Abstract
Amino acids are plant-available organic nitrogen (N) that can be directly absorbed, but their availability relies on microbial decomposition of organic matter in the soil. Natural variation in Lysine-Histidine-Type Transporter-1 (OsLHT1) (NCBI Gene ID: 3974662) is associated with higher amino acid uptake in japonica rice than in indica. However, how this genetic variation influences rhizosphere microbiome assembly and its subsequent impact on amino acid acquisition remains unclear. In this study, we demonstrate that the OsLHT1a allele in japonica is prevalent in rice grown in high-organic-N soils, where it recruits a distinct rhizosphere microbiome to enhance amino acid acquisition. A synthetic microbiota composed of bacteria enriched by the OsLHT1a allele in japonica enhanced amino acid production in soil through organic matter decomposition and increased root amino acid uptake by upregulating OsLHT1 gene expression. The rhizosphere colonization of the synthetic microbiota was specifically driven by the function of OsLHT1. Notably, organic fertilization facilitated this colonization, thereby improving organic N use efficiency and rice yield. This root–rhizosphere microbiome functional synergy under organic fertilization presents a promising strategy to increase organic fertilizer use efficiency and demonstrates the potential for harnessing plant-gene-associated rhizosphere microbiomes for sustainable agriculture.
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Data availability
The raw 16S rRNA sequence data that support the findings of this study are openly available via the Beijing Institute of Genomics Data Center, Chinese Academy of Sciences, under BioProject accession no. PRJCA038661 at https://ngdc.cncb.ac.cn/bioproject/. Source data are provided with this paper.
Code availability
This study only used base R packages, which are publicly available and can be downloaded from CRAN. Python analyses relied on pandas (v2.2.2), available on Python Package Index (PyPI) and installable via ‘pip install pandas’.
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Acknowledgements
This research was financially supported by the National Key Research and Development Program (grant nos 2021YFF1000403 to G.X. and R.Z. and 2022YFF1001804 to R.Z.), the National Natural Science Foundation of China (grant nos 32172661 and 32361143785 to R.Z. and 32272803 to W.X.) and the Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education of China (grant no. JYB2025XDXM703 to R.Z.). The authors are grateful to N. Guo from Yangzhou University for her valuable suggestions on the experimental design.
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R.Z., G.X., W.X., Q.S., A.M. and S.Z. designed the study. A.M. and S.Z. performed the experimental work and conducted the sampling. A.M., S.L. and H.H. conducted the DNA purification and organized the sequencing. G.X., S.Z. and W.W. provided the rice materials. A.M. carried out the bioinformatics and statistical analysis. W.X. and A.M. drafted the manuscript, and R.Z., G.X., W.X. and S.Z. revised it. All authors helped review, edit and complete the manuscript.
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Extended data
Extended Data Fig. 1 Total nitrogen content in roots and shoots of OsLHT1a and OsLHT1b haplotypes under organic and inorganic fertilized soils.
a. Total nitrogen in root. b. Total nitrogen in shoot. n = 42 biologically independent samples (including 7 cultivars with 6 biological replicates per cultivar). Values represent means ± s.d. Two-way ANOVA showed significant effects of Genotype (F(1, 136) = 25.64, p < 0.0001), Fertilization (F(1, 136) = 20.52, p < 0.0001), and their interaction (F(1, 136) = 25.98, p < 0.0001) on roots. For shoots, significant effects of Genotype (F(1, 136) = 24.49, p < 0.0001), Fertilization (F(1, 136) = 13.89, p = 0.0003), and a marginal effect of Genotype:Fertilization interaction (F(1, 136) = 3.89, p = 0.051). Different letters above bars indicate significant differences between groups (p < 0.05) based on one-way ANOVA followed by Tukey’s HSD post-hoc test. A two-sided t-test was performed to compare the total nitrogen in the shoot and in the root of OsLHT1a and OsLHT1b grown in organic and inorganic N fertilization soils.
Source data
Extended Data Fig. 2 Enzyme activity and amino acid production of the isolated strains.
a. Protease activity (U·ml⁻¹), b. Asparagine (mg·L⁻¹), c. Glutamine (mg·L⁻¹), d. Nitrate (mg·L⁻¹) e. Ammonium (mg·L⁻¹). Different letters above bars indicate significant differences between groups (p < 0.05) based on one-way ANOVA followed by Tukey’s HSD post-hoc test. Values represent means ± s.d., n = 3 biologically independent samples.
