In our discussion of energy metabolism in Chapters 7 and 8, we emphasized oxidation–reduction (redox) chemistry. In redox reactions, a pair of molecules reacts, one molecule becoming more oxidized and the other becoming more reduced. If we follow the transfer of electrons in a redox reaction, we see that the molecule that is reduced gains electrons, whereas the molecule that is oxidized loses electrons. Reduction therefore requires a source of electrons, or an electron donor, and oxidation requires a sink for electrons, or an electron acceptor.

In photosynthesis carried out by plants, algae, and cyanobacteria (Chapter 8), carbon dioxide (CO₂) is reduced to form carbohydrates, and water is oxidized to oxygen gas (O₂). Water is the electron donor needed to reduce CO₂, generating O₂ as a by-product. In respiration, as described in Chapter 7, organic molecules are oxidized to CO₂, and O₂ is reduced to water. In this case, O₂ serves as the electron acceptor needed to oxidize organic molecules.

In all known photosynthetic eukaryotes, the photosynthetic reaction is oxygenic, or oxygen producing. There is a good reason for this. Water occurs nearly everywhere and, in the oxygen-rich environments where most eukaryotic organisms thrive, no other molecule is available to donate electrons. Nonetheless, where oxygen is limited or absent, other electron donors such as hydrogen sulfide (H₂S) are available for photosynthesis and are utilized by photosynthetic microorganisms. Similarly, essentially all respiration in eukaryotic cells is aerobic, or oxygen utilizing. Again, this makes good chemical sense because oxidation of carbohydrates using oxygen generates far more energy than can be obtained using other oxidants. Once again, however, where oxygen is absent, other electron acceptors can be used for respiration. The organisms that can use these alternative electron donors and electron acceptors are Bacteria and Archaea.

We’ve already noted that Bacteria and Archaea differ from Eukarya in cell structure and genome organization, but it is the distinctive ways in which Bacteria and Archaea gather carbon and harvest energy that make them indispensable parts of nature. Prokaryotic organisms are thus the real foundation of the carbon cycle, capable of building and dismantling organic molecules throughout the full breadth of habitats on Earth.