Bacteria are nature made biofuel producers, such as methane, hydrogen and organic molecules which can be converted into biodiesel. However the nature has more on its mind than just making biomass and food (fuel) for other organisms including humans. Genetically modified bacteria can be modified to produce more H₂, CH₄ or membrane lipids, which can be converted into biodiesel.

Biodiesel is good because it would require few changes to our energy infrastructure. Since biodiesel gobbles up as much carbon dioxide as it releases when it is burned in the engines, it doesn’t contribute to rising atmospheric CO₂ level and global warming. The ASU research program in biodiesel is focused on engineering cyanobacteria which have larger portion of membranes in their cells. 600 km² of cyanobacteria may provide the biomass to fuel a 1.6 GW power plant (a large plant for US standards; sufficient for the national demand in smaller African and S. Asian countries) and take up all of the CO₂ produced.

Methane is a key component of compressed natural gas, and, when combined with other hydrocarbons, offers a cleaner burning fuel already used in today's vehicles. The ASU research program is focused on improvement of methane production that occurs in wastewater treatment. For example, running wastewater through a high-voltage generator, causes the release of simple sugars and the breakdown of complex biomass molecules. This result in more food for the microorganisms and more production of methane.

Hydrogen can be produced by cyanobacteria in variety of natural habitats cyanobacteria, which means that unless there is some way the cells exclude oxygen from the process, their hydrogenase (enzyme for hydrogen production) must be oxygen tolerant. ASU research program is focused on finding hydrogenase, which can operate in the presence of oxygen. In the modified cyanobacterial system we intend to divert electrons from their normal pathways and push them into new pathways that result in hydrogen production.