The Carbon Cycle

Carbon is the backbone of all organic molecules and is the most prevalent element in cellular (organic) material. In its most oxidized form, CO₂, it can be viewed as an "inorganic" molecule (no C - H bond). Autotrophs, which include plants, algae, photosynthetic bacteria, lithotrophs, and methanogens, use CO₂ as a sole source of carbon for growth, which reduces the molecule to organic cell material (CH₂O). Heterotrophs require organic carbon for growth, and ultimately convert it back to CO₂.

Thus, a relationship between autotrophs and heterotrophs is established wherein autotrophs fix carbon needed by heterotrophs, and heterotrophs produce CO₂ used by the autotrophs.

CO₂ + H₂O-----------------> CH₂O (organic material)   autotrophy

CH₂O + O₂-----------------> CO₂ + H₂O heterotrophy

Since CO₂ is the most prevalent greenhouse gas in the atmosphere, it isn't good if these two equations to get out of balance (i.e. heterotrophy predominating over autotrophy, as when rain forests are destroyed and replaced with cattle).

Autotrophs are referred to as primary producers at the "bottom of the food chain" because they convert carbon to a form required by heterotrophs. Among procaryotes, the cyanobacteria, the lithotrophs and the methanogens are a formidable biomass of autotrophs that account for a corresponding amount of CO₂ fixation in the global carbon cycle.

The lithotrophic bacteria and archaea that oxidize reduced N and S compounds and play important roles in the natural cycles of N and S (discussed below), are virtually all autotrophs. The prevalence of these organisms in sulfur-rich environments (marine sediments, thermal vents, hot springs, endosymbionts, etc. may indicate an unappreciated role of these procaryotes as primary producers of organic carbon on earth.

The methanogens play a dual role in the carbon cycle. These archaea are inhabitants of virtually all anaerobic environments in nature where CO₂ and H₂ (hydrogen gas) occur. They use CO₂ in their metabolism in two distinct ways. About 5 percent of CO₂ taken up is reduced to cell material during autotrophic growth; the remaining 95 percent is reduced to CH₄ (methane gas) during a unique process of generating cellular energy. Hence, methane accumulates in rocks as fossil fuel ("natural gas"), in the rumen of cows and guts of termites, in sediments, swamps, landfills and sewage digesters. Since CH₄ is the second-most prevalent of the greenhouse gases, it is best to discourage processes that lead to its accumulation in the atmosphere.

CO₂ + H₂ -----------------> CH₂O (cell material) + CH₄  methanogenesis

Under aerobic conditions, methane and its derivatives (methanol, formaldehyde, etc.) can be oxidized as energy sources by bacteria called methylotrophs. Metabolically this is a version of decomposition or biodegradation during the carbon cycle which is discussed below.

Biodegradation is the process in the carbon cycle for which microbes get most credit (or blame).  Biodegradation is the decomposition of organic material (CH₂O) back to CO₂ + H₂O and H₂. In soil habitats, the fungi play a significant role in biodegradation, but the procaryotes are equally important. The typical decomposition scenario involves the initial degradation of biopolymers (cellulose, lignin, proteins, polysaccharides) by extracellular enzymes, followed by oxidation (fermentation or respiration) of the monomeric subunits. The ultimate end products are CO₂, H₂O and H₂, perhaps some NH₃ (ammonia) and sulfide (H₂S), depending on how one views the overall process. These products are scarfed up by lithotrophs and autotrophs for recycling. Procaryotes which play an important role in biodegradation in nature include the actinomycetes, clostridia, bacilli, arthrobacters and pseudomonads.

Overall Process of Biodegradation (Decomposition)

polymers (e.g. cellulose)-----------------> monomers (e.g. glucose) depolymerization

monomers-----------------> fatty acids (e.g. lactic acid, acetic acid, propionic acid) + CO₂ + H₂ fermentation

monomers + O₂ -----------------> CO₂ + H₂O aerobic respiration

The importance of microbes in biodegradation is embodied in the adage that "there is no known natural compound that cannot be degraded by some microorganism." The proof of the adage is that we aren't up to our ears in whatever it is that couldn't be degraded in the last 3.5 billion years. Actually, we are up to our ears in cellulose and lignin, which is better than concrete, and some places are getting up to their ears in teflon, plastic, styrofoam, insecticides, pesticides and poisons that are degraded slowly by microbes, or not at all.

Figure 1. The Carbon Cycle. Organic matter (CH₂O) derived from photosynthesis (plants, algae and cyanobacteria) provides nutrition for heterotrophs (e.g.  animals and associated bacteria), which convert it back to CO₂. Organic wastes, as well as dead organic matter in the soil and water, are ultimately broken down to CO₂ by microbial processes of biodegradation.

Recently, I asked a colleague, Professor Paul Weimer of the University of Wisconsin Department of Bacteriology, whether mathanogenesis, which utilizes CO₂ while producing CH₄ was better or worse on the greenhouse effect and global warming. This is his response. "Worse. During methanogenesis involving CO₂ reduction, the stoichiometry is 4H₂ + CO₂ --> CH₄ + 2 H₂O, so one mole of a greenhouse gas is exchanged for another. But methane is about 15 times more potent than is CO₂ in terms of heat absorption capability on a per-molecule basis, so the net effect is a functional increase in heat absorption by the atmosphere. Remember also that in most natural environments, around two-thirds of the methane is produced by aceticlastic methanogenesis (CH₃COOH --> CH₄ + CO₂) - an even less welcome situation, as BOTH products are greenhouse gases.