Ridge-furrow mulching with microbial co-inoculation reshapes the maize rhizosphere microbiome to enhance water and nitrogen use efficiency

In rainfed agroecosystems with limited water resources, ridge-furrow plastic film mulching (RFPM) combined with microbial inoculation has shown great potential for enhancing grain yield and water use efficiency (WUE). However, how RFPM reshapes the soil microenvironment to promote the recruitment of beneficial taxa by microbial inoculants and how these interactions vary across maize developmental stages remain poorly understood. Here, we integrated 16S rRNA gene amplicon sequencing and shotgun metagenomics, and field validation to elucidate the microbial mechanisms underlying improved water and nitrogen use efficiency in maize under two cultivation practices, flat planting (FP) and RFPM, combined with the co-inoculation of Rhizophagus irregularis and Bacillus velezensis (FP-AB and RFPM-AB). Compared with the other three treatments, the RFPM-AB treatment increased soil water content (SWC), bacterial diversity, and the enrichment of Klebsiella and Pseudomonas in both the rhizosphere and endosphere at the silking stage (VT), and enhanced the proportion of macroaggregates (250–1000 μm) at the physiological maturity stage (R6). It also enhanced WUE, nitrogen use efficiency (NUE), and grain yield. Compared with the R6 stage, the VT stage was more responsive, showing lower α-diversity, greater network complexity, broader niche breadth, higher abundances of functional genes associated with nitrogen (N) and phosphorus (P) cycling. At the VT stage, RFPM-AB treatment particularly enhanced the abundances of genes involved in anammox, N fixation and ABC transporter in the rhizosphere. The RFPM-AB treatment enriched the rhizosphere with Klebsiella and Pseudomonas, which are linked to nitrogen fixation (nifH, nifD, nifK), nitrification (amoB), and nitrite reduction (nirB). Strain-level characterization and pot inoculation assays confirmed that Klebsiella sp. YCMR11 and Pseudomonas sp. MR464 possessed diverse plant growth-promoting traits, and field inoculation experiments demonstrated that these strains increased maize grain yield by up to 25.92% relative to uninoculated controls. Collectively, RFPM combined with co-inoculation of R. irregularis and B. velezensis improves soil water content, promotes stage-specific enrichment of rhizosphere taxa and enhances the abundance of genes involved in N cycling, thereby improving maize WUE, NUE, and grain yield under semiarid conditions. This integrated strategy offers a mechanistic foundation for sustainable crop production in water-limited agroecosystems.