Long-term organic fertilizer amendment improves citrus yield and quality in calcareous soil mainly by shaping the microbiome and mobilizing soil phosphorus

Abstract Background and aims Citrus, the largest fruit globally, often encounters nutritional imbalances, notably phosphorus (P) deficiency, when cultivated in calcareous soil. Although organic fertilizers outperform inorganic alternatives in citrus production, their specific impacts and the microbiome’s role in calcareous soil remain unclear. This study aimed to investigate the effects of rapeseed cakes (RC) and cow manure (CM) on citrus plant-soil performance and their correlations with microbiome composition and functional profiles. Methods We conducted a 5-year long-term positioning field experiment on citrus under calcareous soil conditions. Field experiments combined with amplicon and metagenome sequencing were employed to analyze differences in plant-soil performance and rhizosphere microbiome traits under RC and CM treatments. Isolation-culture verification was further performed to validate the function of key differential microorganisms. Results RC and CM supplementation enhanced fruit yield and quality while facilitating P utilization in calcareous soil, with CM showing a better improvement effect. Both organic fertilizers induced significant alterations in rhizosphere microbiome composition and function. The genus Cupriavidus was significantly enriched in rhizosphere under organic fertilizer treatments. Isolation-culture verification confirmed it enhanced soil P availability by secreting organic acids, alkaline phosphatases and other enzymes, serving as plant-growth-promoting rhizobacteria for citrus. Conclusion Our findings clarify the effects of rapeseed cakes and cow manure on citrus growth and soil P activation in calcareous soil, and reveal the key role of the rhizosphere microbiome represented by Cupriavidus in this process. This study advances our understanding of microbiome-mediated improvement of citrus growth and P utilization via organic fertilizer application.