Organic-inorganic fertilization optimizes phoD-harboring microbial communities and increases phosphorus availability in paddy soils under intensive rice cropping

Alkaline phosphatase (ALP), encoded by phoD , phoA , and phoX genes, plays a crucial role in regulating soil organic phosphorus (OP) transformation. However, the effects of organic-inorganic fertilization on ALP-producing microbes and available phosphorus (AP) under intensive rice cropping systems remain poorly understood. This study investigated a 39-year experiment (1984–2022) involving different fertilization regimes (no fertilization, inorganic fertilizers , or organic-inorganic fertilizers) under rice-rice cultivation. The results demonstrated that long-term fertilization significantly increased soil nutrients and altered the structure and composition of ALP-coding microbial communities . Organic-inorganic fertilization significantly enhanced soil P levels, as well as the functional strength, abundance, and diversity of ALP-producing microorganisms, particularly those harboring the phoD gene, while phoA - and phoX -harboring communities exhibited minimal changes. Moreover, phoD -harboring microorganisms were identified as the primary contributors to soil ALP activity. Bayesian structural equation modeling revealed that the higher OP content in soils receiving organic and chemical fertilizers optimized phoD -harboring microbial communities, enhanced ALP activity, and facilitated the transformation of soil OP, ultimately leading to increased soil AP content. At the phylum level, the composition of phoD -harboring microbes remained consistent across treatments, with Proteobacteria, Actinobacteria , and Acidobacteria being the dominant groups. However, the top 10 microbial genera in each treatment varied in their contributions to soil ALP activity, highlighting the functional diversity within these communities. Thus, organic-inorganic fertilization increases soil OP levels and optimizes phoD -harboring microbial communities, which are vital for increasing soil AP content in paddy soils . This study provides valuable insights into the microbial mechanisms by which organic-inorganic fertilization enhances soil P availability under intensive rice cropping in South China. • Fertilization regimes altered the structure and composition of ALP-coding microbial communities in paddy soil. • Organic-inorganic fertilization enhanced the phoD -harboring microbial community. • No significant changes were observed in phoA - and phoX -harboring microorganisms. • SOC optimized the phoD -harboring microbial community, increasing soil ALP and AP. • Proteobacteria, Actinobacteria, and Acidobacteria were the main contributors to ALP.