Soil microbial mechanisms promoting ultrahigh rice yield

Abstract Improving rice yield potential is crucial for global food security. Taoyuan, China, is famous worldwide as a special ecosite for ultrahigh rice yield. Climatological factors affecting this phenomenon have been identified, but the potential molecular processes and environmental mechanisms promoting ultrahigh yield remain mysteries. This study presents detailed results on factors from soil microbial community structure to metagenomic functions during four key rice growth stages, together with results from nitrogen enrichment experiments and rice root transcriptome analysis, to identify potential soil biotic factors affecting ultrahigh yield. Our results show that Taoyuan has more diverse bacterial taxa, less diverse fungal taxa, and a 10-fold-stronger connection among microbial taxa as well as a significantly higher proportion of nutrient transport functions than a regular site. Notably, our metagenomic analysis shows that Taoyuan contains more taxa with nitrogen metabolism functions and a higher abundance of genes involved in the nitrification process (e.g., hydroxylamine oxidoreductase and nitric oxide dioxygenase), promoting effective transformation of ammonium (NH4+) to nitrate (NO3−) in rice fields and stimulating high expression of nitrate transporters in rice roots, leading to ultrahigh yields. Our results reveal the non-meteorological mechanisms that promote ultrahigh rice yield in Taoyuan, enhancing knowledge regarding the potential soil microbial mechanism in crops with ultrahigh yield.