Sources and Sinks of Essential Elements

Biogeochemical cycles are pathways by which essential elements flow from the abiotic and biotic compartments of the Earth.

Key Takeaways

Reservoirbiogeochemical cycle

Earth's most important substances, including oxygen, nitrogen, and water, undergo transition and cycling between biotic (living) and abiotic (geological, atmospheric, and hydrologic) compartments.In the biogeochemical cycle, nutrients are exchanged from living cells to non-living cells.

Nutrient Cycles and the Biosphere

Biogeochemical cycles are vital to ecosystems.Assimilation of these nutrients into living organisms occurs in all four nitrogen cycles, the phosphorus cycle, the sulfur cycle, and the carbon cycle.Food webs lead to the transfer of these elements between living things, until organisms eventually die and release them back into the earth's crust.


Reservoirs of Essential Elements

In some cases, chemicals are taken out of circulation for long periods of time.Reservoirs are locations where elements are stored for a long period of time.Carbon is a storage mechanism for coal, and coal deposits can store carbon for several thousand years.Nitric oxide is considered to be a reservoir for carbon.

Humans and Biogeochemical Cycles

Although the Earth receives energy from the Sun, its chemical makeup is more or less constant.In general, supplies of essential elements don't change except when matter is added by meteorites.However, human activity can change the proportion of nutrients in reservoirs and circulation.The human use of fossil fuels has released carbon into the atmosphere, which increased the amount of carbon in circulation. Coal, for example, is a reservoir of carbon, but human use has released carbon into the atmosphere.Excess quantities of phosphorus and nitrogen, which are extracted from geological reservoirs and used in polymers, have led to the overgrowth of plant matter and have disrupted many ecosystems.

The Carbon Cycle

The carbon cycle describes the flow of carbon from the atmosphere to the marine and terrestrial biospheres, and the earth’s crust.

Learning Objectives

Outline the flow of carbon through the biosphere and abiotic matter on earth

Key Takeaways

lithospherechemoautotrophiccarbon cycle

The carbon cycle describes the flow of carbon between the biosphere, the geosphere, and the atmosphere, and is essential to maintaining life on earth.

Atmospheric Carbon Dioxide: Carbon in the earth’s atmosphere exists in two main forms: carbon dioxide and methane. Carbon dioxide leaves the atmosphere through photosynthesis, thus entering the terrestrial and marine biospheres. Carbon dioxide also dissolves directly from the atmosphere into bodies of water (oceans, lakes, etc.), as well as dissolving in precipitation as raindrops fall through the atmosphere. When dissolved in water, carbon dioxide reacts with water molecules and forms carbonic acid, which contributes to ocean acidity. Human activity over the past two centuries has significantly increased the amount of carbon in the atmosphere, mainly in the form of carbon dioxide, both by modifying ecosystems ‘ ability to extract carbon dioxide from the atmosphere and by emitting it directly, e.g. by burning fossil fuels and manufacturing concrete.

Terrestrial Biosphere: The terrestrial biosphere includes the organic carbon in all land-living organisms, both alive and dead, as well as carbon stored in soils. Although people often imagine plants as the most important part of the terrestrial carbon cycle, microorganisms such as single celled algae and chemoautotrophic bacteria are also important in converting atmospheric CO2 into terrestrial carbon. Carbon is incorporated into living things as part of organic molecules, either through photosynthesis or by animals that consume plants and algae. Some of the carbon in living things is released through respiration, while the rest remains in the tissue. Once organisms die, bacteria break down their tissues, releasing CO2 back into the atmosphere or into the soil.

Marine Biosphere: The carbon cycle in the marine biosphere is very similar to that in the terrestrial ecosystem. CO2 dissolves in the water and algae, plants and bacteria convert it into organic carbon. Carbon may transfer between organisms (from producers to consumers). Their tissues are ultimately broken down by bacteria and CO2 is released back into the ocean or atmosphere.

NASA | A Year in the Life of Earth’s CO2: An ultra-high-resolution NASA computer model has given scientists a stunning new look at how carbon dioxide in the atmosphere travels around the globe. Plumes of carbon dioxide in the simulation swirl and shift as winds disperse the greenhouse gas away from its sources. The simulation also illustrates differences in carbon dioxide levels in the northern and southern hemispheres and distinct swings in global carbon dioxide concentrations as the growth cycle of plants and trees changes with the seasons. The carbon dioxide visualization was produced by a computer model called GEOS-5, created by scientists at NASA Goddard Space Flight Center’s Global Modeling and Assimilation Office. The visualization is a product of a simulation called a “Nature Run.” The Nature Run ingests real data on atmospheric conditions and the emission of greenhouse gases and both natural and man-made particulates. The model is then left to run on its own and simulate the natural behavior of the Earth’s atmosphere. This Nature Run simulates January 2006 through December 2006. While Goddard scientists worked with a “beta” version of the Nature Run internally for several years, they released this updated, improved version to the scientific community for the first time in the fall of 2014.

