Organic Fertilization Enhances Microbial-Mediated Dissolved Organic Matter Composition and Transformation in Paddy Soil

Dissolved organic matter (DOM) is a crucial carbon source for soil microorganisms and plays a vital role in nutrient cycling and carbon (C) sequestration in soils. However, the extent to which soil microbes mediate DOM transformation at the molecular level, and whether this is regulated by different organic fertilization, remains unclear. Here, we designed a field experiment to investigate the transformations of DOM under three types of organic fertilization (straw, biochar, and manure) using Fourier transform ion cyclotron resonance mass spectrometry and metagenomic analysis. Compared to the control, manure fertilization increased the molecular chemodiversity of DOM by 33.2%, with recalcitrant compounds (e.g., highly unsaturated phenolic compounds and lignins) increasing by 47.2%. In contrast, labile compounds (e.g., aliphatics) decreased by 73.5%. Compared to straw treatment, manure application significantly increased the average conversion rate of dissolved organic matter (DOM). This process was accompanied by a significant increase in the Shannon index of the soil microbial community (p < 0.05) and upregulation of ABC transporter-encoding genes (e.g., livK, livM). DOM composition directly governed transformation potential (p < 0.01), whereas functional genes enhanced transformation indirectly by modulating DOM composition. This study elucidates microbial-mediated DOM transformation mechanisms under varying organic fertilization practices, providing a scientific basis for optimizing soil organic matter management in paddy ecosystems.