Long-term soil carbon accumulation and nutrient depletion under intensive chemical fertilization in tropical rice systems

Intensive flooded rice systems are often assumed to sustain soil organic matter (SOM) due to suppressed decomposition under anaerobic conditions. However, whether long-term soil carbon accumulation translates into improved soil fertility remains unclear. This study examined decadal temporal effects of intensive chemical fertilization on SOM accumulation and nutrient pools across two tropical paddy systems. We analyzed archived soil samples (0–15 cm depth) from two long-term experiments in the Philippines: a continuous triple-rice system on a clayey soil (LTCCE, 1985–2019) and a double-rice cropping system on a silty soil (LTFE, 1985–2013). Decadal changes in total carbon (TC), total nitrogen (TN), available nitrogen (AN), available phosphorus (AP), and exchangeable potassium (Ex-K) were quantified. Principal component analysis (PCA) and regression models were applied to assess temporal trends and their relationships with grain yield. In the LTCCE, TC and TN contents increased steadily over more than three decades (e.g., 0.017–0.024% year⁻¹ for TC), despite complete residue removal. Conversely, AN declined consistently across all treatments, halving the AN/TN ratio by 2019, which indicates a progressive deterioration of indigenous soil N-supplying capacity despite increasing SOM stocks. PCA confirmed this paradox: in the LTCCE, grain yield was significantly correlated with short-term nutrient availability (PC2: driven by AN, AP, Ex-K), rather than long-term SOM accumulation (PC1). In the LTFE, TC and TN accumulation was modest, and yield was more closely associated with overall SOM and available P status (PC1). Across both sites, AP accumulated when fertilizer inputs exceeded crop uptake, but stabilized or declined when nutrient balances shifted, suggesting its partial reversibility. In contrast, Ex-K declined markedly under high-yield conditions in the LTCCE, dropping below the 0.2 cmol c kg⁻¹ deficiency threshold, highlighting severe, continuous K mining despite substantial irrigation inputs. These decadal data demonstrate a soil fertility paradox in tropical intensive rice systems, where quantitative SOC accumulation coincides with qualitative degradation. The findings highlight the necessity of coordinated water and nutrient management—such as periodic soil aeration to restore N mineralization, strategic use of residual soil P, and reinforcement of K fertilization—to sustain indigenous nutrient-supplying capacity and ensure the long-term sustainability of intensive rice production systems in tropics.