Harnessing Alpine Lake Bacteria for the Development of Synthetic Communities with Broad-Spectrum Antiviral Activity

In aquatic ecosystems, phagotrophic protists and bacteriophages are major biological factors shaping bacterial populations. However, the extreme environmental conditions and low nutrient concentrations in alpine lakes limit the abundance of protists. Thus, bacteriophages may represent the main biological factor shaping bacterial communities in these ecosystems. We hypothesized that alpine lake bacteria populations harbor diverse antiviral strategies against bacteriophages that could be used to fight against other viral pathogens. To evaluate the presence of bacteria with broad-spectrum antiviral activity in high altitude Swiss lakes, we developed a sampling campaign in 24 alpine lakes in Switzerland. We assessed the decay of two human viruses (echovirus 11 and influenza A virus) in lakewater and characterized the microbial abundance and metabolic diversity in the collected samples. In addition, we obtained a collection of 223 bacterial isolates and selected bacteriophage resistant bacteria to build synthetic communities with enhanced antiviral activity against the two tested human viruses, and one plant virus of commercial significance (Potato Virus X). These results support our hypothesis and reveal, for the first time, an association between bacteriophage resistance and viral inactivation. Our findings emphasize the importance of alpine lakes as hotspots of microbial diversity with unexplored biotechnological applications.