The study of the cycling of chemicals between organisms and the surface environment of the Earth. The chemicals either can be taken up by organisms and used for growth and synthesis of living matter or can be processed to obtain energy. The chemical composition of plants and animals indicates which elements, known as nutrient elements, are necessary for life. The most abundant nutrient elements, carbon (C), hydrogen (H), and oxygen (O), supplied by the environment in the form of carbon dioxide (CO₂) and water (H₂O), are usually present in excess. The other nutrient elements, which are also needed for growth, may sometimes be in short supply; in this case they are referred to as limiting nutrients. The two most commonly recognized limiting nutrients are nitrogen (N) and phosphorus (P).

Biogeochemistry is concerned with both the biological uptake and release of nutrients, and the transformation of the chemical state of these biologically active substances, usually by means of energy-supplying oxidation-reduction reactions, at the Earth's surface. Emphasis is on how the activities of organisms affect the chemical composition of natural waters, the atmosphere, rocks, soils, and sediments. Thus, biogeochemistry is complementary to the science of ecology, which includes a concern with how the chemical composition of the atmosphere, waters, and so forth affects life.Ecology

The two major processes of biogeochemistry are photosynthesis and respiration. Photosynthesis involves the uptake, under the influence of sunlight, of carbon dioxide, water, and other nutrients by plants to form organic matter and oxygen. Respiration is the reverse of photosynthesis and involves the oxidation and breakdown of organic matter and the return of nitrogen, phosphorus, and other elements, as well as carbon dioxide and water, to the environment.Photosynthesis Plant respiration

Biogeochemistry is usually studied in terms of biogeochemical cycles of individual elements. There are short-term cycles ranging from days to centuries and long-term (geological) cycles ranging from thousands to millions of years.

There has been increasing interest in biogeochemistry because the human influence on short-term biogeochemical cycling has become evident. Perhaps the best-known example is the changes in the biogeochemical cycling of carbon due to the burning of fossil fuels and the cutting and burning of tropical rainforests. The cycles of nitrogen and phosphorus have been altered because of the use of fertilizer and the addition of wastes to lakes, rivers, estuaries, and the oceans. Acid rain, which results from the addition of sulfur and nitrogen compounds to the atmosphere by humans, affects biological systems in certain areas.

Carbon is the basic biogeochemical element. The atmosphere contains carbon in the form of carbon dioxide gas. There is a large annual flux of atmospheric carbon dioxide to and from forests and terrestrial biota, amounting to nearly 7% of total atmospheric carbon dioxide. This is because carbon dioxide is used by plants to produce organic matter through photosynthesis, and when the organic matter is broken down through respiration, carbon dioxide is released to the atmosphere. The concentration of atmospheric carbon dioxide shows a yearly oscillation because there is a strong seasonal annual cycle of photosynthesis and respiration in the Northern Hemisphere.

Breakdown of organic matter via respiration is accomplished mainly by bacteria that live in soils, sediments, and natural waters. There is a very large reservoir of terrestrial carbon in carbonate rocks, which contain calcium carbonate (CaCO₃), and in rocks such as shales which contain organic carbon. Major exchange of carbon between rocks and the atmosphere is very slow, on the scale of thousands to millions of years, compared to exchange between plants and the atmosphere, which can even be seasonal.Microbial ecology Soil microbiology

The oceans taken as a whole represent a major reservoir of carbon. Carbon in the oceans occurs primarily as dissolved (HCO₃)^- and to a lesser extent as dissolved carbon dioxide gas and carbonate ion [(CO₃)^2-]. The well-mixed surface ocean (the top 250 ft or 75 m) rapidly exchanges carbon dioxide with the atmosphere. However, the deep oceans are cut off from the atmosphere and mix with it on a long-term time scale of about 1000–2000 years. Most of the biological activity in the oceans occurs in the surface (or shallow) water where there is light and photosynthesis can occur.Maritime meteorology

The main biological process in seawater is photosynthetic production of organic matter by phytoplankton. Some of this organic matter is eaten by animals, which are in turn eaten by larger animals farther up in the food chain. Almost all of the organic matter along the food chain is ultimately broken down by bacterial respiration, which occurs primarily in shallow water, and the carbon dioxide is quickly recycled to the atmosphere.Food web Phytoplankton Seawater

