Covering with orchard abandoned branches exerts positive effects on improving the soil micro-ecological environment and enhancing fruit quality

Aims Branch covering can address the challenge of disposing orchard waste branches; however, its regulatory effects on soil microecology remain unclear. This study investigated the impacts of six-year branch covering in a pear orchard on soil microecology and fruit quality. Methods Soil physicochemical properties, microbial communities, soil transcriptome, soil metabolites, and fruit quality were analyzed under branch covering. Multi-omics approaches were integrated to elucidate changes in the soil microecological system. Results Branch covering significantly increased soil nutrient content and enzyme activity, and improved fruit quality. Although dominant microbial species remained unchanged, covering modulated community composition, reducing high-abundance taxa while enriching low-abundance ones, thereby enhancing microbial community stability and evenness. Microbial assembly was primarily governed by stochastic processes. Key enriched metabolic pathways included "Metabolic pathways" and "Biosynthesis of antibiotics." Critical metabolites identified were 4-guanidinobutanal, theobromine, chorismate, histamine, and D-glucuronic acid 1-phosphate. Six differentially expressed genes (e.g., GC5_TRINITY_DN187820_c0_g1) associated with chorismate regulation and GC2_TRINITY_DN296510_c0_g1 linked to D-glucuronic acid 1-phosphate were identified. It has been clarified that six bacterial microorganisms, including Paraburkholderia caffeinilytica CF1 and Paenarthrobacter aurescens TC1, participate in the regulation of chorismate through chorismate lyase and chorismate synthase. Additionally, covering reduced levels of potentially toxic compounds such as diaminochlorotriazine and histamine, suggesting a possible role in mitigating pesticide residues. Conclusion Branch covering improves soil microecology and enhances fruit quality while offering a sustainable solution for orchard waste management, representing an effective eco-friendly soil management strategy.