NRT1.1B contributes to the host-dependent variation and functional divergence of the root microbiome between rice subspecies

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.