Long-Term Application of Organic Amendments Increases Soybean Yield by Enhancing Soil Quality in Aggregate Scale

Soil aggregates, which form the basic framework of soil structure, exert significant control over soil quality and crop yield. However, the influence of organic amendments on the relationships between aggregate formation and crop yield are still unclear. To investigate this issue, a long-term field experiment was established including four fertilizer treatments: control without fertilization (CK), chemical fertilizer (NPK), NPK combined with straw (NPKS), and NPK combined with organic manure (NPKM). Soil aggregates were fractionated into >2 mm (LMA), 2–0.25 mm (MMA), 0.25–0.053 mm (SMA), and <0.053 mm (MIC) fractions. NPKS and NPKM treatments increased the proportion of large macroaggregates (LMAs) by 8–12% and significantly elevated soil organic carbon (SOC) and nutrient levels relative to CK. NPKS and NPKM significantly increased the soil quality index (SQI) of LMA and MIC by 45.5–116.7% and 21.1–32.1%, compared with CK and NPK. Random forest (RF) analysis revealed that among the nutrient variables across the four aggregate fractions, the SOC content in LMA and the total phosphorus (TP) content in MIC contributed the highest to soybean yield. Partial least squares modeling further confirmed that the SQI of LMA was the dominant factor influencing soybean yield. Therefore, long-term organic amendments improve soybean yield mainly by enhancing soil quality at the aggregate scale, providing a practical pathway for sustaining soil quality and crop productivity.