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Metagenomic analysis reveals how multiple stressors disrupt virus–host interactions in multi-trophic freshwater mesocosms

Author

Listed:
  • Tao Wang

    (Chinese Academy of Sciences
    Chinese Academy of Sciences)

  • Peiyu Zhang

    (Chinese Academy of Sciences
    Chinese Academy of Sciences)

  • Karthik Anantharaman

    (University of Wisconsin-Madison
    University of Wisconsin-Madison
    Indian Institute of Technology Madras)

  • Huan Wang

    (Chinese Academy of Sciences
    Hainan University
    Hainan University)

  • Huan Zhang

    (Chinese Academy of Sciences
    Chinese Academy of Sciences)

  • Min Zhang

    (Huazhong Agricultural University)

  • Jun Xu

    (Chinese Academy of Sciences
    Chinese Academy of Sciences
    Hainan University)

Abstract

Virus–host interactions are vital to microbiome ecology and evolution, yet their responses to environmental stressors under global change remain poorly understood. We perform a 10-month outdoor mesocosm experiment simulating multi-trophic freshwater shallow lake ecosystems. Using a fully factorial design comprising eight treatments with six replicates each, we assess the individual and combined effects of climate warming, nutrient loading, and pesticide loading on DNA viral communities and their interactions with microbial hosts. Metagenomic sequencing recovers 12,359 viral OTUs and 1628 unique prokaryotic metagenome-assembled genomes. Our analysis shows that combined nutrient and pesticide loading causes significant disruption by synergistically reducing viral alpha diversity while altering beta diversity and predator-prey linkages. Stressors lead to the simplification of virus-bacteria cross-kingdom networks, with nutrient-pesticide combinations exerting the strongest influence, although warming impacts diminish in the presence of pesticides. Stressor-driven changes also affect the abundance and composition of viral auxiliary metabolic genes, leading to complex shifts in virus-mediated metabolic pathways under multiple stress conditions. These findings underscore the importance of understanding the regulatory role of viruses on microbial communities to effectively address the challenges posed by global change.

Suggested Citation

  • Tao Wang & Peiyu Zhang & Karthik Anantharaman & Huan Wang & Huan Zhang & Min Zhang & Jun Xu, 2025. "Metagenomic analysis reveals how multiple stressors disrupt virus–host interactions in multi-trophic freshwater mesocosms," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-63162-2
    DOI: 10.1038/s41467-025-63162-2
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