The geochemistry of carbon is the study of the transformations involving the element carbon within the systems of the Earth. To a large extent this study is organic geochemistry, but it also includes the very important carbon dioxide. Carbon is transformed by life, and moves between the major phases of the Earth, including the water bodies, atmosphere, and the rocky parts. Carbon is important in the formation of organic mineral deposits, such as coal, petroleum or natural gas. Most carbon is cycled through the atmosphere into living organisms and then respirated back into the atmosphere. However an important part of the carbon cycle involves the trapping of living matter into sediments. The carbon then becomes part of a sedimentary rock when lithification happens. Human technology or natural processes such as weathering, or underground life or water can return the carbon from sedimentary rocks to the atmosphere. From that point it can be transformed in the rock cycle into metamorphic rocks, or melted into igneous rocks. Carbon can return to the surface of the Earth by volcanoes or via uplift in tectonic processes. Carbon is returned to the atmosphere via volcanic gases. Carbon undergoes transformation in the mantle under pressure to diamond and other minerals, and also exists in the Earth's outer core in solution with iron, and may also be present in the inner core.
Carbon can form a huge variety stable compounds. It is an essential component of living matter. Living organisms can live in a limited range of conditions on the Earth that are limited by temperature and the existence of liquid water. The potential habitability of other planets or moons can also be assessed by the existence of liquid water.
Carbon makes up only 0.08% of the combination of the lithosphere, hydrosphere, and atmosphere. Yet it is the twelfth most common element there. In the rock of the lithosphere, carbon commonly occurs as carbonate minerals containing calcium or magnesium. It is also found as fossil fuels in coal and petroleum and gas. Native forms of carbon are much rarer, requiring pressure to form. Pure carbon exists as graphite or diamond.
The deeper parts of Earth such as the mantle are very hard to discover. Few samples are known, in the form of uplifted rocks, or xenoliths. Even fewer remain in the same state they were in where the pressure and temperature is much higher. Some diamonds retain inclusions held at pressures they were formed at, but the temperature is much lower at the surface. Iron meteorites may represent samples of the core of an asteroid, but it would have formed under different conditions to the Earth's core. Therefore, experimental studies are conducted in which minerals or substances are compressed and heated to determine what happens in similar conditions to the planetary interior.
The two common isotopes of carbon are stable. On Earth, carbon 12, 12C is by far the most common at 98.894%. Carbon 13 is much rarer averaging 1.106%. This percentage can vary slightly and its value is important in isotope geochemistry whereby the origin of the carbon is suggested.
Origins
Formation Carbon can be produced in stars at least as massive as the Sun by fusion of three helium-4 nuclei: 4He + 4He + 4He --> 12C. This is the triple alpha process. In stars as massive as the Sun, carbon-12 is also converted to carbon-13 and then onto nitrogen-14 by fusion with protons. 12C + 1H --> 13C + e+. 13C + 1H --> 14N. In more massive stars, two carbon nuclei can fuse to magnesium, or a carbon and an oxygen to sulfur.
Astrochemistry In molecular clouds, simple carbon molecules are formed, including carbon monoxide and dicarbon. Reactions with the trihydrogen cation of the simple carbon molecules yield carbon containing ions that readily react to form larger organic molecules. Carbon compounds that exist as ions, or isolated gas molecules in the interstellar medium, can condense onto dust grains. Carbonaceous dust grains consist mostly of carbon. Grains can stick together to form larger aggregates.
Earth formation Meteorites and interplanetary dust shows the composition of solid material at the start of the Solar System, as they have not been modified since its formation. Carbonaceous chondrites are meteorites with around 5% carbon compounds. Their composition resembles the Sun's minus the very volatile elements like hydrogen and noble gases. The Earth is believed to have formed by the gravitational collapse of material like meteorites.
Important effects on Earth in the first Hadian Era include strong solar winds during the T-Tauri stage of the Sun. The Moon forming impact caused major changes to the surface. Juvenile volatiles outgased from the early molten surface of the Earth. These included carbon dioxide and carbon monoxide. The emissions probably did not include methane, but the Earth was probably free of molecular oxygen. The Late Heavy Bombardment was between 4.0 and 3.8 billion years ago (Ga). To start with, the Earth did not have a crust as it does today. Plate tectonics in its present form commenced about 2.5 Ga.
Early sedimentary rocks formed under water date to 3.8 Ga. Pillow lavas dating from 3.5 Ga prove the existence of oceans. Evidence of early life is given by fossils of stromatolites, and later by chemical tracers.
Organic matter continues to be added to the Earth from space via interplanetary dust, which also includes some interstellar particles. The amounts added to the Earth were around 60,000 tonnes per year about 4 Ga.
