Carbon Cycle

Carbon is the element that defines life, and as such it is everywhere. The exchange of elements between sources and sinks is referred to as flux. Carbon is present in reduced forms, such as methane (CH4) and organic matter, and in more oxidized forms, such as carbon monoxide (CO) and carbon dioxide (C02).

Carbon fixation

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. 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., the 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 the deep, dark ocean may constitute a significant fraction of marine carbon fixation.

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. Alternatively, inorganic carbon (CO2) and organic carbon can be reduced anaerobically to methane (CH4).

Large amounts of methane are also generated in the guts of ruminant animals. Globally, ruminant animals, sediments found in rice paddies, coal mines, sewage treatment plants, landfills, marshes and mangrove swamps, and even archaea found in termite guts are important sources of methane.

Degradation of carbon compounds is influenced by a series of factors

The degradation of carbon compounds is influenced by a series of factors. These include
( 1) oxidation-reduction potential as determined by the relative abundance of electron donors and electron acceptors in the environment;
(2) availability of competing nutrients;
(3) abiotic conditions such as pH, temperature, 02, and osmotic conditions; and
(4) the microbial community present.

Many of the complex organic substrates used by microorganisms.

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.

Fungi and the streptomycetes 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 at a very slow rate. This diminished biodegradability under anoxic conditions results in accumulation of lignified materials, including the formation of peat bogs.

The term mineralization is used to describe the decomposition of organic matter to simpler, inorganic compounds (e.g., C02, NH3, CH4, H2). These compounds may or may not be recycled within the same environment. Microbes require each macronutrient in specific relative amounts, so if an environment is enriched in one nutrient but relatively deficient in another, the nutrient found in overabundance may not be completely recycled into living biomass.  Protein and chitin (present in insect exoskeletons and fungal cell walls) contain carbon, hydrogen, oxygen, and nitrogen. These compounds may provide more nitrogen than can be used relative to the amount of carbon available. Thus these minerals may be released to the environment. By contrast, nutrients that are converted into biomass become temporarily “tied up” and are unavailable for nutrient cycling; this is sometimes called nutrient immobilization.

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) from 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, growth of many microbes is often nitrogen limited. In other words, if higher concentrations of usable nitrogen (e.g., N03-, NH/) were available, the rate of microbial growth would increase.

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