Global climate change is anticipated to have a tremendous influence on crop productivity and nutrient cycling in legume-based cropping systems. The effect of long-term application of manure and fertilizers on the dynamics of soil organic carbon (SOC) pools and soil physical properties was studied in a soybean (Glycine max Merr. L)-wheat (Triticum aestivum L) system. The temperature sensitivity of C pools and the alterations in microbial composition were determined at 25, 35, and 45 degrees C. Higher levels of microbial biomass C (MBC) and nitrogen (MBN), water soluble carbon (WSC), acid hydrolysable carbohydrates (AHC), particulate organic matter carbon (POMC) and nitrogen (POMN) were observed in the NPK + FYM at a depth of 0-15 cm. Irrespective of the treatment, micro aggregates (53-250 mu m) were a major aggregate size class, comprising 45-57% of the total soil aggregates, followed by macro aggregates (250-2000 mu m at 37.8-45%). Microbial respiration rate increased by 13.9% in most recalcitrant pools (<53 mu m) at 45 degrees C than at 25 degrees C. Furthermore, data on labile C (A(0)) revealed a 4.9-55.4% increase in the substrate pools and a 10.5-32.5% increase in mineralization rate (k) with these treatments at 25-45 degrees C in 250-2000 mu m aggregates. AHC and POMC content decreased by 23-37% and 12-23% of SOC, respectively, when the temperature was raised from 25 to 45 degrees C. It is concluded the gradual depletion of nutrients, structural degradation and changes in microbial composition might have collectively contributed to the decline in crop yields. It was suggested that temperature has a strong effect on C mineralization, depending on the types and extents of substrate utilization. Seasonal rainfall, maximum and minimum temperature and SOC had jointly explained 12-41% of variation in soybean production in NP, NPK and NPK+FYM treatments. However, balanced use of NPK plus FYM is an important management option to arrest the decline of crop yield. (C) 2013 Elsevier B.V. All rights reserved.