Effects of exogenous microbial fertilizer and in situ green manure management on soil microbial community structure and predicted functional potential in Korla fragrant pear orchards

Abstract

Long-term chemical fertilizer overuse has degraded soil quality in Korla fragrant pear orchards of Xinjiang, causing reduced organic matter accumulation, nutrient imbalance, and microbial community shifts. However, the effects of exogenous microbial fertilizers and endogenous green manure, particularly under different planting densities, on soil microbiome regulation in sandy orchards of southern Xinjiang remain unclear. Here, a 7–8-year-old Korla fragrant pear orchard was subjected to six fertilization treatments: conventional fertilization (CK), microbial fertilizer (JF), low- and high-density * Melilotus officinalis * (CM1 and CM2), and low- and high-density sunflower (* Helianthus annuus *) (DK1 and DK2). Soil physicochemical properties, 16S rRNA and ITS amplicon sequencing, and PICRUSt2-based functional prediction were integrated to evaluate treatment effects on soil properties, microbial communities, and predicted functional potential. Organic fertilization generally reduced electrical conductivity (EC) and improved organic matter and available nutrients. Among treatments, CM1 showed relatively favorable soil improvement, reducing EC by 19.20% and increasing alkali-hydrolyzable nitrogen and total nitrogen by 36.20 and 36.83%, respectively. JF significantly increased fungal diversity, with the Chao1 index rising by 48.6%, while green manure species and planting density strongly influenced bacterial and fungal community structures. All organic fertilization treatments reduced the relative abundance of *Fusarium*, with CM1 showing the greatest decrease (29.8–60.0%). Functional prediction revealed distinct microbial responses: JF enhanced pathways related to fatty acid β-oxidation and lysine fermentation, with associated gene abundances increasing by 11.86 and 203.32%, respectively; CM1 increased butyrate fermentation-related predicted functions and reduced several denitrification-related predicted functions; DK1 mainly enhanced glycolysis and the tricarboxylic acid cycle, whereas DK2 showed greater potential in nitrogen cycling and phosphorus transformation-related functions. RDA indicated that bacterial functional profiles were associated with soil available potassium, alkali-hydrolyzable nitrogen, and total nitrogen. Under the conditions of this experiment, different fertilization strategies altered soil microbial communities by modifying environmental conditions and microbial assembly patterns. CM1 showed relatively strong potential for improving soil properties and regulating microbial communities, while microbial fertilizer and sunflower treatments exhibited distinct functional responses. These findings provide insights into green manure and microbial fertilizer management in arid-region pear orchards of southern Xinjiang.