Rhizosphere-triggered viral lysogeny mediates microbial metabolic reprogramming to enhance arsenic oxidation
The rhizosphere is a critical hotspot for metabolic activities involving arsenic (As). While recent studies indicate many functions for soil viruses, much remains overlooked regarding their quantitative impact on rhizosphere processes. Here, we analyze time-series metagenomes of rice (Oryza sativa L.)rhizosphere and bulk soil to explore how viruses mediate rhizosphere As biogeochemistry. We observe the rhizosphere favors lysogeny in viruses associated with As-oxidizing microbes, with a positive correlation between As oxidation and the prevalence of these microbial hosts. Moreover, results demonstrate these lysogenic viruses enrich both As oxidation and phosphorus co-metabolism genes and mediated horizontal gene transfers (HGTs) of As oxidases. In silico simulation with genome-scale metabolic models (GEMs) and in vitro validation with experiments estimate that rhizosphere lysogenic viruses contribute up to 25% of microbial As oxidation. These findings enhance our comprehension of the plant-microbiome-virome interplay and highlight the potential of rhizosphere viruses for improving soil health in sustainable agriculture.
Authors
- Mengcen Wang (ORCID: https://orcid.org/0000-0001-7169-6779)
- Ruichuan Gao
- Dedong Kong (ORCID: https://orcid.org/0009-0002-9329-1574)
- Xianjin Tang (ORCID: https://orcid.org/0000-0002-7515-2047)
- Youjing Wang (ORCID: https://orcid.org/0009-0006-5678-9145)
- Yiling Wang (ORCID: https://orcid.org/0000-0001-8924-2417)
- Fangbai Li (ORCID: https://orcid.org/0000-0001-9027-9313)
- Bin Ma (ORCID: https://orcid.org/0000-0003-4807-4992)
- Yunjie Ruan
- Jianming M. Xu (ORCID: https://orcid.org/0000-0002-2954-9764)
- Di Tong (ORCID: https://orcid.org/0000-0003-4090-578X)
- Xinwei Song (ORCID: https://orcid.org/0000-0002-0188-1319)
- Xiaofei Lv (ORCID: https://orcid.org/0000-0002-1712-630X)
- Kankan Zhao (ORCID: https://orcid.org/0000-0003-3066-9402)
- Yong‐Guan Zhu (ORCID: https://orcid.org/0000-0003-3861-8482)
- Yongming Luo (ORCID: https://orcid.org/0000-0002-2217-3207)
Institutions
- Guangdong Academy of Sciences (CN)
- ZheJiang Academy of Agricultural Sciences (CN)
- Rural Development Institute (CN)
- Research Center for Eco-Environmental Sciences (CN)
- Ministry of Agriculture and Rural Affairs (CN)
- Institute of Soil Science (CN)
- China Jiliang University (CN)
- Zhejiang University of Technology (CN)
- Zhejiang University (CN)
Publication Details
- Journal
- Nature Communications
- Published
- 2025-04-30
- DOI
- https://doi.org/10.1038/s41467-025-58695-5
- Citations
- 11
- Primary Topic
- CRISPR and Genetic Engineering
- Type
- article
- Field-Weighted Citation Impact
- 8.87
Funders
- National Natural Science Foundation of China