Nutrient Cycles

Sources and Sinks of Essential Elements

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

Learning Objectives

Identify sources and sinks of essential elements

Key Takeaways

Key Points

  • Biogeochemical cycles are pathways by which nutrients flow between the abiotic and abiotic compartments of the Earth. The abiotic portion of the Earth includes the lithosphere (the geological component of the Earth) and the hydrosphere (the Earth’s water).
  • Ecosystems rely on biogeochemical cycles. Many of the nutrients that living things depend on, such as carbon, nitrogen, and phosphorous are in constant circulation.
  • Essential elements are often stored in reservoirs, where they can be taken out of circulation for years. For example, coal is a reservoir for carbon.
  • Humans can affect biogeochemical cycles. Humans extract carbon and nitrogen from the geosphere and use them for energy and fertilizer. This has increased the amount of these elements in circulation, which has detrimental effects on ecosystems.

Key Terms

  • Reservoir: Reservoirs are places where essential elements are sequestered for long periods of time.
  • biogeochemical cycle: A pathway by which a chemical element or molecule moves through both biotic (biosphere) and abiotic (lithosphere, atmosphere, and hydropshere) compartments of the planet.

Most important substances on Earth, such as oxygen, nitrogen, and water undergo turnover or cycling through both the biotic (living) and abiotic (geological, atmospheric, and hydrologic) compartments of the Earth. Flows of nutrients from living to non-living components of the Earth are called biogeochemical cycles.

Nutrient Cycles and the Biosphere

Ecosystems hinge on biogeochemical cycles. The nitrogen cycle, the phosphorous cycle, the sulfur cycle, and the carbon cycle all involve assimilation of these nutrients into living things. These elements are transferred among living things through food webs, until organisms ultimately die and release them back into the geosphere.

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The Carbon Cycle: The element carbon moves from the biosphere to the geosphere and the hydrosphere. This flow from abiotic to biotic compartments of the Earth is typical of biogeochemical cycles.

Reservoirs of Essential Elements

Chemicals are sometimes sequestered for long periods of time and taken out of circulation. Locations where elements are stored for long periods of time are called reservoirs. Coal is a reservoir for carbon, and coal deposits can house carbon for thousands of years. The atmosphere is considered a reservoir for nitrogen.

Humans and Biogeochemical Cycles

Although the Earth receives energy from the Sun, the chemical composition of the planet is more or less fixed. Matter is occasionally added by meteorites, but supplies of essential elements generally do not change. However, human activity can change the proportion of nutrients that are in reservoirs and in circulation. For example, coal is a resevoir of carbon, but the human use of fossil fuels has released carbon into the atmosphere, increasing the amount of carbon in circulation. Likewise, phosphorous and nitrogen are extracted from geological reservoirs and used in phosphorous, and excesses of these elements have caused the overgrowth of plant matter and the disruption of 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

Key Points

  • Atmospheric carbon is usually in the form of CO2. Carbon dioxide is converted to organic carbon through photosynthesis by primary producers such as plants, bacteria, and algae.
  • Some organic carbon is returned to the atmosphere as CO2 during respiration. The rest of the organic carbon may cycle from organism to organism through the food chain. When an organism dies, it is decomposed by bacteria and its carbon is released into the atmosphere or the soil.
  • Carbon is also found in the earth’s crust, primarily as limestone and kerogens.

Key Terms

  • lithosphere: The rigid, mechanically strong, outer layer of the earth; divided into twelve major tectonic plates.
  • chemoautotrophic: An organism obtaining its nutrition through the oxidation of non-organic compounds (or other chemical processes); as opposed to the process of photosynthesis.
  • carbon cycle: The physical cycle of carbon through the Earth’s biosphere, geosphere, hydrosphere and atmosphere that includes such processes as photosynthesis, decomposition, respiration and carbonification.

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

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The Carbon Cycle: The carbon cycle describes the flow of carbon between the atmosphere, the biosphere, and the geosphere.

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

Key Points

  • Methanogenic bacteria are only found in the domain Archea, which are bacteria with no nucleus or other organelles.
  • Methanogenesis is a form of respiration in which carbon rather than oxygen is used as an electron acceptor.
  • Bacteria that perform anaerobic fermentation often partner with methanogenic bacteria. During anaerobic fermentation, large organic molecules are broken down into hydrogen and acetic acid, which can be used in methanogenic respiration.
  • There are other examples of syntrophic relationships between methanogenic bacteria and mircoorganisms: protozoans in the guts of termites break down cellulose and produce hydrogen which can be used in methanogenesis.

