The essential functions of freshwater lake ecosystems—such as carbon, nitrogen, and phosphorus cycling, as well as water quality maintenance—are largely sustained by the dynamic equilibrium of microbial interaction networks, which are highly sensitive to human activities and environmental stressors. Viruses act as pivotal regulators of microbial communities, shaping host diversity, adaptability, and ecosystem functioning through strategies such as the “kill-the-winner” (lytic) and “piggyback-the-winner” (lysogenic) models. In addition, auxiliary metabolic genes (AMGs) encoded by viruses can directly modulate host metabolic pathways. Although individual stressors are known to influence virus–host interactions, the combined effects of multiple stressors on these interaction networks remain poorly understood.

Recently, a research team led by Prof. XU Jun from the Institute of Hydrobiology (IHB) of the Chinese Academy of Sciences, together with collaborators across institutions, has provided new insights into how multiple environmental stressors interact to influence freshwater microbiomes. Their findings reveal that viral community responses to multiple stressors are highly complex, underscoring the importance of accounting for coupled stressor effects when assessing ecological risks. The study was published in Nature Communications.

In this study, the researchers conducted a long-term, large-scale mesocosm experiment simulating a multi-trophic freshwater lake food web. Over a ten-month period, 48 experimental systems were subjected to factorial combinations of warming, nutrient enrichment, and exposure to the insecticide imidacloprid. Metagenomic analyses were employed to investigate the responses of viral and bacterial communities, as well as their interactions, under these stressor regimes. 

The results showed that viruses are highly sensitive to combined stressors. Specifically, the synergistic effects of nutrient enrichment and insecticide exposure significantly increased the relative abundance of lysogenic phages while markedly reducing viral diversity, effects that were not observed under single-stressor treatments.

Multiple stressors substantially altered viral community composition, leading to distinct community differentiation. Both warming and the combined nutrient–insecticide treatment significantly reduced the complexity and stability of virus–bacteria interaction networks, and strongly affected the abundance and composition of viral auxiliary metabolic genes. 

As key modulators of microbial communities and biogeochemical cycles, viruses propagate the effects of environmental stressors to their hosts through shifts in life-history strategies and viral auxiliary metabolic genes, thereby influencing the stability of essential ecosystem functions such as carbon cycling.

This study shows that multiple stressors can interact in non-additive ways to restructure virus–host interactions and microbiome stability in freshwater ecosystems. Notably, combined stressors such as nutrient loading and pesticide exposure disrupted viral communities and virus–host interactions even when single stressors had negligible effects. The results demonstrate that viral responses cannot be predicted from single-stressor scenarios, highlighting the importance of incorporating multi-stressor perspectives into ecological theory and risk assessment frameworks. Understanding these responses is essential for predicting ecosystem stability in a rapidly changing world and for guiding the management and conservation of freshwater ecosystems.

Effects of multiple stressors on viral communities and virus–bacteria interaction networks (Image by IHB)

(Editor: MA Yun)