Strategic fertilization enhances crop quality index via changes in soil microbial generalist communities

Partially replacing chemical fertilizers with organic alternatives is a promising strategy for sustainable agriculture, boosting crop yields while mitigating environmental risks. However, the interactions among soil nutrients, microbial communities, and crop quality under organic-inorganic mixed fertilization remain unclear. We hypothesized that mixed fertilization (MF), combining equal proportions of chemical and organic fertilizers, enhances plant and soil functions compared to chemical fertilization alone (CF). In the final year of an eight-year field experiment, we analyzed seasonal samples to assess how MF and CF influence soil multifunctionality, microbial dynamics, and watermelon quality. MF significantly improved soil carbon, nitrogen, and phosphorus cycling, increasing dissolved organic carbon, organic matter, nitrate nitrogen, and available zinc across growth stages. Watermelon quality under MF was 2.48 times higher than CF ( p < 0.01), with notable increases in sugar content, fruit weight, and nutrient accumulation. MF also enhanced bacterial and fungal diversity at key growth stages, altered microbial community structure and assembly processes, and increased plant-growth-promoting bacteria (PGPB), such as Bacillus and Pseudomonas , while reducing Fusarium oxysporum sp. niveum by 0.65–0.88 times compared to CF. Additionally, elevated soil organic matter and nitrogen under MF favored r-strategist generalist microorganisms, supporting beneficial microbial communities essential for plant health. Structural equation modeling identified microbial communities (e.g., PGPB, ribosomal copy number, and beneficial generalists), along with soil carbon and nitrogen, as key drivers of improved watermelon quality. This study highlights MF as a sustainable agricultural approach to enhance soil multifunctionality, regulate beneficial microbes, and improve crop quality, contributing to long-term agricultural sustainability.