A renewable energy source, biogas, comprises of methane (80%) and carbon dioxide (15%), and is a great alternative to the conventional fossil-based fuels, such as coal, gas and oil. Biogas is created during anaerobic biological digestion of waste materials, such as landfill material, animal manure, wastewater, algal biomass, industrial organic waste etc. A biogas potential from organic waste in the United States is estimated at about 9 million tons per year and technology allows capture of greenhouse gases, such as methane and carbon dioxide, into a form of a fuel. In the light of global climate change and efforts to decrease carbon footprint of fuels in daily life, usage of biogas as an alternative fuel to fossil fuels looks especially promising. The goal of this research was to develop and test an approach for optimization of biogas production by engineering microorganisms digesting organic waste. Specifically, bacteria that can digest algal biomass, collected from the wastewater lagoons or open waterbodies. The research also expands on the previous efforts to analyze microbial interactions in wastewater treatment systems. A computational model is developed to aid with prognosis of microbial consortia ability to form complex aggregates in reactors with upflow mode of feeding substrate. Combining modeling predictions and laboratory experiments in organic matter digestion will lead to more stable engineered systems and higher yields of biogas.