From Soil Amendment to Fruit Quality: Evidence and Uncertainties in Organic Amendment-Driven Regulation of the Rhizosphere Microbiome in Fruit Tree Systems

Excessive chemical fertilization causes orchard soil degradation and fruit quality decline. Organic amendments serve dual functions in nutrient supply and ecological restoration. Yet the causal pathway through which they modulate fruit quality via the rhizosphere microbiome remains poorly understood. This review proposes a cascade framework: “soil amendment → microbiome restructuring → root response → quality formation.” Regulatory evidence at each step is synthesized across organic amendment types. Results indicate that evidence for improvements in soil organic matter and aggregate stability is relatively well established. Shifts in microbial community composition are widely confirmed, yet their associations with soil functions remain predominantly correlative. The causal chain from microbiome to fruit quality has been validated in only a few cases; most underlying mechanisms remain hypothetical. These effects are modulated by tree species, rootstock, soil type, climate, and application regime, and are accompanied by risks of pathogen introduction and heavy metal accumulation. Priority research directions are proposed, including nutrient-matched controls, isotope tracing, re-inoculation of synthetic microbial communities, and multi-site long-term field trials. These directions aim to provide a scientific basis for reducing chemical fertilizer use while enhancing production efficiency in orchards.