Two types of enzymes can catalyze the reduction of protons to H₂, namely nitrogenase and hydrogenase. Although much progress has been made in the elucidation of gene expression, structure and regulation of these key enzymes, no practical and economically competitive process for the continuous production of biological H₂ (biohydrogen) has, as yet, been put on the market. One of the difficulties is due to the fact that H₂ output represents an energy loss for the cell and that microbial metabolic network has evolved for rationalization of energy use and optimization of specific growth rate.

The study of the physiology of genetically modified photosynthetic microorganisms has shown that electron flux could be redirected to the bidirectional hydrogenase in a ndhB mutant of Synechocystis and that a change in carbon metabolism in mutants of Rhodobacter capsulatus unable to grow photoautotrophically could affect the flow of reducing equivalent from organic substrates to nitrogenase. Increasing the flux through an existing pathway or redirecting enzyme-catalyzed reactions is an approach referred to as metabolic engineering.

Various “naturally engineered” organisms are found in Nature. An example is provided by the bacterium Dehalococcoides ethenogenes, which is the only bacterium known to reductively dechlorinate the ground water pollutants tetrachloroethene and trichloethene to ethene. D. ethenogenes exhibits an unusual metabolic specialization; it uses only H₂ as an electron donor and chlorinated compounds as electron acceptors to support growth. In accordance, the sequence of its genome has revealed the presence of five hydrogenase complexes.