Key Terms

  • Archea: A domain of single-celled microorganisms. These microbes have no cell nucleus or any other membrane-bound organelles within their cells.
  • syntrophy: A phenomenon where one species lives off the products of another species.
  • methanogenesis: The generation of methane by anaerobic bacteria.

Syntrophy or cross feeding is when one species lives off the products of another species. A frequently cited example of syntrophy are methanogenic archaea bacteria and their partner bacteria that perform anaerobic fermentation.

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Methanogenic Bacteria in Termites: Methanogenic bacteria have a syntrophic relationship with protozoans living in the guts of termites. The protozoans break down cellulose, releasing H2 which is then used in methanogenesis.

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: [latex]\text{CO}_2 + 4\text{H}_2 \rightarrow\text{CH}_4 + 2\text{H}_2\text{O}[/latex]

Carbon Dioxide: [latex]\text{CH}_3\text{COOH} \rightarrow\text{CH}_4 +\text{CO}_2[/latex]

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

Key Points

  • Phosphorous is important for the production of ATP and nucleotides.
  • Inorganic phosphorous is found in the soil or water. Plants and algae assimilate inorganic phosphorus into their cells, and transfer it to other animals that consume them.
  • When organisms die, their phosphorous is released by decomposer bacteria.
  • Aquatic phosphorous follows a seasonal cycle, inorganic phosphorous peaks in the spring causing rapid algae and plant growth, and then declines. As plants die, it is re-released into the water.
  • Phosphorous based fertilizers can cause excessive algae growtin in aquatic systems, which can have negative impacts on the environment.

Key Terms

  • hypertrophication: the ecosystem response to the addition of artificial or natural substances, such as nitrates and phosphates, through fertilizers or sewage, to an aquatic system. This response is usually an increase in primary production.

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.

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The aquatic phosphorous cycle: Phosphorous is converted between its organic and inorganic forms. Plants convert phosphorous to its organic form, and bacteria convert it back to the inorganic form through decomposition

Phosphorous levels follow a seasonal pattern in aquatic ecosystems. In the spring, inorganic phosphorous is released from the sediment by convection currents in the warming water. When phosphorous levels are high, algae and plants reproduce rapidly. Much of the phosphorous is then converted to organic phosphorous, and primary productivity then declines. Later in the summer, the plants and algae begin to die off, and bacteria decompose them, and inorganic phosphorus is released back into the ecosystem. As phosphorous levels begin to increase at the end of the summer, primary plants and algae begin to rapidly grow again.

The phosphorous cycle is affected by human activities. Although phosphorous is normally a limiting nutrient, most agricultural fertilizers contain phosphorous. Run-off and drainage from farms can flood aquatic ecosystems with excess phosphorus. Artificial phosphorous can cause over growth of algae and plants in aquatic ecosytems. When the excess plant material is broken down, the decomposing bacteria can use up all the oxygen in the water causing dead zones. Most bodies of water gradually become more productive over time through the slow, natural accumulation of nutrients in a process called eutrophication. However, overgrowth of algae due to phosphorous fertilizer is called “cultural eutrophication” or “hypertrophication,” and is generally negative for ecosystems.

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Hypertrophication on the Potomac River: The bright green color of the water is the result of algae blooms in response to the addition of phosphorous based fertilizers.

The Nitrogen Cycle

The nitrogen cycle is the process by which nitrogen is converted from organic to inorganic forms; many steps are performed by microbes.

Learning Objectives

Describe the nitrogen cycle and how it is affected by human activity

Key Takeaways

Key Points

  • Nitrogen is converted from atmospheric nitrogen (N2) into usable forms, such as NO2-, in a process known as fixation. The majority of nitrogen is fixed by bacteria, most of which are symbiotic with plants.
  • Recently fixed ammonia is then converted to biologically useful forms by specialized bacteria. This occurs in two steps: first, bacteria convert ammonia in to (nitrites) NO2-, and then other bacteria species convert it to NO3- (nitrate).
  • Nitriates are a form of nitrogen that is usable by plants. It is assimilated into plant tissue as protein. The nitrogen is passed through the food chain by animals that consume the plants, and then released into the soil by decomposer bacteria when they die.
  • De-nitrifying bacteria convert NO2- back into atmospheric nitrogen (N2), completing the cycle.

