Accession PRJCA001214
Title NRT1.1B contributes to the host-dependent variation and functional divergence of the root microbiome between rice subspecies in the field
Relevance Agricultural
Data types Metagenome
Organisms root metagenome
Description The root microbiome extends the functional repertoire of the plant genome and is essential for plant growth and health in natural environments. Variation and functional divergence in the root microbiome among a population of plants and the corresponding host genetic basis remain to be ascertained. We find that two rice subspecies, indica and japonica, recruit distinct root microbiomes with robust biomarker taxa under field conditions. Many indica-enriched bacteria are related to the nitrogen cycle. Notably, NRT1.1B, a nitrate transporter and sensor, regulates a substantial proportion of indica-specific bacterial taxa. Metagenomic sequencing reveals that the ammonification pathway is dramatically impaired in the root microbiome of the nrt1.1b mutant. We establish comprehensive root bacterial culture collections representing more than 70 percent of bacterial species that are reproducibly detectable by culture-independent sequencing. With the synthetic community approach, we found that indica-enriched bacteria have stronger ability to promote rice growth under the organic nitrogen condition than bacteria enriched in japonica. Our results provide insights into the integration of the root microbiome, soil nutrient cycles, host genetic regulation, and plant traits, which could thus facilitate microbiome-based improvements in sustainable agriculture.
Sample scope Multispecies
Release date 2019-01-25
PubMed ID Article title Journal name DOI Year
NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice Nature Biotechnology 10.1038/s41587-019-0104-4 2019
Agency program Grant ID Grant title
Chinese Academy of Sciences (CAS) XDB11020700
Chinese Academy of Sciences (CAS) XDA08010104
Submitter Yong-Xin    Liu  (
Organization Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
Submission date 2019-01-17

Project Data

Resource name Description
BioSample (834)  show -
GSA (2) -
CRA001362 Rice nrt1.1b related root metagenome
CRA001372 Rice subspecies indica and japonica, and NRT1.1b related 16S amplicon sequencing