Investigating the role of lake microbial communities on virus inactivation using continuous culture systems

Authors: MORALES, L. DANIELA - Ecole Polytechnique Federale De Lausanne (EPFL); WYNN, HTET KYI - Ecole Polytechnique Federale De Lausanne (EPFL); MEIBOM, JOSEPHINE - Ecole Polytechnique Federale De Lausanne (EPFL); Heffron, Joseph; KOHN, TAMAR - Ecole Polytechnique Federale De Lausanne (EPFL)

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 4/1/2025
Publication Date: 6/17/2025
Citation: Morales, L., Wynn, H., Meibom, J., Heffron, J.A., Kohn, T. 2025. Investigating the role of lake microbial communities on virus inactivation using continuous culture systems. Meeting Abstract. 1.

Interpretive Summary:

Technical Abstract: Introduction: In aquatic environments, multiple abiotic and biotic factors challenge the environmental stability of enteric viruses. While abiotic factors (temperature, sunlight, etc.) have been well studied, biotic factors remain uncharacterized. Our lab has previously shown that certain bacteria isolated from Lake Geneva reduced the infectivity of Echovirus 11 (E11) and Coxsackievirus A9 (CVA9). However, bacteria in nature are found in complex communities, and their interactions impact their physiology and metabolism. Here, we aim to further characterize the role of lake bacterial communities in viral inactivation. Methods: We developed a method to grow bacterial communities from lakewater using chemostats. Chemostats are culture systems with a continuous inflow of nutrients and removal of microbial metabolic waste. We collected surface water from Lake Geneva and used it to seed chemostats at varying dilutions to manipulate diversity . Chemostats were incubated in the dark at room temperature for 14 days and fed with sterile lakewater. Flow cytometry (Attune CytPix Flow Cytometer) was used to track bacterial cell growth. SYTO13 was used to stain and differentiate bacterial cells. On day 14, chemostats were homogenized, and E11 was spiked into batch cultures from each chemostat. Viral titre was monitored by sampling the batch cultures and comparing the infectivity of the samples over time (55 hours ). In addition, DNA was extracted for 16S sequencing to compare microbial diversity within the chemostats. Results: Bacterial communities from Lake Geneva were successfully grown and maintained inside the chemostats. All chemostats reached cell concentrations around 1E+05 and 1E+06 events/mL after four days, and cell numbers were maintained throughout the experiment. After eight days of growth , aggregates accumulated on the walls of the chemostats and the bacterial cells in the effluent decreased. This was likely due to biofilm formation. As intended, the different chemostats yielded microbial communities of different diversity. All microbial communities decreased the infectivity of E11 by >1 log after 24 hours and >2 log after 48 hours in all batch cultures, though the inactivation rates were community specific. Discussion: Human pathogenic viruses have beneficial and detrimental interactions with bacteria. To date, most research on bacteria-virus interactions has focused on human bacteria commensals. Here we cultured lake water microbial communities using chemostats. These culture systems allowed us to grow and maintain bacteria in exponential growth phase for 14 days. In addition, we showed that microbial communities from Lake Geneva successfully inactivate E11, though the resulting inactivation rates depend on the community composition. Conclusion: This work provides new insights into how bacteria modulate the stability of human pathogenic viruses in nature. Future research will focus on further characterizing the metabolism of these lake water communities using a combination of “-omics” and biochemical approaches to better elucidate the mechanisms behind viral inactivation. The molecular mechanisms behind viral inactivation by bacteria could be potentially used to improve water treatment and decrease viral outbreaks.