Related Experiment Video
Updated: Feb 5, 2026
09:55
Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere
Published on: May 2, 2018
28.2K
Large-scale multi-omics unveils host-microbiome interactions driving root development and nitrogen acquisition
Nannan Li1, Guoliang Li2, Xiaofang Huang3,4,5
1College of Resources and Environment, and Academy of Agricultural Sciences, Southwest University, Chongqing, China. linannan2013@swu.edu.cn.
Nature Plants
|February 3, 2026
Summary
Understanding the plant root microbiome is key for crop nutrition. This study links plant genetics, root gene regulation, and microbiome assembly to nitrogen uptake, identifying Sphingopyxis as a beneficial bacterium for crop improvement.
Area of Science:
- Plant Science
- Microbiome Research
- Genetics
Background:
- The rhizosphere microbiome significantly impacts plant health and nutrition.
- Mechanisms connecting host genetics, root gene regulation, and microbiome assembly to plant nutritional traits are not well understood.
Purpose of the Study:
- To investigate the interplay between host genetic variation, root gene expression, and rhizosphere microbiome assembly.
- To understand how these factors collectively influence plant nutritional traits, specifically nitrogen uptake.
Main Methods:
- Integration of 1,341 paired datasets: root transcriptomes, bacterial 16S rRNA profiles, and root ionomes from 175 Brassica napus ecotypes.
- Genome-wide association studies (GWAS) to identify host loci regulating microbial abundance.
- Isolate-level inoculation, whole-genome sequencing, metabolite profiling, and confocal imaging to functionalize bacterial roles.
Main Results:
- Identified 203 highly heritable bacterial amplicon sequence variants (ASVs), many associated with root nitrogen (N) levels.
- Host gene expression and microbial features explained up to 45% of variation in N uptake.
- Discovered host loci regulating ASV abundance, linked to carbon and N metabolism.
- Demonstrated that Sphingopyxis modulates auxin biosynthesis, promoting lateral root development for enhanced N acquisition.
Conclusions:
- Sphingopyxis is a functionally relevant bacterial genus that enhances nitrogen acquisition.
- This study provides insights into microbiome-assisted breeding for developing nutrient-efficient crops.
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