Organic manure and grass mulching are widely recognized as modifiers of soil microbial communities and nutrient dynamics; however, the combined effects of these practices on nitrogen fractionation and microbial functionality in orchard ecosystems remain poorly understood. This study conducted a comprehensive evaluation of soil nitrogen fractions, enzymatic activity, microbial diversity and functional traits in walnut orchards under three management practices: organic manure (OM), grass mulching combined with manure (GM), and chemical fertilization (CF) in China’s Loess Plateau. The results revealed that OM and GM significantly enhanced soil nutrient pools, with GM elevating total nitrogen by 1.96-fold, soil organic carbon by 97.79%, ammonium nitrogen by 128%, and nitrate nitrogen by 54.56% relative to CF. Furthermore, the OM significantly increased the contents of total hydrolysable nitrogen, amino sugar nitrogen, amino acid nitrogen, ammonia nitrogen, hydrolysable unidentified nitrogen, non-acid-hydrolyzable nitrogen compared to the CF and GM treatments. Meanwhile, ASN and AN had significant effects on mineral and total nitrogen. The OM and GM had higher activities of leucine aminopeptidase enzymes (LAP), α-glucosidase enzyme, β-glucosidase enzyme (βG), and N-acetyl-β-D-glucosidase enzyme (NAG). Microbial community analysis revealed distinct responses to different treatments: OM and GM enhanced bacterial Shannon index, while suppressing fungal diversity, promoting the relative abundance of copiotrophic bacterial phyla such as Proteobacteria and Chloroflexi. Moreover, GM favored the enrichment of lignocellulose-degrading Ascomycota fungi. Functional annotation indicated that Chemoheterotrophy (43.54%) and Aerobic chemoheterotrophy (42.09%) were the dominant bacterial metabolic pathways. The OM significantly enhanced the abundance of fermentation-related genes. Additionally, fungal communities under the OM and GM showed an increased relative abundance of saprotrophic taxa, and a decrease in the relative abundances of potential animal and plant pathogenic taxa. The Random forest model further confirmed that βG, LAP, and NAG, as well as Basidiomycota, Mortierellomycota, and Ascomycota served as pivotal mediators of soil organic nitrogen fraction. Our findings demonstrated that combined organic amendments and grass mulching can enhance soil N retention capacity, microbial functional redundancy, and ecosystem stability in semi-arid orchards. These insights support the implementation of integrated organic management as a sustainable approach to enhance nutrient cycling and minimize environmental trade-offs in perennial fruit production systems.

Apple is notoriously difficult to propagate by cuttings, which severely restricts the large-scale production of own-rooted dwarfing rootstocks. ‘Y-1’ is a promising apple dwarfing rootstock that has been newly bred in China, but its recalcitrant rooting limits its application as an own-rooted stock. In this study, three-year-old ‘Y-1’ stock plants were subjected to three shading rates (40%, 60% and 80%) for 7, 14 and 21 days before cutting collection, and the rooting performance, endogenous hormone and phenolic profiles, antioxidant enzyme activities, and transcriptomic responses of the shoots and cuttings were systematically investigated. Shading of stock plants significantly promoted adventitious rooting, with the combination of 60% shading for 14 days giving the highest rooting rate (39.74%), compared with 5.13% in the unshaded control at the same stage. During shading, leaf chlorophyll content increased with shading intensity and peaked at day 14; phloem indole-3-acetic acid (IAA) and gibberellin (GA₃) contents remained higher than the control, whereas abscisic acid (ABA) and major phenolics (phloridzin, chlorogenic acid, quercitrin and rutin) declined. Transcriptome analysis of the phloem (full light vs. 60% shading at days 7 and 14) identified up to 10,944 differentially expressed genes (DEGs), which were significantly enriched in plant hormone signal transduction, MAPK signaling and plant–pathogen interaction pathways. Shading up-regulated auxin biosynthesis and transport genes (YUCCA6, ARG7, LAX2/LAX3, PIN2) and SAUR genes (SAUR20/50/72/78) while down-regulating auxin signaling repressors and receptors (IAA3/13/14/16/17/26/29/30, TIR1, AFB2, ARF5/6/17/19, PIN3) and the ABA-responsive factor DPBF3. During subsequent rooting, shaded cuttings exhibited four rooting phases (callus formation, root primordium induction, root emergence and elongation); higher IAA and GA₃ and lower ABA and total phenols, together with earlier peaks of POD, PPO, and IAAO activities, characterized the shaded, easy-to-root cuttings. These results indicate that pre-cutting shading creates a “rooting-competent” physiological and transcriptional state in stock-plant shoots that is inherited by the cuttings, providing a practical protocol for ‘Y-1’ cutting propagation and mechanistic insight into light-mediated regulation of adventitious rooting in apple.