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Semi-arid tropical soils have low soil organic carbon and microbial biomass carbon with limited available macroand micronutrients for crop plants. These soils may have future yield sustainability problems due to intensive cropping, erosion and limited adoption of nutrient management strategies. Therefore monitoring the abundance, community shift and physiological status of the soil microbiome in response to agricultural practices is vital to understand soil fertility sustainability. We measured the long term effects of organic and inorganic nutrient management practices on bacterial communities and soil biochemical processes. Samples were from a long term nutrient experiment field trial on an Alfisol established in 1909. The abundance of bacterial 16S rRNA, nifH and amoA genes was measured in soil samples for two consecutive years, 2009 and 2010 using quantitative real-time polymerase chain reaction (qPCR). The 16S rRNA and nifH genes were abundant in organically managed soil while the inorganic nutrient amendments increased the abundance of amoA gene. Respiration studies indicated that organic management encouraged higher substrate induced respiration rates compared to inorganically fertilized and control soils. However, the metabolic quotient of the soil remained unaffected by long term nutrient management regimes. The inorganic fertilizer amended soil showed higher nitrification potential compared to organically managed and control soils. Multivariate regression analysis revealed that soil organic carbon, microbial biomass carbon and substrate induced respiration rate significantly drive the abundance of 155 rRNA and nitH gene; while for amoA, the drivers were available nitrogen, substrate induced respiration rate and nitrification potential. Our results show that long term organic and inorganic nutrient managements had strong influences on the abundance of key bacterial genes and related biochemical processes in a semi-arid tropical Alfisol. This study further underlines the importance of fertility management options for improving or sustaining the biological properties of tropical soils. (C) 2014 Elsevier B.V. All rights reserved.