Regulatory role of rhizosphere microbial structure and function in yield formation of ratooning season rice

In ratoon rice cultivation, the formation of tillers from stubble following the harvest of the main crop rice is crucial for achieving high and stable yields during the ratooning season. This study employed two rice varieties, YongYou1540 (YY1540) and JinHui809 (JH809), which exhibited comparable yields in the main crop season but markedly different yields in the ratooning season. We systematically compared changes in the physicochemical properties of the rhizosphere soil, as well as the microbial community structure and functional characteristics, between the two varieties at different growth stages during their ratooning seasons (0, 10, and 20 days after harvest). Our results revealed that microbial nutrient-acquiring enzyme activities were significantly higher in YY1540 compared to JH809. Analysis of rhizosphere microbial communities indicated that community diversity (e.g., Chao1) and network properties (e.g., robustness) had limited effects on the yield of ratooning season rice. In contrast, the functional features of the microbiome-particularly the abundances of carbon fixation genes (e.g., acsA, acsB), carbon degradation genes (e.g., malQ, pulA), and phosphorus cycling genes (e.g., pstS, ppx)-were significantly higher in YY1540. Furthermore, Mantel tests indicated that nutrient-cycling functional genes in the rhizosphere microbiome were significantly associated with soil nutrient indices, such as available phosphorus (AP), extractable organic carbon (EOC), and dissolved organic carbon (DOC), as well as the status of microbial nutrient limitation (e.g., VA) and yield of ratooning season rice. Notably, functional genes involved in carbon and phosphorus cycling exhibited particularly strong associations with AP, EOC, and yield of ratooning season rice. Collectively, the increased abundances of key functional genes (e.g., acsA and pstS), along with elevated activities of β-1,4-glucosidase and acid phosphatase, alleviated carbon and phosphorus limitations, improved nutrient supply efficiency during the regrowth stage, and ultimately enabled YY1540 to achieve higher yields in ratooning season rice. This study provides initial evidence for the crucial role of rhizosphere microbial functions in the yield formation of ratooning season rice. It offers a novel theoretical framework and practical pathway for the precision management and sustainable intensification of ratoon rice through microbial regulation.