# 6.2 Biogeochemical Cycles
Biogeochemical cycles refer to the pathways by which essential elements, such as $\ce{C}$, $\ce{N}$, and $\ce{P}$, cycle through the Earth's ecosystems. These cycles involve the interaction of biological, geological, and chemical processes that facilitate the transfer of these materials between living organisms and their environment. These cycles also involve processes such as photosynthesis, respiration, decomposition, weathering, and nutrient uptake and release by plants and animals.
The biogeochemical cycles help to maintain the balance of essential elements and compounds in the Earth's ecosystems. Changes to these cycles through human activities like deforestation, land use change, or pollution, can have significant impacts on the health and functioning of ecosystems.
In this section, you will explore:
- nutrient pollution,
- agricultural importance, and
- CZ function and dynamics in relation to nutrient cycling.
## The Carbon Cycle
The carbon cycle describes the movement of $\ce{C}$ between the atmosphere, oceans, land, and living organisms. It involves both biotic and abiotic processes, including photosynthesis, respiration, decomposition, and the exchange of $\ce{CO2}$ between the atmosphere and oceans.
```{figure} https://openstax.org/apps/archive/20230220.155442/resources/e8f44d6ce2709457ad741448a53b4fecc7b51aa7
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$\ce{CO2}$ gas exists in the atmosphere and is dissolved in water. Photosynthesis converts $\ce{CO2}$ gas to organic carbon, and respiration cycles the organic carbon back into $\ce{CO2}$ gas. Long-term storage of organic carbon occurs when matter from living organisms is buried deep underground and becomes fossilized. Volcanic activity and, more recently, human emissions bring this stored carbon back into the carbon cycle.
Image source: [20.2 Biogeochemical Cycles - Concepts of Biology | OpenStax](https://openstax.org/books/concepts-biology/pages/20-2-biogeochemical-cycles)
```
The $\ce{C}$ cycle is most easily studied as two interconnected subcycles: one dealing with rapid carbon exchange among living organisms and the other dealing with the long-term cycling of carbon through geologic processes.
### The Biological Carbon Cycle
Living organisms are connected in many ways, even between ecosystems. A good example of this connection is the exchange of $\ce{C}$ between heterotrophs and autotrophs within and between ecosystems by way of atmospheric $\ce{CO2}$. $\ce{CO2}$ is the basic building block that autotrophs use to build multi-$\ce{C}$, high-energy compounds, such as glucose. The energy harnessed from the Sun is used by these organisms to form the covalent bonds that link $\ce{C}$ atoms together. These chemical bonds store this energy for later use in the process of respiration. Most terrestrial autotrophs obtain their $\ce{CO2}$ directly from the atmosphere, while marine autotrophs acquire it in the dissolved form (bicarbonate, $\ce{HCO3-}$). However the $\ce{CO2}$ is acquired, a byproduct of fixing carbon in organic compounds is $\ce{O2}$. Photosynthetic organisms are responsible for maintaining approximately $\pu{21 \%}$ of $\ce{O2}$ content of the atmosphere that we observe today.
The partners in biological carbon exchange are the heterotrophs (especially the primary consumers, largely herbivores). Heterotrophs acquire the high-energy carbon compounds from the autotrophs by consuming them and breaking them down by respiration to obtain cellular energy, such as ATP. The most efficient type of respiration, aerobic respiration, requires oxygen obtained from the atmosphere or dissolved in water. Thus, there is a constant exchange of $\ce{O2}$ and $\ce{CO2}$ between the autotrophs (which need the carbon) and the heterotrophs (which need the oxygen). Autotrophs also respire and consume the organic molecules they form: using $\ce{O2}$ and releasing $\ce{CO2}$. They release more $\ce{O2 (g)}$ as a waste product of photosynthesis than they use for their own respiration; therefore, there is excess available for the respiration of other aerobic organisms. Gas exchange through the atmosphere and water is one way that the carbon cycle connects all living organisms on Earth.
### The Biogeochemical Carbon Cycle
The movement of $\ce{C}$ through land, water, and air is complex, and, in many cases, it occurs much more slowly geologically than the movement between living organisms. Carbon is stored for long periods in what are known as carbon reservoirs, which include the atmosphere, bodies of liquid water (mostly oceans), ocean sediment, soil, rocks (including fossil fuels), and Earth’s interior.
As stated, the atmosphere is a major reservoir of carbon in the form of $\ce{CO2}$ that is essential to the process of photosynthesis. The level of $\ce{CO2}$ in the atmosphere is greatly influenced by the reservoir of carbon in the oceans. The exchange of carbon between the atmosphere and water reservoirs influences how much carbon is found in each, and each one affects the other reciprocally. $\ce{CO2}$ from the atmosphere dissolves in water and, unlike oxygen and nitrogen gas, reacts with water molecules to form ionic compounds. Some of these ions combine with $\ce{Ca^2+}$ in the seawater to form $\ce{CaCO3}$, a major component of the shells of marine organisms. These organisms eventually form sediments on the ocean floor. Over geologic time, the $\ce{CaCO3}$ forms limestone, which comprises the largest carbon reservoir on Earth.
