Abstract
Arsenic (As), a toxic element widespread in paddy soils worldwide, is mobilized by microbial processes, posing risks to environmental quality, food safety and human health. The rice rhizosphere is a dynamic environment with day–night cycles in chemical conditions and microbial activity. However, how arsenic itself changes over these daily cycles remains unexplored. Here we conduct metatranscriptomic and biogeochemical analyses in a greenhouse study to investigate the diurnal rhythms of As dynamics in the rice rhizosphere. We observed consistent diel fluctuations in arsenite (As(III)) concentrations, increasing from 1.8 to 2.9 mg l‒1 at night, alongside a 24.9% rise in ferrous iron (Fe(II)). Redox potential decreased to ~100 mV at night, promoting As/Fe reduction. Transcriptional activity of key functional genera involved in dissimilatory As/Fe reduction (for example, Geomobilimonas and Geobacter) increased at night, reflected in higher transcript abundances of reduction genes (arrA, omcS, omcZ and mtrC), without corresponding changes in relative abundance. These patterns were confirmed in a field study. Under constant darkness, these diel patterns disappeared. Together, these findings suggest managing rice cultivation to align with natural daily cycles may reduce contamination risks and optimize nutrient management.
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Data availability
All data that support the findings of this study are publicly available. All raw sequence data generated in this study have been deposited in the National Genomics Data Center under project accession code PRJCA051357 and in the Genome Sequence Archive (GSA) under accession CRA033909. Source data are provided with this paper.
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Acknowledgements
This study was supported by the National Natural Science Foundation of China (42330711, 42595620), the Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education of China (JYB2025XDXM909), the Fundamental Research Funds for the Central Universities (226-2025-00004) and China Agriculture Research System (CARS-01). Seeds of rice (Oryza sativa L. subsp. japonica ‘Nipponbare’) were provided by Y. Zhang from China National Rice Research Institute. We thank K. Zhao for providing the field experiment data, X. Song for data analysis and X. Tang for his guidance on analytical methods. We also thank H. Zhu, X. Xiong, Z. Wu, X. Wang and Y. Liu for their help with sampling.
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J.X. designed the research; H.Y., Y.W. and D.T. performed data collection and measurements; H.Y. and J.X. wrote the original paper; J.X., B.M., L.H., Y.L., X.L., R.A.D. and H.Y. reviewed and edited the paper.
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Extended data
Extended Data Fig. 1 Diurnal pH changes in the rice rhizosphere under light-dark cycles.
(a) pH values in the rice rhizosphere under light-dark cycles sampled every 10 s. (b) Box plot showing diel variations of pH in the rice rhizosphere day and night groups (n = 9); boxes show IQR, medians are center lines, whiskers extend to 1.5× IQR. (c) Linear regressions of As(III) concentrations with pH in rhizosphere. Regression lines represent the fitted model; shaded areas represent 95% confidence intervals. For panels (b) and (c), each data point represents a biologically independent replicate. The P-values were calculated by a two-sided Wilcoxon test.
Source Data
Extended Data Fig. 2 Heatmap showing transcript abundance of dissimilatory As/Fe reduction genes harbored by functional genera between day and night groups.
The P-values were calculated by a two-sided Wilcoxon test. *P < 0.05, **P < 0.01, ***P < 0.001.
Source Data
Extended Data Fig. 3 Diel variation of As- and Fe- reduction genes and functional taxa in the rice rhizosphere of field experiment.
(a) Transcript abundance (metaT) of As- and Fe- reduction genes for day and night groups (n = 9). (b) Transcript abundance (metaT) of key functional families. Error bars represent ± 1 s.d. around mean values. Each data point represents a biologically independent replicate. The P-values were calculated by a two-sided Wilcoxon test. *P < 0.05, **P < 0.01, ***P < 0.001.
Source Data
Extended Data Fig. 4 Diel variation of As and Fe concentrations, and associated genes in the rice rhizosphere under constant dark conditions.
(a) Diel variations of As(III) and Fe(II) concentrations in rice rhizosphere under constant dark conditions (n = 9). (b) Transcript abundance (metaT) of As- and Fe- related genes for day and night groups (n = 9). Error bars represent ± s.d. around mean values. (c) Transcript abundance (metaT) of key dissimilatory As/Fe reduction genes (arrA, omcS, mtrC, and omcZ) between day and night groups (n = 9). (d) Heatmap of transcriptional activity (metaT/metaG ratio) for key functional taxa under constant dark conditions; no significant differences were observed between day and night groups (P > 0.05) under constant dark conditions. Each data point represents a biologically independent replicate. For panels (a) and (c), boxes show IQR, medians are center lines, whiskers extend to 1.5× IQR. The p-values were calculated by a two-sided Wilcoxon test. *P < 0.05, **P < 0.01, ***P < 0.001.
Source Data
Extended Data Fig. 5 Metagenomics of As- and Fe-related reduction genes.
Relative abundance (metaG) of As and Fe reduction subtype genes between day and night groups (n = 9). Boxes show IQR, medians are center lines, whiskers extend to 1.5× IQR. Each data point represents a biologically independent replicate. The P-values were calculated by a two-sided Wilcoxon test.
Source Data
Extended Data Fig. 6 qPCR of As- and Fe-related reduction genes and taxa.
Absolute abundance of functional genes and microbial taxa in day and night groups measured by qPCR (n = 9). Boxes show IQR, medians are center lines, whiskers extend to 1.5× IQR. These data provide validation for the metagenomic findings. Each data point represents a biologically independent replicate. The P-values were calculated by a two-sided Wilcoxon test.
Source Data
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Yu, H., Wang, Y., Tong, D. et al. Day–night shifts in microbial activity affecting arsenic and iron in the rice rhizosphere.
Nat. Geosci. (2026). https://doi.org/10.1038/s41561-026-01999-y
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DOI: https://doi.org/10.1038/s41561-026-01999-y
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