Geologic Carbon: The earth’s crust also contains carbon. Much of the earth’s carbon is stored in the mantle, and has been there since the earth formed. Much of the carbon on the earth’s lithosphere (about 80%) is stored in limestone, which was formed from the calcium carbonate from the shells of marine animals. The rest of the carbon on the earth’s surface is stored in Kerogens, which were formed through the sedimentation and burial of terrestrial organisms under high heat and pressure.

Syntrophy and Methanogenesis

Bacteria that perform anaerobic fermentation often partner with methanogenic archea bacteria to provide necessary products such as hydrogen.

Learning Objectives

Assess syntrophy methanogenesis

Key Takeaways


Synthrophy, or cross feeding, occurs when one species eats the products of another.In anaerobic fermentation, methanogenic archaea bacteria and their partners are frequently cited as an example of syntrophy.

Methanogenesis in microbes is a form of anaerobic respiration, performed by bacteria in the domain Archaea. Unlike other microorganisms, methanogens do not use oxygen to respire; but rather oxygen inhibits the growth of methanogens. In methanogenesis, carbon is used as the terminal electron receptor instead of oxygen. Although there are a variety of potential carbon based compounds that are used as electron receptors, the two best described pathways involve the use of carbon dioxide and acetic acid as terminal electron acceptors.

Acetic Acid: \text{CO}_2 + 4\text{H}_2 \rightarrow\text{CH}_4 + 2\text{H}_2\text{O}

Carbon Dioxide: \text{CH}_3\text{COOH} \rightarrow\text{CH}_4 +\text{CO}_2

Many methanogenic bacteria that live in close association with bacteria produce fermentation products such as fatty acids longer than two carbon atoms, alcohols longer than one carbon atom, and branched chain and aromatic fatty acids. These products cannot be used in methanogenesis. Partner bacteria of the methanogenic archea therefore process these products. By oxydizing them to acetate, they allow them to be used in methanogenesis.

Methanogenic bacteria are important in the decomposition of biomass in most ecosystems. Only methanogenesis and fermentation can occur in the absence of electron acceptors other than carbon. Fermentation only allows the breakdown of larger organic compounds, and produces small organic compounds that can be used in methanogenesis. The semi-final products of decay (hydrogen, small organics, and carbon dioxide) are then removed by methanogenesis. Without methanogenesis, a great deal of carbon (in the form of fermentation products) would accumulate in anaerobic environments.

Methanogenic archea bacteria can also form associations with other organisms. For example, they may also associate with protozoans living in the guts of termites. The protozoans break down the cellulose consumed by termites, and release hydrogen, which is then used in methanogenesis.

The Phosphorus Cycle

Phosphorus, important for creating nucleotides and ATP, is assimilated by plants, then released through decomposition when they die.

Learning Objectives

Explain the phosphorous cycle

Key Takeaways


Phosphorus is an important element for living things because it is neccesary for nucleotides and ATP. Plants assimilate phosphorous from the environment and then convert it from inorganic phosphorous to organic phosphorous. Phosphorous can be transfered to other organisms when they consume the plants and algae. Animals either release phosphorous through urination or defecation, when they die and are broken down by bacteria. The organic phosphorous is released and converted back into inorganic phosphorous through decomposition. The phosphorous cycle differs from other nutrient cycles, because it never passes through a gaseous phase like the nitrogen or carbon cycles.

Phosphorous levels in aquatic ecosystems vary by season.In the spring, sediments that contain inorganic phosphorus are released by convection currents in warm waters.Plants and algae reproduce rapidly in phosphorus-rich waters.Phosphorous is then converted into organic phosphorous, and primary productivity declines.During the summer, plants and algae begin to wither, and bacteria decompose them, releasing inorganic phosphorus back into the ecosystem.When the phosphorous levels start to rise at the end of summer, primary plants and algae grow quickly again. Human activities influence the phosphorous cycle.Compared to other nutrients, phosphorus is considered a limiting nutrient.Farm run-off and drainage may contaminate aquatic ecosystems with excess phosphorus.A significant amount of artificial phosphorous may cause algae and plants to overgrow in aquatic ecosystems.If the excess plant material is broken down, the bacteria that decompose it can consume all of the oxygen in the water, causing dead zones.During eutrophication, bodies of water slowly become more productive as their nutrients accumulate.However, overgrowth of algae as a result of phosphorus fertilizers is called "eutrophication" or "hypertrophication," which generally causes harm to ecosystems.