Isotope Biological sequestration of carbon causes enrichment of carbon-12, so that substances that originate from living organisms have a higher carbon-12 content. Due to the kinetic isotope effect, chemical reactions can happen faster with lighter isotopes, so that photosynthesis fixes lighter carbon-12 faster than carbon-13. Also lighter isotopes diffuse across a biological membrane faster. Enrichment in carbon 13 is measured by delta 13C(o/oo) = [(13C/12C)sample/(13C/12C)standard - 1] * 1000. The common standard for carbon is Cretaceous Peedee formation belemnite.
Stereoisomers Complex molecules, in particular those containing carbon can be in the form of stereoisomers. With abiotic processes they would be expected to be equally likely, but in carbonaceous chondrites this is not the case. The reasons for this are unknown.
Crust The outer layer of the Earth, the crust along with its outer layers contain about 1020 kg of carbon. This is enough for each square meter of the surface to have 200 tons of carbon.
Sedimentation Carbon added to sedimentary rocks can take the form of carbonates, or organic carbon compounds. In order of source quantity the organic carbon comes from phytoplankton, plants, bacteria and zooplankton. However terrestrial sediments may be mostly from higher plants, and some oxygen deficient sediments from water may be mostly bacteria. Fungi and other animals make insignificant contributions.Killops page 24 On the oceans the main contributor of organic matter to sediments is plankton, either dead fragments or faecal pellets termed marine snow. Bacteria degrade this matter in the water column, and the amount surviving to the ocean floor is inversely proportional to the depth. This is accompanied by biominerals consisting of silicates and carbonates. The particulate organic matter in sediments is about 20% of known molecules 80% of material that cannot be analysed. Detritivores consume some of the fallen organic materials. Aerobic bacteria and fungi also consume organic matter in the oxic surface parts of the sediment. Coarse-grained sediments are oxygenated to about half a meter, but fine grained clays may only have a couple of millimetres exposed to oxygen. The organic matter in the oxygenated zone will become completely mineralized if it stays there long enough.
Deeper in sediments where oxygen is exhausted, anaerobic biological processes continue at a slower rate. These include anaerobic mineralization making ammonium, phosphate and sulfide ions; fermentation making short chain alcohols, acids or methyl amines; acetogenesis making acetic acid; methanogenesis making methane, and sulfate, nitrite and nitrate reduction. Carbon dioxide and hydrogen are also outputs. Under freshwater, sulfate is usually very low, so methanogenesis is more important. Yet other bacteria can convert methane, back into living matter, by oxidising with other substrates. Bacteria can reside at great depths in sediments. However sedimentary organic matter accumulates the indigestible components.
Deep bacteria may be lithotrophes, using hydrogen, and carbon dioxide as a carbon source.
In the oceans and other waters there is much dissolved organic materials. These are several thousand years old on average, and are called gelbstoff (yellow substance) particularly in fresh waters. Much of this is tannins. The nitrogen containing materials here appear to be amides, perhaps from peptidoglycans from bacteria. Microorganisms have trouble consuming the high molecular weight dissolved substances, but quickly consume small molecules.
From terrestrial sources black carbon produced by charring is an important component. Fungi are important decomposers in soil.
Macromolecules Proteins are normally hydrolysed slowly even without enzymes or bacteria, with a half-life of 460 years, but can be preserved if they are desiccated, pickled or frozen. Being enclosed in bone also helps preservation. Over time the amino acids tend to racemize, and those with more functional groups are lost earlier. Protein still will degrade on the timescale of a million years. DNA degrades rapidly, lasting only about four years in water. Cellulose and chitin have a half-life in water at 25° of about 4.7 million years. Enzymes can accelerate this by a factor of 1017. About 1011 tons of chitin are produced each year, but it is almost all degraded.
Lignin is only efficiently degraded by fungi, white rot, or brown rot. These require oxygen.
Lipids are hydrolysed to fatty acids over long time periods. Plant cuticle waxes are very difficult to degrade, and may survive over geological time periods.
Preservation More organic matter is preserved in sediments if there is high primary production, or the sediment is fine-grained. The lack of oxygen helps preservation greatly, and that also is caused by a large supply of organic matter. Soil does not usually preserve organic matter, it would need to be acidified or water logged, as in the bog. Rapid burial ensures the material gets to an oxygen free depth, but also dilutes the organic matter. A low energy environment ensures the sediment is not stirred up and oxygenated. Salt marshes and mangroves meet some of these requirements, but unless the sea level is rising will not have a chance to accumulate much. Coral reefs are very productive, but are well oxygenated, and recycle everything before it is buried.
Sphagnum bog In dead Sphagnum, sphagnan a polysaccharide with D-lyxo-5-hexosulouronic acid is a major remaining substance. It makes the bog very acidic, so that bacteria cannot grow. Not only that, the plant ensures there is no available nitrogen. Holocellulose also absorbs any digestive enzymes around. Together this leads to major accumulation of peat under sphagnum bogs.
Mantle Earth's mantle is a significant reservoir of carbon. The mantle contains more carbon than the crust, oceans, biosphere, and atmosphere put together. The figure is estimated to be very roughly 1022 kg. Carbon concentration in the mantle is very variable, varying by more than a factor of 100 between different parts.