Freshwater Microbiomes Shape Viral Inactivation in Continuous Cultures

In freshwater environments, bacteria are known to enhance the removal and inactivation of human viruses. Rates of inactivation differ across freshwater ecosystems, though the influence of community diversity and composition on this process remain poorly understood. Here, we used dilution-to-extinction to generate 64 distinct freshwater communities from three lakes and three aquifers. After establishing freshwater communities in chemostat cultures, each community was challenged with two viruses, coxsackievirus B5 and human adenovirus 2. Both viruses were inactivated more rapidly in lake-derived than in groundwater-derived communities, and adenovirus was inactivated faster than coxsackievirus in both freshwater types. Community-level parameters (e.g., cell numbers, richness) were not significant predictors of viral inactivation. Instead, differential abundance analyses identified bacterial OTUs associated with inactivation: Acidovorax sp. were associated across sources and Brevundimonas sp., Sphingopyxis sp., and Hydrogenophaga sp. showed source-specific associations. Together, these findings provide new insights into the ecological drivers of viral stability and suggest that viral inactivation may depend more strongly on specific microbial taxa and their environmental context than on overall community diversity. Identifying these associations improves our understanding of the factors governing viral stability in freshwater environments.