Biogeography and host interactions of CPR and DPANN viruses in acid mine drainage sediments

Zhi-Liang Lin, Shao-Ming Gao, Sheng-Xuan Peng, Ling-Yun Tang, Zhen-Hao Luo, Xuan-Wen Lao, Si-Yu Zhang, Wen-Sheng Shu, Fangang Meng () and Li-Nan Huang ()
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Zhi-Liang Lin: Sun Yat-sen University, State Key Laboratory for Biocontrol, School of Life Sciences
Shao-Ming Gao: Sun Yat-sen University, State Key Laboratory for Biocontrol, School of Life Sciences
Sheng-Xuan Peng: Sun Yat-sen University, State Key Laboratory for Biocontrol, School of Life Sciences
Ling-Yun Tang: Sun Yat-sen University, State Key Laboratory for Biocontrol, School of Life Sciences
Zhen-Hao Luo: Sun Yat-sen University, State Key Laboratory for Biocontrol, School of Life Sciences
Xuan-Wen Lao: Sun Yat-sen University, State Key Laboratory for Biocontrol, School of Life Sciences
Si-Yu Zhang: Sun Yat-sen University, State Key Laboratory for Biocontrol, School of Life Sciences
Wen-Sheng Shu: South China Normal University, School of Life Sciences
Fangang Meng: Sun Yat-sen University, School of Environmental Science and Engineering
Li-Nan Huang: Sun Yat-sen University, State Key Laboratory for Biocontrol, School of Life Sciences

Nature Communications, 2025, vol. 16, issue 1, 1-14

Abstract: Abstract The CPR and DPANN superphyla are globally distributed in anoxic habitats including extreme environments. However, the biogeography and potential ecological functions of their viruses remain unexplored. Here, we recover diverse CPR/DPANN metagenomic viral genomes from 90 acid mine drainage (AMD) sediments sampled across southeast China. Our data reveal deterministic processes as the primary driver of virome assembly shaping the distinct distribution patterns of CPR and DPANN viruses. While lifestyle prediction shows higher lytic virus diversity associated with DPANN, both CPR/DPANN viruses likely use the Piggyback-the-winner (PtW) strategy to co-exist with hosts in AMD sediments, with CPR viromes exhibiting increased lysis in low host-density regimes under intensive acidity/salinity conditions. A subsequent metatranscriptomic analysis uncovers diverse functional genes encoded by CPR and DPANN viruses actively expressed in situ, potentially supplementing host metabolisms yet diverging in replication, transcription, and translation-related functions. Furthermore, partial correlation network analysis suggests that putative symbiotic hosts of the CPR/DPANN may confer protection against viral infection through enhanced antiviral defense. Our results highlight the complex interplays between viruses, DPANN and CPR organisms, and their symbiotic hosts.

Date: 2025
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DOI: 10.1038/s41467-025-65461-0

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