Large-scale multi-omics unveils host–microbiome interactions driving root development and nitrogen acquisition

nature plants Article https://doi.org/10.1038/s41477-025-02210-7 Large-scale multi-omics unveils host– microbiome interactions driving root development and nitrogen acquisition Received: 24 April 2025 Accepted: 11 December 2025 Published online: 3 February 2026 Check for updates Nannan Li 1,13 , Guoliang Li 2,13, Xiaofang Huang 3,4,5,13, Lige Ma1,13, Danning Wang6,13, Yu Luo1,13, Xulv Cao1, Yantao Zhu7, Jianxin Mu7, Ran An7, Jianhua Zhao7, Yongfeng Wang8, Cuiling Yang8, Hao Chen8, Ying Xu9, Lixi Jiang 9, Meng Luo10, Xiaodan Li10, Yachen Dong10, Xinping Chen 1,11, Frank Hochholdinger12, Yong Jiang 2, Jochen C. Reif 2, Daojie Wang 8 , Yanfeng Zhang 7 , Yang Bai 5 & Peng Yu 3,4 The rhizosphere microbiome plays a crucial role in determining plant performance and fitness. Nevertheless, regulatory mechanisms linking host genetic variation, root gene regulation and microbiome assembly— and their collective influence on plant nutritional traits—remain poorly understood. Here we generated and integrated 1,341 paired datasets, including root transcriptomes, rhizosphere bacterial 16S rRNA profiles and root ionomes, across 175 resequenced Brassica napus ecotypes grown at two contrasting field sites. We identified 203 highly heritable bacterial amplicon sequence variants (ASVs), many of which were significantly associated with root nitrogen (N) levels. Host transcriptome-wide gene expression and these microbial features together explained up to 45% of natural variation in N uptake while genome-wide association analyses revealed host loci regulating ASV abundance, many of which were under the control of eQTL hotspots linked to carbon and N metabolism. Isolate-level inoculation, whole-genome sequencing, metabolite profiling and confocal imaging demonstrated that the dominant, genetically regulated bacterial genus Sphingopyxis modulates auxin biosynthesis and promotes lateral root development to enhance N acquisition under stress. This study therefore identifies Sphingopyxis as a functionally relevant taxon with potential for microbiome-assisted breeding of nutrient-efficient crops. The rhizosphere, defined as the soil region surrounding plant roots, is a unique and dynamic environment where complex biological interactions occur between the plant root system and the diverse array of soil microbes collectively known as the rhizosphere microbiome1. The rhizosphere microbiome influences root traits and functions that directly impact plant health2, contributes to nutrient homeostasis in the host3, offers protection against both biotic and abiotic stresses4, modulates the plant’s developmental program5 and is a key driver of A full list of affiliations appears at the end of the paper. Nature Plants | Volume 12 | February 2026 | 319–336 broader ecosystem functioning6. Microbes residing in the rhizosphere and on plant roots harbour a diverse range of functional traits, including metabolic properties7–10 and immune system-related functions11,12. Even small host-mediated changes in the microbiome can substantially affect host fitness13. Interestingly, while the host genotype does influence the microbiome, its effect is relatively modest compared to the strong impact of soil edaphic factors14,15. Genome-wide association studies (GWAS) provide an efficient means to identify genetic variations e-mail: ; ; ; ; 319 Article https://doi.org/10.1038/s41477-025-02210-7 associated with specific microbial communities16. Quantitative analyses of microbiome composition, along with plant genetic diversity, have facilitated the identification of heritable microbial traits, enabling their incorporation into GWAS as potential phenotypes17–23. Nevertheless, despite these advancements, a comprehensive understanding of how the rhizosphere microbiome forms and is regulated by host gene expression beyond its influence on plant fitness and agroecosystem functions species remains elusive in crops. Nitrogen is the most important macro-mineral element for plants in terms of quantity, playing a critical role in crop yield and overall plant health. However, the excessive use of nitrogen fertilizers in agriculture has become a global environmental concern, posing dramatic threats to ecosystems and human health24,25. Over the past decades, nitrogen fertilizer application to terrestrial soils has contributed to ~60% of the increase in atmospheric nitrous oxide emissions, a potent greenhouse gas26,27. Mineral nutrients, including nitrogen, are absorbed by plants through their elaborate root systems, which interact with the surrounding rhizosphere28. Numerous studies have shown that beneficial symbiotic relationships between plant roots and rhizosphere microbes can enhance plant performance by improving nutrient uptake, including nitrogen29,30. Growing genetic evidence suggests that the root microbiome plays a pivotal role in enhancing plant nutrient uptake, for example, nitrogen acquisition31–33. Furthermore, the microbiome is involved in directly sensing phosphate stress in the soil, as shown in research on plant–microbe interactions34. These findings highlight the importance of the rhizosphere microbiome in regulating nutrient dynamics, with implications for both sustainable agriculture and minimizing the environmental impact of fertilizer use. In this context, understanding the genetic basis and regulatory variation of host–microbiome associations is crucial for deciphering the mechanisms that underlie the formation and function of the crop microbiome, particularly in relation to plant nutrition. The present study takes an integrative approach, combining rhizosphere microbiome analyses with host GWAS and transcriptome-wide association studies (TWAS) across two independent environments. By quantifying the interactions among genotypes, environmental factors and plant nutritional status, the study aims to predict the overall fitness and health of rapeseed (Brassica napus) plants. The findings provided insights into the beneficial associations between the soil microbiome and the plant root system, offering a pathway for developing crop varieties with optimized root phenotypes. Such varieties would be designed to recruit and activate microbiomes that confer a range of benefits, including enhanced crop productivity, more efficient nutrient acquisition and improved agroecosystem resilience. By leveraging the genetic basis, gene regulation and microbiome interactions identified in this study, it may be possible to improve crop health and sustainability in agricultural systems, ultimately contributing to more efficient and eco-friendly farming practices. Results Fig. 1 | Genomic and transcriptomic analyses of host–bacterial microbiome association and plant nutritional traits in B. napus. a, A schematic overview of omics datasets used in this study. WGS SNPs data for rapeseed accessions (n = 175) were derived from ref. 44. RNA-seq SNP data were extracted from RNA sequencing results for both KF and YL locations. Iono (...truncated)