A method and apparatus is provided for microbial seeding and amendment of traditional alternative fuels production systems and processes using immobilized microbe bioreactors. The system addition utilizes attachment of yeast or other microbial consortia to a substrate to enhance alternative fuels production in fermentation processes. The system allows for the maintenance of a constant concentrated microbial population, thus enhancing alternative fuels production by stabilizing microbial populations. Desired aerobic and anaerobic conditions are maintained using a microbubble aeration device coupled to the Immobilized Microbe Bioreactor (IMBR) seeding reactors. Generation of the microbial populations for seeding requires control of aerobic and anaerobic conditions to ensure growth of a microbial population acclimated to elevated alternative fuels concentrations.