Objectives Phosphorus is one of the major limiting factors affecting crop productivity. This study aimed to investigate the effects of long-term different fertilization on soil phosphorus transformation and functional microbial communities, providing a theoretical basis for efficient phosphorus management and sustainable agricultural development.

Methods This study was based on a long-term fertilization experiment under a double-cropping rice system in Nanchang, Jiangxi Province, China. Five treatments were selected: no fertilization (CK), nitrogen and phosphorus fertilization (NP), nitrogen and potassium fertilization (NK), phosphorus and potassium fertilization (PK), and balanced nitrogen, phosphorus, and potassium fertilization (NPK). Soil phosphorus fractions were determined using the modified Hedley phosphorus fractionation method. Soil phosphatase (PHOS) activity was measured using a fluorometric microplate enzyme assay. High-throughput sequencing was employed to analyze the functional microbial communities encoding acid phosphatase (phoC) and alkaline phosphatase (phoD). Mantel test and Partial least squares path modeling were used to analyze the relationships among fertilization treatments, microbial communities, and phosphorus fractions.

Results Long-term phosphorus application (NP, PK, NPK) significantly increased the contents of soil total phosphorus (TP), Olsen-P, H₂O-Pi, NaHCO₃-Pi, NaHCO₃-Po, NaOH-Pi, NaOH-Po, and HCl-Pi during both early and late rice seasons. The proportions of labile phosphorus (LP), moderately labile phosphorus (MLP), and non-labile phosphorus (NLP) in the soil ranged from 7.41% to 18.70%, 35.31% to 49.81%, and 33.00% to 51.80%, respectively. Long-term phosphorus fertilization significantly increased the proportions of LP and MLP while decreasing the proportion of NLP in soils collected during both early and late rice seasons. Soil phosphatase (PHOS) activity was highest under the NPK treatment, followed by the NK and NP treatments, although no significant differences were observed among them. Moreover, the NPK treatment significantly increased the α-diversity (Chao and Shannon indices) of both phoC- and phoD-harboring functional microbial communities. The α-diversity of phoD harboring microorganisms was significantly positively correlated with the content and proportion of LP, as well as with NaOH-Pi and Olsen-P contents. Furthermore, fertilization significantly influenced the community composition of microorganisms harboring the phoD and phoC genes in soils during the early and late rice seasons. Long-term nitrogen application reduced the relative abundance of dominant phoC-harboring microbial taxa, with a significant decrease in the relative abundance of Stenotrophomonas under nitrogen fertilization. In contrast, phosphorus application increased the relative abundance of dominant phoD-harboring microbial taxa, with significant increases in the relative abundance of Ralstonia and Pseudolabrys. Partial least squares path modeling revealed that fertilization mainly promoted the transformation of soil phosphorus fractions by influencing the community composition of phoD-harboring microorganisms.

Conclusions Long-term phosphorus fertilization effectively increased the accumulation of different phosphorus fractions in the soil, while balanced NPK fertilization effectively enhances soil phosphatase (PHOS) activity and the diversity of phoC- and phoD-harboring functional microorganisms, thereby promoting soil phosphorus cycling. Compared with phoC-harboring microorganisms, phoD-harboring microorganisms may play a more important role in the process of soil phosphorus transformation in this system.