TECHNOLOGY FOCUS - BIOLOGY - Preferred Method: The water source is surface water, which is pond, lake, and/or waste lagoon; or subterranean water, which is associated with geological formation that includes a hydrocarbon material. The subterranean water is injected into a geological formation that includes a hydrocarbon material. The method further comprises injecting a portion(s) of the nutrient rich water into a geological formation that includes a hydrocarbon material; allowing the population of microorganisms to propagate using the hydrocarbon material and nutrient compounds from the industrial waste stream; and recovering the bio-energy product from the geological formation. Injecting includes injecting liquid water into the geological formation and/or injecting an aerosol into the geological formation. At least some microbes in the microbial population are indigenous to the geological formation. The microbial population includes methanogenic microorganism(s) capable of producing biotic methane in the geological formation. The method further comprises recovering a portion(s) of the biotic methane from the geological formation. The industrial waste stream is a gaseous waste stream or gaseous fluid stream. The gaseous industrial waste stream is flue gas from an industrial power plant, which is a coal fired power plant. The industrial waste stream is a liquid waste stream. It is from a food processing plant. The salt concentration in the nutrient rich water is 35, preferably 10-300 pts./thousand (ppt). The nutrient rich water has a carbon content of 100-120 mg/L; nitrogen content of 10-20 mg/L; phosphorus content of 1-3 mg/L; and sulfur content of 1-2 mg/L. The population of microorganisms includes greater than or equal to 10 wt.% algae belonging to Dunaliella; and greater than or equal to 10 wt.% bacteria, i.e. halobacterium. The bio-energy product comprises biomass. The method further comprises processing the biomass to produce a hydrocarbon fuel and to recover heavy metals. The industrial waste stream has a temperature equal to or greater than that of the water. It is mixed with the water using an infuser system. The method further comprises recovering a portion(s) of the bacterial and/or algal population from the nutrient rich body of water; and processing the recovered portion of the bacterial and/or algal population to recover heavy metals. Sunlight is used to supplement microbial and/or algal growth. The bacterial and/or algal population includes Cyanophyta for sequestration of carbon dioxide (CO2), sulfur oxide (SOx), and/or nitrogen oxide (NOx). It is used to produce high concentrations of fuel precursor compounds selected from glycerol, lignins, and/or lipids. The biological product includes biomass used to produce biofuel. The microbial component(s) includes enzymes and surfactants to facilitate biotic methane production and/or microbial growth in the geological formation. It is derived from the microbial population. The method further comprises providing a first microbial population and a first nutrient and/or a first microbial component within the geological formation; and providing a second microbial population and a second nutrient and/or a second microbial component within the geological formation. The first and second nutrients are derived from the industrial waste stream. The first microbial population and/or the microbial component(s) degrade the hydrocarbon material in the geological formation to produce humic acids and/or colloidal polymers. The second microbial population and/or second microbial component degrade the humic acids and/or colloidal polymers to produce fatty acids, sugars, amino acids, ammonia, hydrogen sulfide (H2S), hydrogen, acetate, and/or methane. The geological formation is a coal bed, an oil shale bed, depleted oil field, or tar sand deposit. The hydrocarbon material has been fractured. The method further comprises injecting a fracturing fluid into the geological formation to crack the hydrocarbon material and increase the surface area. The fracturing fluid includes carbon dioxide and hydrocarbon. Providing the microbial population within the geological formation includes injecting a portion(s) of the microbial population into the geological formation. The microbial population includes extremophile(s), which includes halophile(s). The industrial waste stream provides carbonates, sulfates, phosphates, and/or transition metals. The nutrient rich water is salt or brine water. The salt concentration in the brine water is greater than 400, preferably 10-300 ppt. The aerosol includes aqueous portion, nutrient portion derived from industrial waste stream, and/or microbial portion derived from the microbial population. The water source comprises fresh water, brackish water, or salt water. The indigenous population of microorganisms includes microorganism(s) to produce methane precursor material for the methanogenic microorganism. The nutrient rich water further includes the population of microorganisms for propagation in the subterranean geological formation.