Stochastic assembly of rhizosphere microbial communities drives super rice yield variation via enhanced nutrient metabolism

Understanding the mechanisms underlying yield differences among rice planting regions is crucial for boosting the yield potential of low-producing regions and ensuring global food security. Although climate factors affecting rice yields in different sites have been widely studied, the microbial ecological processes and environmental mechanisms that promote super rice yields remain poorly understood. This study analyzed the composition, assembly mechanisms, and functions profiles of rhizosphere and soil microbial communities in five representative super rice production regions across China, including Handan (Hebei, temperate zone, drab soil), Xinyang (Henan, subtropical zone, clay loam soil), Xupu and Longhui (Hunan, subtropical zone, paddy soils), and Gejiu (Yunnan, tropical highland paddy soil). Our results revealed that the assembly mechanisms of rhizosphere microbial communities were primarily dominated by stochastic processes (accounting for 79.54 %), mainly including dispersal limitation and undominated processes. In contrast, bulk soil microbial communities were predominantly shaped by deterministic processes (contributing to 72.18 %), primarily homogeneous selection. Distance-decay relationships indicated that bulk soil microbial communities were more susceptible to latitude and environmental factors (R 2 = 0.13, p < 0.001), while rhizosphere microbial communities exhibited greater stability due to the buffered rhizosphere microenvironment. Partial Least Squares Path Modeling further demonstrated that rhizosphere microbes exerted stronger influences on rice growth compared with bulk soil microbes. Further predictions showed that the high-yielding Gejiu site selectively recruited rhizosphere microbes enriched in nutrient cycling and transport pathways, including glyoxylate and dicarboxylate metabolism, inositol phosphate metabolism, and nitrogen metabolism. These functions enhanced nutrient availability and supported higher biomass (70.96 g plant −1 ). Collectively, our findings suggest that the stochastic assembly of rhizosphere microbial communities confers functional stability, and their enrichment in nutrient cycling functions represents a key biological mechanism driving regional differences in super rice yields. • Ecological niche differentiation: rhizosphere (stochastic) and bulk soil (deterministic) • Rhizosphere microbes show higher stability than bulk soil across regions. • Rhizosphere microbes influence super rice productivity more strongly than bulk soil. • High-yield regions recruit microbes enriched in nitrogen-related nutrient cycling. • Enhancing rhizosphere nutrient transformation may sustainably reduce yield gaps.