NRT1.1B contributes to subspeciation of root microbiome between rice subspecies in the field. Oryza Sativa root microbiome

Plant roots associate with a great diversity of soil borne microbial community, root microbiome, which extend the functional repertoire of plant genome. The stable interaction between root microbiome and host plants is essential for plant growth and health in natural environments. High-throughput sequencing has provided new insights into root microbiome composition in several model and crop plants. However, little is known about the variation pattern of root microbiome in a population of host plants, and the corresponding genetics basis is unknown. In this work, we explored the root microbiome variation between rice subspecies, indica and japonica, in the field conditions. We found that rice root microbiome varied significantly between representative indica and japonica cultivars. Robust biomarker taxa can serve as an indicative trait to differentiate indica and japonica. Many indica or japonica specific bacteria were related with nutrient cycles. Notably, NRT1.1B regulated a substantial amount of indica specific bacterial taxa. Metagenomic sequencing revealed that ammonification pathway was dramatically reduced in the root microbiome of the nrt1.1b mutant. Indica enriched root microbiome members including bacteria related with ammonification positively correlated with rice tilling process. Our results provide insight into integration of root microbiome, host genetic regulation and plant traits, with potentials for microbiome-based improvements in sustainable agriculture.