Abstract
Anaerobic oxidation of methane (AOM) can mitigate global warming by converting methane into either carbon dioxide or soil organic carbon (SOC). However, it is unclear whether soil viruses influence AOM and the associated carbon sequestration processes. Here we quantify the impact of viruses on the carbon sink formed through AOM and reveal the underlying mechanisms using 13C labelling and metagenomics. Our findings show that viruses can substantially increase SOC associated with AOM and alter the amount of iron-bound organic carbon (Fe-bound OC). However, the magnitude and direction of these effects depend on the type of virus. Specifically, mitomycin C-induced viruses contributed 54.5% of the newly formed SOC and caused a 73.1% loss of 13C-Fe-bound OC by facilitating the survival of related microbes, such as iron-reducing bacteria, under anaerobic conditions. In contrast, free extracellular viruses increased both 13C-SOC (+115.5%) and 13C-Fe-bound OC (+35.8%) via viral lysis, due to the high affinity of lysate dissolved organic matter for sorption onto iron(hydr)oxides. These results highlight the substantial impact of soil viruses on the stabilization of methane-derived carbon in soils, and advance our understanding of viral-controlled soil carbon biogeochemical cycles.
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Data availability
The original sequence data were deposited into the National Center for Biotechnology Information Sequence Read Archive database under project ID PRJNA1412534. Data used in this study are available from the figshare data repository (https://doi.org/10.6084/m9.figshare.31563373 (ref. 91)). Source data are provided with this paper.
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Acknowledgements
This study was supported by the National Natural Science Foundation of China (42595620, 42330711), the Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education of China (JYB2025XDXM703), the Fundamental Research Funds for the Central Universities (226-2025-00004), the 111 Project (B17039) and China Postdoctoral Science Foundation (GZC20251623).
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The experiment was designed by J.X. Soil sampling and microcosm incubation were performed by D.T., Y.W., H.Y., Y. Zhou, Y.L. and B.M. Y. Zhang and D.T. carried out measurements of soil properties. X.S. and D.T. performed statistical analyses. Visualization was provided by D.T. and J.X. The original draft was written by D.T. and J.X. The paper was reviewed and edited by J.X., C.T., R.A.D. and D.T.
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Extended data
Extended Data Fig. 1 Dynamics of CH4 and CO2 concentrations for different viral groups.
(a) The fraction of 13CO2 enrichment (F13CO2 = 13CO2/(13CO2 + 12CO2), (b) cumulative partial anaerobic oxidation of methane, and (c) cumulative full anaerobic oxidation of methane during incubation with 13CH4 in the no virus-added group (NoV), inactive virus-added group (InV), free extracellular virus-added group (FreeV), and virus induced by mitomycin C group (MMC_V). The spheres and stars show the control groups with Ar and 12CH4 injection. The data are shown as the mean ± std dev (n = 3).
Source Data
Extended Data Fig. 2 Changes in fluorescence index (FI) (a), β/α (b) and HIX (c) of dissolved organic matter (DOM) at 60 and 90 days after incubation among different groups.
Changes in fluorescence index (FI) (a), β/α (b) and HIX (c) of dissolved organic matter (DOM) at 60 and 90 days after incubation with treatments receiving no virus (NoV), inactive virus (InV), free extracellular virus (FreeV), and virus induced by mitomycin C (MMC_V). The FI and β/α represent autochthonous DOM inputs to the soil, which indicates the relative contribution of recent microbial-derived DOM to total DOM. The HIX indicates the humification degree of DOM. The bar plots show the data as the mean ± std dev and overlay the corresponding data points as dot plots. Different letters above the bars indicate statistically significant differences between the treatments (n = 3), as determined by a one-way ANOVA followed by an LSD post hoc test (two-sided, P < 0.05).
Source Data
Extended Data Fig. 3 Abundance of AOM-related microbes, bacteria and archaea after the pre-incubation period.
The abundance of ANME-2d (a), NC10 (b), iron-reducing bacteria (FeRB; c), sulfate-reducing bacteria (SRB; e), bacteria (f), archaea (g), and methanogens (h). The bar plots show the data as the mean ± std dev and overlay the corresponding data points as dot plots. Different letters above the bars indicate statistically significant differences between the treatments (n = 3), as determined by a one-way ANOVA followed by an LSD post hoc test (two-sided, P < 0.05).
Source Data
Extended Data Fig. 4 Changes in concentrations of 13C-SOC/SOC, soil organic C and dissolved organic C at 1, 60 and 90 days during incubation.
(a)Ratio (mean ± std dev) of 13C-SOC to total soil organic C (SOC) in treatments receiving no virus (NoV), inactive virus (InV), free extracellular virus (FreeV), and virus induced by mitomycin C (MMC_V). Grey spheres indicate the corresponding control groups with argon injection. (b) Changes in SOC and DOC (c) during incubation. Different letters indicate statistically significant differences between the treatments (n = 3), as determined by a one-way ANOVA followed by an LSD post hoc test (two-sided, P < 0.05).
Source Data
Extended Data Fig. 5 Changes in Fe species and Fe-bound OC (mean ± std dev) after incubation with 13CH4 for 1, 60 and 90 days.
(a) Ferrous iron [Fe(II)] and ferric iron [Fe(III)], (b) Changes of Fe-bound OC, (c) amorphous Fe oxides (Feo) and (d) crystalline Fe oxides (Fec) in treatments receiving no virus (NoV), inactive virus (InV), free extracellular virus group (FreeV), and virus induced by mitomycin C (MMC_V). Different lowercase letters within a given time point indicate statistically significant differences between the treatments (n = 3), as determined by a one-way ANOVA followed by an LSD post hoc test (two-sided, P < 0.05).
Source Data
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Tong, D., Wang, Y., Song, X. et al. Viral mediation of anaerobic methane oxidation to carbon sequestration in paddy soil.
Nat. Geosci. (2026). https://doi.org/10.1038/s41561-026-01998-z
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DOI: https://doi.org/10.1038/s41561-026-01998-z
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