Rhizosphere Soil Microbiome and Metabolome Responses of Sesame to Different Nitrate-to-Ammonium Nitrogen Ratios: A Multi-Omics Approach

Understanding how rhizosphere microbial communities and root-associated metabolites respond to nitrate-to-ammonium nitrogen ratios is critical for optimizing sesame nitrogen management. Three NO3−-N:NH4+-N ratios (NB1 = 10:0, NB2 = 6:4, and NB4 = 0:10) were applied to assess their effects on sesame agronomic traits, yield, microbial community structure, functional profiles, and metabolomic profiles via metagenomic sequencing and untargeted metabolomics. Samples were collected from four compartments: rhizosphere (H0 and D0) and bulk soils (H1 and D1) of both healthy (H) and diseased (D) plants. The results showed that the NB2 treatment (6:4) achieved the highest seed yield (923.43 kg·ha−1), representing a 7.04% increase compared to NB1 (10:0). The LEfSe analysis identified significantly differential taxa across treatments, with NB2RH0 harboring eight differential bacterial taxa (s_Methylobacterium radiodurans, s_Flavisolibacter ginsenosidimutans, s_Sphingomonas sp_LK11, etc.) and 3 differential fungal taxa (g_Cercospora, o_Mycosphaerellales, and f_Mycosphaerellaceae). Functional annotation via KEGG, CAZy, eggNOG, and GO revealed treatment-specific enrichment of pathways related to Peroxisome (map04146), Biosynthesis of various plant secondary metabolites (map00999), EC 4.1.1.48, GH78, and M00848. PLS-DA and univariate analyses identified multiple metabolites closely associated with disease resistance, including Hamaudol, Nodakenin, Psoralenoside, Rhapontigenin, and Columbianetin acetate in positive ion mode, which were significantly more abundant in healthy-plant rhizosphere soils. In negative ion mode, Pyranonigrin A, Pteroic acid, and Botryaloic acid acetate showed significantly lower abundances in rhizosphere soils of healthy plants than in those of diseased plants. Overall, these findings demonstrate that they significantly shaped rhizosphere microbial communities, functional profiles, and metabolomic profiles. This study provides valuable insights into nitrogen form management for improving soil health in sesame cultivation.