Light but no oxygen penetrates into the purple layer in Fig. 26.7b, and neither light nor oxygen penetrates into the black layer deep within the microbial mat. Yet both layers are inhabited by a diversity of heterotrophic Bacteria and Archaea that metabolize organic molecules originally synthesized by photosynthetic bacteria higher in the mat community.

Because there is no oxygen in these layers, these organisms must use other molecules as electron acceptors in cellular respiration, including oxidized forms of nitrogen (NO₃–), sulfur (SO₄^2–), manganese (Mn⁴⁺), iron (Fe³⁺), and even arsenic (AsO₄^3–). Such microorganisms thrive in many environments where oxygen is absent.

Still other types of heterotrophs live in deeper layers of microbial mats. Fermentation provides an alternative to cellular respiration as a way of extracting energy from organic molecules. Whereas cellular respiration is the full oxidation of carbon compounds to CO₂, fermentation is the partial oxidation of carbon compounds to molecules that are less oxidized than CO₂ (Chapter 7). Fermentation has an advantage over cellular respiration in that it does not require an external electron acceptor, such as O₂. On the other hand, fermentation yields only a modest amount of energy.

Fermentation plays an important role in oxygen-poor environments that are rich in organic matter, such as landfills and the digestive tracts of animals. Here the breakdown of organic molecules typically requires more than one organism, each able to metabolize a different intermediate. These cooperating groups of fermenters enable the breakdown of substances that could not be metabolized by any one organism alone. Groups of fermenters thus form what is essentially an ecological solution to the metabolically difficult problem of gaining energy from complex organic molecules. Fermentation is widespread in Bacteria and Archaea, but is of only minor importance in most Eukarya, the exception being yeasts, which thrive in the sugar-rich environment of rotting fruit, as well as in breweries throughout the world.

In summary, where O₂ is present, many different kinds of organisms participate in the carbon cycle. Photosynthetic plants, algae, and cyanobacteria all transform CO₂ into organic molecules, and animals, fungi, single-celled eukaryotes, bacteria, and archaeons return CO₂ to the environment by aerobic respiration. In Chapter 25, we noted that some of the organic carbon produced by photosynthesis escapes aerobic respiration and accumulates in oxygen-depleted waters or sediments. Only prokaryotic heterotrophs can complete the recycling of organic carbon in oxygen-poor environments. Thus, in carrying out anaerobic respiration or a diversity of fermentation reactions, prokaryotes play a major role in the carbon cycle.