AimsLong-term application of organic materials has been shown to significantly enhance the content of soil organic matter (SOM), underscoring the critical need to examine the components of soil organic carbon for a deeper understanding of SOM functionalities. Thus, the structural changes and microbial driving mechanisms of water extractable organic matter (WEOM), fulvic acid (FA) and humic acid (HA) were investigated in black soil by a long-term fertilization experiment.MethodsThis 33-year experiment comprises five treatments: no fertilizer (CK), chemical fertilizer (NPK), chemical fertilizer with low-rate straw (NPKJ1), chemical fertilizer with high-rate straw (NPKJ2), and chemical fertilizer with organic manure (NPKM). We also conducted a detailed study of WEOM, FA, HA, and the microbial community structure in both the 0-20 cm and 20-40 cm soil layers.ResultsOur findings indicate that organic material application primarily sourced WEOM, FA, and HA from microbial metabolism and plant-derived origins, exhibiting humus and aromatization characteristics with high molecular weight. WEOM was rich in fulvic acid-like and humic acid-like compounds, while FA and HA contained more protein-like components. Organic material use altered WEOM, FA, and HA structures by impacting soil microbial biomass carbon (MBC) and fungal/bacterial biomass. In 0-20 cm soil layer, SOM content was mainly influenced by humus, especially the HA fraction, whereas in 20-40 cm soil layer, it was predominantly affected by WEOM.ConclusionsThe present study emphasizes that the application of organic materials can influence the structure of microbial communities, thereby affecting the composition of WEOM, FA, and HA, consequently influencing the organic matter content in different soil layers.