Effect of rice (Oryza sativa L.) genotype on yield: Evidence from recruiting spatially consistent rhizosphere microbiome

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.