In the process of phosphate fertilizer production, adding humic acid to produce humic-acid-value-added phosphate fertilizer can improve fertilizer efficiency and promote crop growth. Although studies have primarily focused on investigating the impact of humic acid’s structure and function on phosphorus availability in humic-acid-added phosphate fertilizers, there is limited research on the regulatory effects of phosphorus fertilizer structure and the synergistic mechanisms involving microorganisms. Therefore, this study aimed to examine the chemical and biological mechanisms underlying the increased efficiency of humic-acid-added phosphate fertilizers by implementing various treatment processes. These processes included physically blending humic acid with phosphate fertilizer (HA+P), chemically synthesizing humic acid phosphate fertilizer (HAP), using commercially available humic acid phosphate fertilizer (SHAP), employing ordinary potassium phosphate fertilizer (P), and implementing a control treatment with no phosphate fertilizer (CK). Investigating the synergistic mechanism of humic-acid-added phosphate fertilizers holds significant importance. The results showed that during the preparation of HAP at high temperature, a new absorption peak appeared at 1101 cm−1, and a new chemical bond -O- was formed. The hydroxyl fracture in humic acid combined with phosphoric acid to form a phosphate ester (P-O-C=O) structure. HAP residues were concentrated on the surface and loaded with more soil minerals. The content of highly active oxygen-containing functional groups—such as aromatic C-O, carboxyl/amide carbon and carbonyl carbon—increased significantly, while the content of alkyl carbon, oxyalkyl carbon, and aromatic carbon decreased. Upon combining humic acid with potassium phosphate, the carboxyl group and calcium ions formed the HA-m-P complex, increasing the content of soluble phosphate (H2PO4−) in the soil by 1.71%. Compared to HA+P treatment, HAP treatment significantly increased the soil’s available P content by 13.8–47.7% (P < 0.05). The plant height, stem diameter, and above-ground biomass of HAP treatment were increased by 21.3%, 15.31%, and 61.02%, respectively, and the total accumulations of N, P, and K nutrient elements were increased by 6.71%, 31.13%, and 41.40%, respectively, compared to the control treatment. The results of high-throughput sequencing showed that the rhizosphere soil of HA+P and HAP treatment was rich in bacterial groups, the soil microbial structure was changed, and the bacterial community diversity was increased under HAP treatment. The number of genes encoding phytase and alkaline phosphatase associated with organophosphorus dissolution increased by 3.23% and 2.90%, respectively, in HAP treatment. Humic acid phosphate fertilizer forms phosphate esters in the process of chemical preparation. After application, the soil’s microbial community structure is changed, and soil enzyme activity related to phosphorus transformation is improved to promote tomatoes’ absorption of soil nutrients, thus promoting tomato plant growth and nutrient accumulation.
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