Long-Term Biogas Digestate Application Reshapes Root-Zone Soil Microbiomes, Enhancing Fruit Quality and Leaf Physiology in Pear Trees

Biogas residue is a valuable by product of organic waste recycling with potential to enhance soil quality. However, its long-term effects on root-zone soil microbial communities, leaf physiology, and fruit quality in perennial fruit crops such as pear remain poorly understood. In this study, a ‘Huangguan’ pear orchard managed with five consecutive years of biogas digestate application (Z) was compared against a treatment without digestate history (CK) in North China. Soil organic matter, bacterial (16S) and fungal (ITS) community profiles, fruit quality traits, and leaf physiological and anatomical parameters were comprehensively evaluated. Compared with CK, long-term biogas digestate application significantly increased soil organic matter content by 16.45% and 18.27% at soil depths of 20 cm and 40 cm, respectively. Principal coordinate analysis revealed pronounced structural divergence in both bacterial and fungal communities between orchards. At 20 cm depth, the bacterial Chao1 and Shannon diversity indices in Z were significantly higher by 15.23% and 3.98%, respectively, accompanied by a 479.59% surge in the relative abundance of Bacillus. In the 40 cm layer, fungal OTU richness increased by 45.34%. The application of biogas digestate promoted the enrichment of functional microbial taxa, including Solicoccozyma aeria, Sphingomonas, Chaetomiaceae, Lophotrichus, Bacillus, Streptomyces, and Acinetobacter pittii. Fruit soluble solids content in Z consistently exceeded CK by 22.36% in 2024 and 7.56% in 2025. Single fruit weight was 10.21% greater in 2024. Leaf water content increased by 23.08% in 2024 and 97.22% in 2025, alongside a 28.57% enhancement in the leaf effective quantum yield of the photosystem in 2025. Overall, long-term biogas digestate application reshapes the root-zone soil microbial community and augments soil fertility; meanwhile, fruit quality and leaf physiological function were improved in pears.