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Extended Data Fig. 3 Functional relationship of rhizosphere bacterial strains.
a. OsLHT1 expression. b. Amino acid in rhizosphere soil(mg·kg⁻¹). c. Amino acid in shoot(mg·kg⁻¹). d. Amino acid in root(mg·kg⁻¹). Different letters above bars indicate significant differences between groups (p < 0.05) based on one-way ANOVA followed by Tukey’s HSD post-hoc test. The F-values indicate the ratio of between-group variance to within-group variance, p-values represent the statistical significance of the differences, and partial R² indicates the effect size, representing the proportion of total variance explained by the treatment factor. Values represent means ± s.d. For a, n = 72 biologically independent samples, representing 10 varieties, with 4 OsLHT1a haplotypes and 4 OsLHT1b haplotypes. Each haplotype had 6 biologically independent samples, with 12 biologically independent samples for the LHT1/LHT1 and LHT1/lht1 genotypes. For b,c and d, n = 30 biologically independent samples, representing 10 cultivars, with 3 biologically independent samples per cultivar.
Source data
Extended Data Fig. 4 SynM enhances growth and organic N uptake in OsLHT1 genotypes under organic and inorganic fertilization.
a-b. Shoot height, Total nitrogen in shoot and root of lht1/lht1, LHT1/LHT1, and LHT1/lht1 under CK and SynM treatments in organic (a) and inorganic N (b) fertilization soil. A two-sided t-test was performed to compare the differences between the non-inoculated (CK) and SynM-inoculated groups, values represent means ± s.d. (n = 3 biologically independent samples).
Source data
Extended Data Fig. 5 Effect of SynM on OsLHT1a and OsLHT1b in cross-generation experiment.
a-b. Shoot height, shoot dry weight, Total nitrogen in shoot and root of 4 OsLHT1a and 4 OsLHT1b haplotypes under CK and SynM treatments across first and second generations in organic (a) and inorganic N (b) fertilization soil. A two-sided t-test was performed to compare the differences between the non-inoculated (CK) and SynM-inoculated groups, values represent means ± s.d., The analysis was based on 16 biologically independent samples for shoot height and shoot dry weight (4 cultivars with 4 replicates per cultivar), and 12 biologically independent samples for total nitrogen in shoot and total nitrogen in root (4 cultivars with 3 replicates per cultivar).
Source data
Extended Data Fig. 6 Effect of SynM on LHT1/LHT1, LHT1/lht1 and lht1/lht1 in cross-generation experiment.
a-b. Shoot height, shoot dry weight, Total nitrogen in shoot and root, and Amino acid in shoot and root of lht1/lht1, LHT1/LHT1, and LHT1/lht1 under CK and SynM treatments across first and second generations in organic (a) and inorganic N (b) fertilization soil. A two-sided t-test was performed to compare the differences between the non-inoculated (CK) and SynM-inoculated groups, values represent means ± s.d., n = 3 biologically independent samples.
Source data
Extended Data Fig. 7 SynM enhances growth and organic N uptake of OsLHT1a and OsLHT1b cultivars under field conditions.
a-b. Shoot height, tillering number, Total nitrogen in shoot and root of 4 OsLHT1a and 4 OsLHT1b haplotypes under CK and SynM treatments during the tillering stage under long-term organic (a) and inorganic N fertilization (b). A two-sided t-test was performed to compare the differences between the non-inoculated (CK) and SynM-inoculated groups. Values represent means ± s.d., the analysis was based on 16 biologically independent samples for shoot height and tiller number (4 cultivars with 4 replicates per cultivar), and 12 biologically independent samples for total nitrogen in shoot and total nitrogen in root (4 cultivars with 3 replicates per cultivar).
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Ma, A., Xun, W., Zhang, S. et al. Amino-acid-transporter-mediated assembly of rhizosphere microbiota enhances soil organic nitrogen acquisition in rice.
Nat. Plants (2026). https://doi.org/10.1038/s41477-025-02217-0
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DOI: https://doi.org/10.1038/s41477-025-02217-0
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