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

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.

植物根系与种类繁多的土壤源性微生物群落——根际微生物组（root microbiome）——形成共生关联，该群落可拓展植物基因组的功能谱。根际微生物组与宿主植物的稳定互作，对于自然环境中植物的生长与健康至关重要。高通量测序技术已为多种模式植物与作物的根际微生物组组成研究带来全新视角。然而，目前学界对宿主植物种群内根际微生物组的变异模式仍知之甚少，其对应的遗传基础亦尚未阐明。本研究在田间条件下，针对水稻两个亚种——籼稻（indica）与粳稻（japonica）——的根际微生物组变异展开探究。研究发现，代表性籼稻与粳稻品种的根际微生物组存在显著差异。稳健的生物标记物类群可作为区分籼、粳稻的指示性状。诸多籼稻或粳稻特异性细菌类群与养分循环过程密切相关。值得注意的是，NRT1.1B调控了大量籼稻特异性细菌类群。宏基因组测序结果显示，nrt1.1b突变体的根际微生物组中，氨化通路显著下调。富集于籼稻根际的微生物类群（包括与氨化作用相关的细菌）与水稻分蘖过程呈显著正相关。本研究结果为整合根际微生物组、宿主遗传调控与植物性状提供了新的认知，为基于微生物组的可持续农业改良提供了潜在可能。