NOVELTY - A method (M1) for producing a biofuel using genetically modified ammonia-oxidizing bacteria (AOB), involves: providing an AOB that have been genetically modified to include a particular metabolic pathway to enable them to generate a particular biofuel; feeding a first source of ammonia to the AOB; feeding carbon dioxide to the AOB; and producing at least the biofuel, nitrite, and an AOB biomass.    USE - For producing a biofuel (particularly isobutanol) and a chemical (particularly commodity chemical, specialty chemical, feedstocks such as acid, amino acid or carbohydrate) using genetically modified ammonia-oxidizing bacteria (claimed).    ADVANTAGE - The methods and systems include the application of chemolithoautotrophic AOB for concomitant carbon dioxide fixation, conversion of the carbon dioxide to a biofuel such as isobutanol, and oxidation of ammonia to nitrite. The nitrite produced upon ammonia oxidation is electrochemically reduced back to ammonia. The bioreactors included in methods and systems are typically operated in a continuous flow mode to maximize the conversion of the substrates to the products. The methods and systems do not include the electrochemical regeneration of ammonia; and use only abundant, inexpensive redox mediators. They do not use costly rare earth elements or organic redox shuttles, and thus can be potentially deployed economically at scale. They potentially exceed an overall efficiency greater than one percent and butanol has desirable fuel properties and is compatible with transportation-fuel infrastructure. The systems and methods can utilize ammonia from ammonia-rich streams derived from a wastewater treatment process to not only fix CO2 using chemolithoautotrophic bacteria, but also converting the fixed CO2 to a desirable fuel such as isobutanol.    DETAILED DESCRIPTION - INDEPENDENT CLAIMS are included for the following:    (1) a system for producing biofuels using genetically modified ammonia-oxidizing bacteria comprising: a bioreactor including AOB that have been genetically modified to include a particular metabolic pathway to enable them to generate a particular biofuel; a first source of ammonia in fluid communication with the bioreactor; a source of carbon dioxide in fluid communication with the bioreactor; and a electrochemical reactor in fluid communication with the bioreactor, where the reactor configured to electrochemically reduce nitrite produced in the bioreactor to a second source of ammonia; and    (2) a method (M2) for producing a chemical using genetically modified ammonia-oxidizing bacteria, involving: providing an AOB that have been genetically modified to include a particular metabolic pathway to enable them to generate a particular chemical; feeding a first source of ammonia to the AOB; feeding carbon dioxide to the AOB; producing at least the chemical, nitrite, and an AOB biomass; electrochemically reducing the nitrite to a second source of ammonia; and feeding the second source of ammonia to the AOB.