Key Terms

  • de-nitrification: A microbially facilitated process of nitrate reduction that may ultimately produce molecular nitrogen (N2) through a series of intermediate gaseous nitrogen oxide products.
  • nitrification: The biological oxidation of ammonia with oxygen into nitrite followed by the oxidation of these nitrites into nitrates.
  • ammonification: The formation of ammonia or its compounds from nitrogenous compounds, especially as a result of bacterial decomposition.

The nitrogen cycle describes the conversion of nitrogen between different chemical forms. The majority of the earth’s atmosphere (about 78%) is composed of atmospheric nitrogen, but it is not in a form that is usable to living things. Complex species interactions allow organisms to convert nitrogen to usable forms and exchange it between themselves. Nitrogen is essential for the formation of amino acids and nucleotides. It is essential for all living things.

Fixation: In order for organisms to use atmospheric nitrogen (N2), it must be “fixed” or converted into ammonia (NH3). This can happen occasionally through a lightning strike, but the bulk of nitrogen fixation is done by free living or symbiotic bacteria. These bacteria have the nitrogenase enzyme that combines gaseous nitrogen with hydrogen to produce ammonia. It is then further converted by the bacteria to make their own organic compounds. Some nitrogen fixing bacteria live in the root nodules of legumes where they produce ammonia in exchange for sugars. Today, about 30% of the total fixed nitrogen is manufactured in chemical plants for fertilizer.

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The role of soil bacteria in the Nitrogen cycle: Nitrogen transitions between various biologically useful forms.

Nitrificaton: Nitrification is the conversion of ammonia (NH3) to nitrate (NO3). It is usually performed by soil living bacteria, such as nitrobacter. This is important because plants can assimilate nitrate into their tissues, and they rely on bacteria to convert it from ammonia to a usable form. Nitrification is performed mainly by the genus of bacteria, Nitrobacter.

Ammonification /Mineralization: In ammonification, bacteria or fungi convert the organic nitrogen from dead organisms back into ammonium (NH4+). Nitrification can also work on ammonium. It can either be cycled back into a plant usable form through nitrification or returned to the atmosphere through de-nitrification.

De-Nitrification: Nitrogen in its nitrate form (NO3) is converted back into atmospheric nitrogen gas (N2) by bacterial species such as Pseudomonas and Clostridium, usually in anaerobic conditions. These bacteria use nitrate as an electron acceptor instead of oxygen during respiration.

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

Key Points

  • The sulfur cycle describes the movement of sulfur through the geosphere and biosphere. Sulfur is released from rocks through weathering, and then assimilated by microbes and plants. It is then passed up the food chain and assimilated by plants and animals, and released when they decompose.
  • Many bacteria can reduce sulfur in small amounts, but some specialized bacteria can perform respiration entirely using sulfur. They use sulfur or sulfate as an electron receptor in their respiration, and release sulfide as waste. This is a common form of anaerobic respiration in microbes.
  • Sulfur reducing pathways are found in many pathogenic bacteria species. Tuberculosis and leprosy are both caused by bacterial species that reduce sulfur, so the sulfur reduction pathway is an important target of drug development.

Key Terms

  • extremophile: An organism that lives under extreme conditions of temperature, salinity, and so on. They are commercially important as a source of enzymes that operate under similar conditions.
  • assimilatory sulfate reduction: The reduction of 3′-Phosphoadenosine-5′-phosphosulfate, a more elaborated sulfateester, leads also to hydrogen sulfide, the product used in biosynthesis (e.g., for the production of cysteine because the sulfate sulfur is assimilated).

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

Key Points

  • Iron is an important limiting nutrient for plants, which use it to produce chlorophyll. Photosynthesis depends on adequate iron supply. Plants assimilate iron from the soil into their roots.
  • Animals consume plants and use the iron to produce hemoglobin, the oxygen transports protein found in red blood cells. When animals die, decomposing bacteria return iron to the soil.
  • The marine iron cycle is very similar to the terrestrial iron cycle, except that phytoplankton and cyanobacteria assimilate iron.
  • Iron fertilization has been studied as a method for sequestering carbon. Scientists have hoped that by adding iron to the ocean, plankton might be able to sequester the excess CO2 responsible for climate change. However, there is concern about the long term effects of this strategy.

Key Terms

  • hemoglobin: the iron-containing oxygen transport metalloprotein in the red blood cells of all vertebrates

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.

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Algal bloom: Algae bloom in the Bering Sea after a natural iron fertilization event.