In an aspect, a method of decontaminating a hydrocarbon fluid comprises applying an ultrasonic wave to the hydrocarbon fluid in a storage tank to maintain or reduce an amount of a microorganism in the storage tank; wherein a source of the ultrasonic wave is located within the storage tank and the storage tank has at least one of an inner volume of greater than or equal to 20 meters cubed and/or that is capable of storing 55 to 160,000 liters of the hydrocarbon fluid. In another aspect, a method of decontaminating a hydrocarbon fluid comprises applying an ultrasonic wave to the hydrocarbon fluid to disrupt a cell membrane of a microorganism to form a disrupted microorganism and to reduce a particle size of the disrupted microorganism to be less than or equal to 1.5 micrometers thereby forming a clean hydrocarbon fluid suitable for injecting through an injection nozzle.