Maize stalk lodging causes substantial yield losses worldwide. Although stalk strength is a genetically determined trait, its molecular mechanisms—particularly the dynamic changes during key developmental stages—remain inadequately characterized due to limitations of single-omics approaches. This study employed an integrated transcriptomic and metabolomic analysis strategy to compare stalk tissues from three maize genotypes with contrasting lodging resistance: the highly resistant inbred line PHB1M, the susceptible inbred line Chang 7-2, and their recombinant inbred line 23NWZ561 (abbreviated as P, C, and Z, respectively). Dynamic sampling of all three genotypes was conducted at both grain-filling and maturity stages, with simultaneous measurement of physiological traits related to stalk strength. Phenotypic analysis revealed that the resistant genotype PHB1M exhibited superior rind penetration strength, cell wall composition (cellulose, hemicellulose, and lignin) content, and vascular bundle development. Multi-omics analysis indicated that the molecular basis of lodging resistance is primarily established during the maturity stage. The transcriptomic and metabolomic profiles of the recombinant inbred line Z shifted from clustering with the susceptible parent C at the grain-filling stage to grouping with the resistant parent P at maturity. Key pathways including phenylpropanoid biosynthesis were significantly enriched specifically at maturity, accompanied by upregulation of related genes (PAL, HCT, CCR) and accumulation of metabolites such as lignin precursors in PHB1M. Integrated analysis identified a core co-expression network within the phenylpropanoid pathway comprising three genes and three metabolites. This study systematically demonstrates that lodging resistance in maize is regulated by transcriptional and metabolic reprogramming during late stalk developmental stages, particularly at maturity, where enhanced activation of the phenylpropanoid biosynthesis pathway plays a central role. These findings provide valuable candidate genes and metabolic markers for breeding lodging-resistant maize varieties.

In mitigating agricultural nitrous oxide (N₂O) emissions, partially substituting chemical nitrogen (N) fertilizers with organic amendments is widely advocated for; however, the effectiveness of this approach varies, and the optimal substitution ratio remains unclear. This study employed a long-term field experiment in a maize cropping system, integrating in situ N₂O flux monitoring, soil analysis, and metagenomic sequencing to investigate the effects of substituting synthetic N fertilizer with sheep manure at different ratios (one-sixth, one-third, and full substitution) on cumulative N₂O emissions and underlying microbial mechanisms. The results showed that substituting one-third of chemical N with sheep manure (OF2) most effectively reduced cumulative N₂O emissions, by 18.64% (2021) and 47.00% (2022), compared to conventional chemical fertilization (NPK). This treatment optimized key soil properties, significantly lowering soil nitrate (NO₃⁻-N) and ammonium (NH₄⁺-N) concentrations while increasing soil organic matter. Metagenomic analysis revealed that the mitigation was primarily driven by a coordinated shift in the nitrogen-cycling microbial functional gene network: OF2 significantly enhanced the abundance of N₂O reductase genes (nosZ clades I and II) and increased the nosZ/(nirK + nirS) gene ratio, thereby strengthening the genetic potential for complete denitrification (N₂O → N₂). Partial least squares path modeling confirmed that soil properties indirectly reduced N₂O emissions, primarily by regulating the microbial community and functional gene abundances. This study provides mechanistic evidence that partial organic substitution (with one-third sheep manure) mitigates N₂O emissions by optimizing the soil habitat and reprogramming the functional gene network of nitrogen-cycling microbes, with a key emphasis on enhancing the N₂O reduction pathway.