Biodesulfurization has emerged as potential alternative to oxidative desulfurization and hydrodesulfurization. However, main impediment in commercial application of biodesulfurization process is its slow kinetics. Ultrasound irradiation (or sonication) has been reported to enhance the kinetics of biodesulfurization. The present study has attempted to establish the physical mechanism of this enhancement by identifying links between physics of ultrasound/cavitation and chemistry of biodesulfurization. The model reaction system comprises of dibenzothiophene (DBT) as model sulfur compound, toluene as model fuel and Rhodococcus rhodochrous cells (in free and immobilized form) as microbial culture. The investigation has three approaches: (1) fitting of experimental profiles of DBT oxidation to kinetic model using Genetic Algorithm, (2) simulations of cavitation bubble dynamics and (3) analysis of secondary structure of the intracellular Dsz enzymes (involved in metabolic pathway) by circular dichroism. It is revealed that strong micro-convection generated by ultrasound and cavitation induces conformational changes in the secondary structure of the enzyme, which augments their catalytic efficiency. Oxidizing radicals generated through transient cavitation also provides a parallel pathway of oxidation of DBT to sulfoxide and sulfone, which are intermediates of DBT metabolism. This assists faster consumption of DBT by microbial cells. The results of this study clearly demonstrate the role of physical and chemical effects of ultrasound and cavitation in enhancing metabolism of biodesulfurization. (C) 2016 Elsevier B.V. All rights reserved.