evolutionary responses differed. The EM1 virus showed an increased mutation rate, reduced infectivity against the native host, and expanded host range when other viruses were present, suggesting a previously unrecognized form of virus-virus interaction, in which coexisting viruses influence each others evolutionary paths promoting viral diversification. In contrast, Sal. ruber M1 exhibited higher mutation rates evolving with other strains, indicating that in our system, intraspecific competition, rather than viral pressure, drives bacterial evolution. These findings demonstrate that incorporating biological complexity reveals distinct selective pressures acting on hosts and viruses, and is therefore essential for accurately predicting virus-host evolution in natural microbial ecosystems.