Although the 13C (13Carbon) natural abundance method is used to study soil C dynamics, scanty information is available on long‐term fertilization effects on soil C sequestration rates along with δ13C in surface (0–30 cm) and deep (30–90 cm) soil layers and their relationships with crop productivities in subtropics. Hence, soil aggregation, δ13C in bulk soils and aggregates, C pools, and sequestration rates were studied in an Indian Alfisol under a 43‐year old wheat (Triticum aestivum L.)‐based cropping system. Treatments were as follows: no mineral fertilizer and no manure (unfertilized control), 100% recommended dose of nitrogen (N), 100% N and 100% recommended phosphorus (NP), 100% N, 100% P, and 100% recommended potassium (NPK), NPK + lime (NPKL), 150% recommended NPK (1.5NPK), and NPK + farmyard manure at 10 Mg ha−1 (NPKF). Plots with NPKF contained 50% higher soil organic C than NPKL in surface soil (0–15‐cm layer). In the 0–90‐cm profile, soil organic C accumulation and sequestration rates in NPKF were ~0.15 and 0.11 Mg ha−1 yr−1 higher than NPKL plots, respectively. The NPKF plots had higher glomalin‐related soil protein and greater recalcitrant C than NPKL, 1.5NPK, and NPK in surface soil. The NPKF plots had higher δ13C values within bulk soils and their aggregates than NPKL and NPK. There were significant correlations between deep soil C sequestration rates with mean crop productivities and δ13C with deep soil C sequestration rates. Overall, NPKF application had the largest surface and deep soil C sequestration with highest crop productivity and hence is recommended.
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