Organic phosphorus (Po) may play a vital role in phosphorus availability via its mineralization by alkaline phosphatase (ALP), being encoded by phoD gene, in calcareous soil. Understanding the effects of long-term fertilization on the community of phoD harboring bacteria and the related alteration of the P availability owing to the changes in ALP secretion may offer a chance to elucidate the Po contribution to soil available P. Based on a long-term experiment, we analyzed the phoD gene harboring microbial diversity, abundance and composition, ALP and Po forms, and their relationship. The treatments involved were control without any fertilizers (CK), synthetic nitrogen and potassium (NK), synthetic nitrogen, phosphorus and potassium (NPK), NPK and crop stalk return (SNPK), and NPK plus organic manure (MNPK). Fertilization increased the abundance and diversity of phoD gene harboring microbial over CK. Those receiving NPK and NPK treatments integrated with organic supplements significantly improved the relative abundance of Proteobacteria but decreased Gemmatimonadetes at the phylum level, while all fertilized treatments appreciably increased the relative abundance of Lysobacter but decreased that of Gemmatirosa and Afipia, at the genus level. SNPK and MNPK treatments noticeably increased the relative abundance of Methylobacter but reduced Pseudomonas and Streptomyces relative to those receiving synthetic fertilizer treatments. Long-term fertilization markedly raised ALP activity, which was significantly and positively correlated with the relative abundance of the phylum Proteobacteria as represented by the genera Methylobacterium and Lysobacter. ALP was closely associated with moderately labile Po, followed by enzyme P, recalcitrant Po, and labile Po. The changes in phoD bacteria and ALP were mainly driven by soil organic carbon, Olsen P and pH. We concluded that the long-term fertilization, especially the addition of organic supplements, profoundly modified the soil properties and subsequently changed the diversity and relative abundance of phoD gene harboring bacteria, which promoted the activity of ALP, and thus the mineralization of various forms of Po (mainly moderately labile Po) to enhance the P availability.

The combination of organic manure and inorganic fertilizer plays a role in increasing crop yield and nutrient efficiency, but such effectiveness varies with crop, soil, management, and climate. Here, a 6-year field experiment was conducted to evaluate the effects of substituting organic manure with inorganic fertilizer on crop yield, grain protein content, and nitrogen and phosphorus efficiency under a winter wheat-summer maize cropping system on Anthrosol. Five treatments were included: recommended nitrogen (N), phosphorus (P) and potassium (K) fertilizers (NPK), 75% NPK + 25% organic manure (M), 50% NPK + 50% M, 25% NPK + 75% M, and 100% M, respectively. Wheat, maize, and annual yield were 1643–8438 kg ha⁻¹, 4847–11,104 kg ha⁻¹, and 10,007–17,496 kg ha⁻¹. Organic manure treatments produced the same crop yield as NPK treatment except for 100% M. Grain protein content of wheat and maize was 7.9–15.1% and 5.6–12.6%. Organic manure treatments yielded significantly lower wheat grain protein content but had no significant effect on maize grain protein content relative to NPK treatment. Nitrogen uptake efficiency and nitrogen use efficiency at the cropping system level were 0.67–1.16 and 35.7–60.5 kg kg⁻¹. Phosphorus uptake efficiency and phosphorus use efficiency were 0.28–0.75 and 167–531 kg kg⁻¹. Compared with NPK treatment, 50% M, 75% M, and 100% M improved nitrogen use efficiency but decreased nitrogen uptake efficiency and phosphorus efficiencies. Annual N and P budgets were −1.3–79.1 kg ha⁻¹ a⁻¹ and 25.6–100.1 kg ha⁻¹a⁻¹, and both increased with the increase in organic manure input. Based on crop yield, grain protein content, nitrogen, and phosphorus efficiency and their budget, substitution of 25% inorganic fertilizer with organic manure is the rational combination under the winter wheat–summer maize system on an Anthrosol.