Another major biological process is the secretion of shells and other hard structures by marine organisms. A biogeochemical cycle of calcium and bicarbonate exists within the oceans, linking the deep and shallow water areas. Bottom dwellers in shallow water, such as corals, mollusks, and algae, provide calcium carbonate skeletal debris. Since the shallow waters are saturated with respect to calcium carbonate, this debris accumulates on the bottom and is buried, providing the minerals that form carbonate rocks such as limestone and dolomite. Calcium carbonate is also derived from the shells of organisms inhabiting surface waters of the deep ocean; these are tiny, floating plankton such as foraminiferans, pteropods, and coccoliths. Much of the calcium carbonate from this source dissolves as it sinks into the deeper ocean waters, which are undersaturated with respect to calcium carbonate. The undissolved calcium carbonate accumulates on the bottom to form deep-sea limestone. The calcium and the bicarbonate ions [Ca²⁺ and (HCO₃)^-] dissolved in the deep ocean water eventually are carried to surface and shallow water, where they are removed by planktonic and bottom-dwelling organisms to form their skeletons.

The long-term biogeochemical carbon cycle occurs over millions of years when the calcium carbonate and organic matter that are buried in sediments are returned to the Earth's surface. There, weathering occurs which involves the reaction of oxygen with sedimentary organic matter with the release of carbon dioxide and water (analogous to respiration), and the reaction of water and carbon dioxide with carbonate rocks with the release of calcium and bicarbonate ions. Weathering processes

Fossil fuels (coal and oil) represent a large reservoir of carbon. Burning of fossil fuels releases carbon dioxide to the atmosphere, and an increase in the atmospheric concentration of carbon dioxide has been observed since the mid-1950s. While much of the increase is attributed to fossil fuels, deforestation by humans accompanied by the decay or burning of trees is another possible contributor to the problem.

When estimates are made of the amount of fossil fuels burned from 1959 to 1980, only about 60% of the carbon dioxide released can be accounted for in the atmospheric increase in carbon dioxide. The remaining 40% is known as excess carbon dioxide. The surface oceans are an obvious candidate for storage of most of the excess carbon dioxide by the reaction of carbon dioxide with dissolved carbonate to form bicarbonate. Because the increase in bicarbonate concentration in surface waters due to excess carbon dioxide uptake would be small, it is difficult to detect whether such a change has occurred. Greater quantities of excess carbon dioxide could be stored as bicarbonate in the deeper oceans, but this process takes a long time because of the slow rate of mixing between surface and deep oceans.

An increase in atmospheric carbon dioxide is of concern because of the greenhouse effect. The carbon dioxide traps heat in the atmosphere; notable increases in atmospheric carbon dioxide should cause an increase in the Earth's surface temperature by as much as several degrees. This temperature increase would be greater at the poles, and the effects could include melting of polar ice, a rise in sea level, and changes in rainfall distribution, with droughts in interior continental areas such as the Great Plains of the United States.Drought Greenhouse effect

Nitrogen is dominantly a biogenic element and has no important mineral forms. It is a major atmospheric constituent with a number of gaseous forms, including molecular nitrogen gas (N₂), nitrogen dioxide (NO₂), nitric oxide (NO), ammonia (NH₃), and nitrous oxide (N₂O). As an essential component of plant and animal matter, it is extensively involved in biogeochemical cycling. On a global basis, the nitrogen cycle is greatly affected by human activities.

Nitrogen gas (N₂) makes up 80% of the atmosphere by volume; however, nitrogen is unreactive in this form. In order to be available for biogeochemical cycling by organisms, nitrogen gas must be fixed, that is, combined with oxygen, carbon, or hydrogen. There are three major sources of terrestrial fixed nitrogen: biological nitrogen fixation by plants, nitrogen fertilizer application, and rain and particulate dry deposition of previously fixed nitrogen. Biological fixation occurs in plants such as legumes (peas and beans) and lichens in trees, which incorporate nitrogen from the atmosphere into their living matter; about 30% of worldwide biological fixation is due to human cultivation of these plants. Nitrogen fertilizers contain industrially fixed nitrogen as both nitrate and ammonium.Fertilizer

