The rhizosphere microbiome facilitates a range of beneficial functions for its host plant. Thus, exploring the functionality of the rhizosphere microbiome and its underlying driving factors are fundamental for understanding how host plants benefit from their microbial symbionts. Herein, we utilized deep metagenomics sequencing to explore the rhizosphere microbiome in three rice (Oryza sativa L.) cultivars (hybrid rice and two japonica cultivars) that were planted in three spatially distant locations. Although rhizosphere prokaryotic communities were primarily affected by planting location, rice genotype signs were still detected. After the effect of planting location was ruled out, the top 24 genotype-discriminatory taxa were found to contribute 85.2% of the diagnostic accuracy for rice cultivars. The significant associations between the measured enzyme activities and the relative abundances of their coding genes validated that the recruitment of different rhizosphere microbes by hybrid rice and japonica cultivars further resulted in divergences in microbe-mediated functions. Compared with that in japonica, the rhizosphere in hybrid rice more efficiently mineralized N and P from organic matter, while mitigated N and K losses. The structural equation model depicted that the rice cultivars imposed direct (host-genotype-associated feature) and indirect (recruitment of specific rhizosphere microbiomes) effects on yield. Collectively, a conceptual model was constructed to infer the collective interplay among rice cultivars, rhizosphere microbiomes, and yield. Our findings provided novel insights into the molecular mechanism underlying the associations among rice cultivars, rhizosphere microbiomes, and yield.

根际微生物组为其寄主植物提供了一系列有益的功能。因此，探索根际微生物组的功能及其潜在驱动因素对于了解宿主植物如何从其微生物共生体中受益至关重要。在此，我们利用深度宏基因组学测序来探索三种水稻（Oryza sativa L.）栽培品种（杂交水稻和两种粳稻）的根际微生物群落。栽培品种），种植在三个空间遥远的位置。尽管根际原核生物群落主要受种植地点的影响，但仍检测到水稻基因型迹象。在排除种植地点的影响后，发现前 24 个基因型判别类群对水稻品种的诊断准确率贡献了 85.2%。测量的酶活性与其编码基因的相对丰度之间的显着关联证实，杂交水稻和粳稻品种对不同根际微生物的募集进一步导致了微生物介导功能的差异。与粳稻相比，杂交水稻的根际更有效地从有机物质中矿化了 N 和 P，同时减轻了 N 和 K 的损失。结构方程模型描述了水稻品种对产量产生直接（宿主基因型相关特征）和间接（特定根际微生物群的招募）影响。总的来说，构建了一个概念模型来推断水稻品种、根际微生物群落和产量之间的集体相互作用。我们的研究结果为水稻品种、根际微生物群落和产量之间关联的分子机制提供了新的见解。