Multiple long-term observations reveal a strategy for soil pH-dependent fertilization and fungal communities in support of agricultural production

Agricultural fertilization plays a crucial role in crop production, and the fungal communities catalyze transformation of soil nutrients in support of crop production. However, it remains controversial about the optimal strategy for fertilizer inputs and the adaptive mechanisms of fungal communities across China. By using seven long-term field fertilization experiments in China, we analyzed crop yields, soil properties and fungal communities in soils that were treated for > 25 years with no fertilizer (control), inorganic fertilizers (NPK) and organic-inorganic fertilizers (NPKM). Long-term NPK resulted in significant acidification up to a decline by 1.20 pH units, while NPKM prevented acidification and increased pH up to 6.39 in three acidic soils with pH < 5.70. NPKM increased crop yields by 1.19–8.72 folds in acidic soils, being significantly higher than NPK. Specific saprotroph Mortierella and Pseudaleuria in acidic soils were exclusively enriched by NPKM. Soil pH was directly related to the abundance of Mortierella, and the enrichment of Mortierella species further caused a positive direct effect on crop yield. In four alkaline soils with pH > 8.11, both NPK and NPKM led to only marginal decline of soil pH, and NPK and NPKM showed comparable crop yields. Some members of Ascomycota in alkaline soils were both enriched by NPKM and NPK. Soil available P and C:N ratio, rather than pH, directly or indirectly affect crop yield in alkaline soils. High crop yield can be achieved by the sole use of inorganic fertilizers in alkaline soils, but acidic soil productivity should be maintained by organic amendment to counteract acidification by inorganic fertilization. Our study advances a mechanistic understanding for optimizing fertilization strategies towards sustainable agriculture under increasingly intensified fertilizer inputs.