Key Takeaways


It describes the transformation of nitrogen between different chemical forms.Approximately 78 percent of the Earth's atmosphere is composed of atmospheric nitrogen, but it is not in a form that can be utilized by living things.Various organisms exchange nitrogen among themselves and convert nitrogen into usable forms through complex species interactions.The production of amino acids and nucleotides requires nitrogen.This is true of all living things. Nitrogen (N2) that can be used by organisms must be fixed or converted into ammonia (NH3).Occasionally, lightning strikes can do this, but the majority of nitrogen fixation is achieved by bacteria living free in nature or symbiotically with them.As a result of the nitrogenase enzyme, these bacteria produce ammonia from gaseous nitrogen and hydrogen.After this, the bacteria further transform the ammonia into organic compounds.Lentils have nitrogen fixing bacteria that produce ammonia in exchange for sugars in their root nodules.In chemical plants, about 30% of the total fixed nitrogen is manufactured.

.It is usually carried out by bacteria in the soil, such as nitrobacter.Biologically, plants can absorb nitrate into their tissues, but they must be converted into usable form by bacteria in order to use it.This process is accomplished mainly by the bacteria genus Nitrobacter. Mineralization: Ammonification is the process of converting organic nitrogen, including nitrogen from dead organisms, into ammonium (NH4+).NITRIFICATION can also be used to convert ammonium.Through nitrification it can be recycled into a plant-available form or de-nitrified and returned to the atmosphere. ext[CH]_4 + ext[H]_2 ext[O]-ightarrow

The Sulfur Cycle

Many bacteria can reduce sulfur in small amounts, but some bacteria can reduce sulfur in large amounts, in essence, breathing sulfur.

Learning Objectives

Describe the sulfur cycle

Key Takeaways

extremophileassimilatory sulfate reduction

The Sulfur Cycle

The sulfur cycle describes the movement of sulfur through the atmosphere, mineral forms, and through living things. Although sulfur is primarily found in sedimentary rocks or sea water, it is particularly important to living things because it is a component of many proteins.

Sulfur is released from geologic sources through the weathering of rocks. Once sulfur is exposed to the air, it combines with oxygen, and becomes sulfate SO4. Plants and microbes assimilate sulfate and convert it into organic forms. As animals consume plants, the sulfur is moved through the food chain and released when organisms die and decompose.

Some bacteria – for example Proteus, Campylobacter, Pseudomonas and Salmonella – have the ability to reduce sulfur, but can also use oxygen and other terminal electron acceptors. Others, such as Desulfuromonas, use only sulfur. These bacteria get their energy by reducing elemental sulfur to hydrogen sulfide. They may combine this reaction with the oxidation of acetate, succinate, or other organic compounds.

The most well known sulfur reducing bacteria are those in the domain Archea, which are some of the oldest forms of life on Earth. They are often extremophiles, living in hot springs and thermal vents where other organisms cannot live. Lots of bacteria reduce small amounts of sulfates to synthesize sulfur-containing cell components; this is known as assimilatory sulfate reduction. By contrast, the sulfate-reducing bacteria considered here reduce sulfate in large amounts to obtain energy and expel the resulting sulfide as waste. This process is known as dissimilatory sulfate reduction. In a sense, they breathe sulfate.

Sulfur metabolic pathways for bacteria have important medical implications. For example, Mycobacterium tuberculosis (the bacteria causing tuberculosis) and Mycobacterium leprae (which causes leoprosy) both utilize sulfur, so the sulfur pathway is a target of drug development to control these bacteria.

The Iron Cycle

Iron is an important limiting nutrient required for plants and animals; it cycles between living organisms and the geosphere.

Learning Objectives

Compare the terrestrial and marine iron cycles

Key Takeaways


Iron (Fe) follows a geochemical cycle like many other nutrients. Iron is typically released into the soil or into the ocean through the weathering of rocks or through volcanic eruptions.

The Terrestrial Iron Cycle: In terrestrial ecosystems, plants first absorb iron through their roots from the soil. Iron is required to produce chlorophyl, and plants require sufficient iron to perform photosynthesis. Animals acquire iron when they consume plants, and iron is utilized by vertebrates in hemoglobin, the oxygen-binding protein found in red blood cells. Animals lacking in iron often become anemic and cannot transmit adequate oxygen. Bacteria then release iron back into the soil when they decompose animal tissue.

The Marine Iron Cycle: The oceanic iron cycle is similar to the terrestrial iron cycle, except that the primary producers that absorb iron are typically phytoplankton or cyanobacteria. Iron is then assimilated by consumers when they eat the bacteria or plankton. The role of iron in ocean ecosystems was first discovered when English biologist Joseph Hart noticed “desolate zones,” which are regions that lacked plankton but were rich in nutrients. He hypothesized that iron was the limiting nutrient in these areas. In the past three decades there has been research into using iron fertilization to promote alagal growth in the world’s oceans. Scientists hoped that by adding iron to ocean ecosystems, plants might grown and sequester atmospheric CO2. Iron fertilization was thought to be a possible method for removing the excess CO2 responsible for climate change. Thus far, the results of iron fertilization experiments have been mixed, and there is concern among scientists about the possible consequences of tampering nutrient cycles.