Fixed nitrogen in rain is in the forms of nitrate [(NO₃)^-] and ammonium [(NH₄)⁺] ions. Major sources of nitrate, which is derived from gaseous atmospheric nitrogen dioxide (and nitric oxide), include (in order of importance) combustion of fossil fuel, especially by automobiles; forest fires (mostly caused by humans); and lightning. Nitrate in rain, in addition to providing soluble fixed nitrogen for photosynthesis, contributes nitric acid (HNO₃), a major component of acid rain. Sources of ammonium, which is derived from atmospheric ammonia gas (NH₃), include animal and human wastes, soil loss from decomposition of organic matter, and fertilizer release.Acid rain

The basic land nitrogen cycle involves the photosynthetic conversion of the nitrate and ammonium ions dissolved in soil water into plant organic material. Once formed, the organic matter may be stored or broken down. Bacterial decomposition of organic matter (ammonification) produces soluble ammonium ion which can then be either taken up again in photosynthesis, released to the atmosphere as ammonia gas, or oxidized by bacteria to nitrate ion (nitrification).

Nitrate ion is also soluble, and may be used in photosynthesis. However, part of the nitrate may undergo reduction (denitrification) by soil bacteria to nitrogen gas or to nitrous oxide which are then lost to the atmosphere. Compared to the land carbon cycle, the land nitrogen cycle is considerably more complex, and because of the large input of fixed nitrogen by humans, it is possible that nitrogen is building up on land. However, this is difficult to determine since the amount of nitrogen gas recycled to the atmosphere is not known and any changes in the atmospheric nitrogen concentration would be too small to detect.Nitrogen cycle

The oceans are another major site of nitrogen cycling: the amount of nitrogen cycled biogenically, through net primary photosynthetic production, is about 13 times that on land. The main links between the terrestrial and the oceanic nitrogen cycles are the atmosphere and rivers. Nitrogen gases carried in the atmosphere eventually fall as dissolved inorganic (mainly nitrate) and organic nitrogen and particulate organic nitrogen in rain on the oceans. The flux of river nitrogen lost from the land is only about 9% of the total nitrogen recycled biogeochemically on land each year and only about 25% of the terrestrial nitrogen flux from the biosphere to the atmosphere.

River nitrogen is an important nitrogen source to the oceans; however, the greatest amount of nitrogen going into ocean surface waters comes from the upwelling of deeper waters, which are enriched in dissolved nitrate from organic recycling at depth. Dissolved nitrate is used extensively for photosynthesis by marine organisms, mainly plankton. Bacterial decomposition of the organic matter formed in photosynthesis results in the release of dissolved ammonium, some of which is used directly in photosynthesis. However, most undergoes nitrification to form nitrate, and much of the nitrate may undergo denitrification to nitrogen gas which is released to the atmosphere. A small amount of organic-matter nitrogen is buried in ocean sediments, but this accounts for a very small amount of the nitrogen recycled each year. There are no important inorganic nitrogen minerals such as those that exist for carbon and phosphorus, and thus there is no mineral precipitation and dissolution.Upwelling

Phosphorus, an important component of organic matter, is taken up and released in the form of dissolved inorganic and organic phosphate. Phosphorus differs from nitrogen and carbon in that it does not form stable atmospheric gases and therefore cannot be obtained from the atmosphere. It does form minerals, most prominently apatite (calcium phosphate), and insoluble iron (Fe) and aluminum (Al) phosphate minerals, or it is adsorbed on clay minerals. The amount of phosphorus used in photosynthesis on land is large compared to phosphorus inputs to the land. The major sources of phosphorus are weathering of rocks containing apatite and mining of phosphate rock for fertilizer and industry. A small amount comes from precipitation and dry deposition.

Phosphorus is lost from the land principally by river transport, which amounts to only 7% of the amount of phosphorus recycled by the terrestrial biosphere; overall, the terrestrial biosphere conserves phosphorus. Humans have greatly affected terrestrial phosphorus: deforestation and agriculture have doubled the amount of phosphorus weathering; phosphorus is added to the land as fertilizers and from industrial wastes, sewage, and detergents. Thus, about 75% of the terrestrial input is anthropogenic; in fact, phosphorus may be building up on the land.

