Carbon is the element that defines life, and as such, it is everywhere. The carbon cycle is often regarded in terms of sources, sinks, and reservoirs of CO2. Sources, such as heterotrophic microbes, release carbon as CO2, whereas sinks include plants and phytoplankton, which take up CO2 from the atmosphere.
Reservoirs store carbon for geological periods of time. The exchange of elements between sources and sinks is referred to as flux. Carbon is present in reduced forms, such as methane (CH4) and other, more complex organic matter, and in the oxidized, inorganic forms, carbon monoxide (CO) and carbon dioxide (CO2).
Although carbon is continuously transformed from one form to another, for the sake of clarity, we shall say that the cycle “begins” with carbon fixation—the conversion of CO2 into organic matter (figure).
Plants such as trees and crops are often regarded as the principal CO2-fixing organisms, but at least half the carbon on Earth is fixed by microbes, particularly marine photosynthetic bacteria and protists (e.g., cyanobacteria in the genera Prochlorococcus and Synechococcus, and diatoms, respectively).
Importantly, microbes also fix carbon in anoxic environments using anoxygenic photosynthesis as well as by chemolithoautotrophy in the absence of light. In fact, recent evidence suggests that bacterial chemolithoautotrophy in deep, dark subsurface sediments may constitute a significant fraction of global carbon fixation.
Alternatively, inorganic carbon (CO2) can be reduced anaerobically to methane (CH4). Recall that only archaea form methane from either H2 + CO2 or H2 + acetate. methane produced in sediments is then oxidized either aerobically by proteobacteria or anaerobically by archaea or newly discovered bacteria that couple methane oxidation with denitrification (figure).
Large amounts of methane are also generated in the guts of ruminant animals. Globally, sediments found in rice paddies, coal mines, sewage treatment plants, landfills, marshes and mangrove swamps, and archaea found in the guts of ruminant animals and even termites are important sources of methane.
All fixed carbon enters a common pool of organic matter that can then be oxidized back to CO2 through aerobic or anaerobic respiration and fermentation (i.e., heterotrophy). In the carbon cycle, no distinction is made between the different types of organic matter formed and degraded.
This is a marked oversimplification because organic matter varies widely in terms of elemental composition, the structure of basic repeating units, and linkages between repeating units.
Its degradation is also influenced by other factors, including
- oxidation-reduction potential;
- availability of competing nutrients;
- abiotic conditions such as pH, temperature, O2, and osmotic conditions; and
- the microbial community present. Many of the complex organic substrates used by microorganisms are summarized in table.
Lignin, an important structural component in mature plant materials, is notoriously stable. Lignin is actually a family of complex amorphous polymers linked by carbon-carbon and carbon-ether bonds (see figure).
Filamentous microorganisms—fungi and the streptomycetes— secrete hydrolytic enzymes that degrade lignin by oxidative depolymerization, a process that requires oxygen.
A few microbes, such as the purple bacterium Rhodopseudomonas palustris, can degrade lignin anaerobically but very slowly. This diminished biodegradability under anoxic conditions results in the accumulation of lignified materials, including the formation of peat bogs.
Two terms are helpful in considering the fate and availability of organic materials in nature: mineralization and immobilization.
Mineralization describes the decomposition of organic matter to simpler, inorganic compounds (e.g., CO2, NH3, CH4, H2). These compounds may or may not be recycled within the same environment.
By contrast, nutrients (including carbon) that are converted into biomass become temporarily unavailable for nutrient cycling; this is called nutrient immobilization. Saprophytes, which degrade dead organic material, as well as viruses, protists, and other predators are important in recycling immobilized organic compounds.
Many complex substrates contain only carbon, hydrogen, and oxygen. Growth using these substrates demands that microbes acquire the remaining nutrients (e.g., N, P, S, and Fe) elsewhere in the environment.
This is often very difficult, as the concentration of nitrogen, phosphorus, and iron may be very low. When the supply of a macronutrient is insufficient to support maximal growth, that nutrient is said to be limiting. For instance, in open-ocean microbial communities, the growth of many microbes is often nitrogen limited.
In other words, if higher concentrations of usable nitrogen (e.g., NO3–, NH4+) were available, the rate of microbial growth would increase.
This phenomenon is called Leibig’s law of the minimum, named after the nineteenth-century chemist Justus van Leibig