In the oceans, phosphorus occurs predominantly as dissolved orthophosphates [PO₄^3-, (HPO₄)^2- and (H₂PO₄)^-]. Since it follows the same cycle as do carbon and nitrogen, dissolved orthophosphate is depleted in surface ocean waters where both photosynthesis and respiration occur, and the concentration builds up in deeper water where organic matter is decomposed by bacterial respiration. The major phosphorus input to the oceans is from rivers, with about 5% coming from rain. However, 75% of the river phosphorus load is due to anthropogenic pollutants; humans have changed the ocean balance of phosphorus. Most of the dissolved oceanic orthophosphate is derived from recycled organic matter. The output of phosphorus from the ocean is predominantly biogenic: organic phosphorus is buried in sediments; a smaller amount is removed by adsorption on volcanic iron oxides. In the geologic past, there was a much greater inorganic precipitation of phosphorite (apatite) from seawater than at present, and this has resulted in the formation of huge deposits which are now mined.

Biogeochemical cycling of phosphorus and nitrogen in lakes follows a pattern that is similar to oceanic cycling: there is nutrient depletion in surface waters and enrichment in deeper waters. Oxygen consumption by respiration in deep water sometimes leads to extensive oxygen depletion with adverse effects on fish and other biota. In lakes, phosphorus is usually the limiting nutrient.

Many lakes have experienced greatly increased nutrient (nitrogen and phosphorus) input due to human activities. This stimulates a destructive cycle of biological activity: very high organic productivity, a greater concentration of plankton, and more photosynthesis. The result is more organic matter falling into deep water with increased depletion of oxygen and greater accumulation of organic matter on the lake bottom. This process, eutrophication, can lead to adverse water quality and even to the filling up of small lakes with organic matter.Eutrophication Limnology

A dominant flux in the global sulfur cycle is the release of 65–70 teragrams of sulfur per year to the atmosphere from burning of fossil fuels. Sulfur contaminants in these fuels are released to the atmosphere as sulfur dioxide (SO₂) which is rapidly converted to aerosols of sulfuric acid (H₂SO₄), the primary contributor to acid rain. Forest burning results in an additional release of sulfur dioxide. Overall, the broad range of human activities contribute 75% of sulfur released into the atmosphere. Natural sulfur sources over land are predominantly the release of reduced biogenic sulfur gases [mainly hydrogen sulfide (H₂S) and dimethyl sulfide] from marine tidal flats and inland waterlogged soils and, to much lesser extent, the release of volcanic sulfur. The atmosphere does not have an appreciable reservoir of sulfur because most sulfur gases are rapidly returned (within days) to the land in rain and dry deposition. There is a small net flux of sulfur from the atmosphere over land to the atmosphere over the oceans.

Ocean water constitutes a large reservoir of dissolved sulfur in the form of sulfate ions [(SO₄)^2-]. Some of this sulfate is thrown into the oceanic atmosphere as sea salt from evaporated sea spray, but most of this is rapidly returned to the oceans. Another major sulfur source in the oceanic atmosphere is the release of oceanic biogenic sulfur gases (such as dimethyl sulfide) from the metabolic activities of oceanic organisms and organic matter decay. Marine organic matter contains a small amount of sulfur, but sulfur is not a limiting element in the oceans.

Another large flux in the sulfur cycle is the transport of dissolved sulfate in rivers. However, as much as 43% of this sulfur may be due to human activities, both from burning of fossil fuels and from fertilizers and industrial wastes. The weathering of sulfur minerals, such as pyrite (FeS₂) in shales, and the evaporite minerals, gypsum and anhydrite, make an important contribution to river sulfate. The major mechanism for removing sulfate from ocean water is the formation and burial of pyrite in oceanic sediments, primarily nearshore sediments. (The sulfur fluxes of sea salt and biogenic sulfur gases do not constitute net removal from the oceans since the sulfur is recycled to the oceans.)

The main processes affecting atmospheric oxygen are photosynthesis and respiration; however, these processes are almost perfectly balanced against one another and, thus, do not exert a simple effect on oxygen levels. Only the very small excess of photosynthesis over respiration, manifested by the burial of organic matter in sediments, is important in raising the level of oxygen. This excess is so small, and the reservoir of oxygen so large, that if the present rate of organic carbon burial were doubled and the other rates remained constant, it would take 5–10 million years for the amount of atmospheric oxygen to double. Nevertheless, this is a relatively short time from a geological perspective.Atmosphere Atmospheric chemistry Biosphere Geochemistry Hydrosphere Marine sediments