On land, carbon is stored in soil as organic carbon as a result of the decomposition of living organisms or from weathering of terrestrial rock and minerals. Deeper under the ground, at land and at sea, are fossil fuels, the anaerobically decomposed remains of plants that take millions of years to form. Fossil fuels are considered a non-renewable resource because their use far exceeds their rate of formation. A non-renewable resource is either regenerated very slowly or not at all. Another way for carbon to enter the atmosphere is from land (including land beneath the surface of the ocean) by the eruption of volcanoes and other geothermal systems. Carbon sediments from the ocean floor are taken deep within Earth by the process of subduction: the movement of one tectonic plate beneath another. Carbon is released as $\ce{CO2}$ when a volcano erupts or from volcanic hydrothermal vents.
$\ce{CO2}$ is also added to the atmosphere by the animal husbandry practices of humans. The large number of land animals raised to feed Earth’s growing human population results in increased carbon-dioxide levels in the atmosphere caused by their respiration. This is another example of how human activity indirectly affects biogeochemical cycles in a significant way. Although much of the debate about the future effects of increasing atmospheric carbon on climate change focuses on fossils fuels, scientists take natural processes, such as volcanoes, plant growth, soil carbon levels, and respiration, into account as they model and predict the future impact of this increase.
## The Nitrogen Cycle
The nitrogen cycle is the biogeochemical cycle by which $\ce{N}$ is converted into various chemical forms as it circulates among the biosphere, geosphere, hydrosphere, and atmosphere. The principal forms of $\ce{N}$ are gaseous dinitrogen ($\ce{N2}$), ammonia ($\ce{NH3}$), ammonium ($\ce{NH4+}$), and nitrate ($\ce{NO3−}$).
```{figure} https://openstax.org/apps/archive/20230220.155442/resources/fcd7625eabb80c9af5a289cf8b2ea6389950c9a1
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Nitrogen enters the living world from the atmosphere through nitrogen-fixing bacteria. This nitrogen and nitrogenous waste from animals is then processed back into gaseous nitrogen by soil bacteria, which also supply terrestrial food webs with the organic nitrogen they need.
Image source: [20.2 Biogeochemical Cycles - Concepts of Biology | OpenStax](https://openstax.org/books/concepts-biology/pages/20-2-biogeochemical-cycles)
```
Getting nitrogen into the living world is difficult. Plants and phytoplankton are not equipped to incorporate nitrogen from the atmosphere (which exists as tightly bonded, triple covalent $\ce{N2}$) even though this molecule comprises approximately $\pu{78 \%}$ of the atmosphere. Nitrogen enters the living world via free-living and symbiotic bacteria, which incorporate nitrogen into their macromolecules through nitrogen fixation (conversion of $\ce{N2}$). Cyanobacteria live in most aquatic ecosystems where sunlight is present; they play a key role in nitrogen fixation. Cyanobacteria are able to use inorganic sources of nitrogen to “fix” nitrogen. _Rhizobium_ bacteria live symbiotically in the root nodules of legumes (such as peas, beans, and peanuts) and provide them with the organic nitrogen they need. Free-living bacteria, such as _Azotobacter_, are also important nitrogen fixers.
Organic nitrogen is especially important to the study of ecosystem dynamics since many ecosystem processes, such as primary production and decomposition, are limited by the available supply of nitrogen. the nitrogen that enters living systems by nitrogen fixation is eventually converted from organic nitrogen back into nitrogen gas by bacteria. This process occurs in three steps in terrestrial systems: ammonification, nitrification, and denitrification. First, the ammonification process converts nitrogenous waste from living animals or from the remains of dead animals into ammonium ($\ce{NH4+}$) by certain bacteria and fungi. Second, this ammonium is then converted to nitrites ($\ce{NO2−}$) by nitrifying bacteria, such as _Nitrosomonas_, through nitrification. Subsequently, nitrites are converted to nitrates ($\ce{NO3−}$) by similar organisms. Lastly, the process of denitrification occurs, whereby bacteria, such as _Pseudomonas_ and _Clostridium_, convert the nitrates into nitrogen gas, thus allowing it to re-enter the atmosphere.
Human activity can release nitrogen into the environment by two primary means: the combustion of fossil fuels, which releases different nitrogen oxides, and by the use of artificial fertilizers (which contain nitrogen and phosphorus compounds) in agriculture, which are then washed into lakes, streams, and rivers by surface runoff. Atmospheric nitrogen (other than $\ce{N2}$) is associated with several effects on Earth’s ecosystems including the production of acid rain (as nitric acid, $\ce{HNO3}$) and greenhouse gas effects (as nitrous oxide, $\ce{N2O}$), potentially causing climate change. A major effect from fertilizer runoff is saltwater and freshwater eutrophication, a process whereby nutrient runoff causes the overgrowth of algae and a number of consequential problems.
A similar process occurs in the marine nitrogen cycle, where the ammonification, nitrification, and denitrification processes are performed by marine bacteria and archaea. Some of this nitrogen falls to the ocean floor as sediment, which can then be moved to land in geologic time by uplift of Earth’s surface, and thereby incorporated into terrestrial rock. Although the movement of nitrogen from rock directly into living systems has been traditionally seen as insignificant compared with nitrogen fixed from the atmosphere, a recent study showed that this process may indeed be significant and should be included in any study of the global nitrogen cycle.
## The Phosphorus Cycle
Phosphorus is an essential nutrient for living processes; it is a major component of nucleic acids and phospholipids, and, as calcium phosphate, makes up the supportive components of our bones. Phosphorus is often the limiting nutrient (necessary for growth) in aquatic, particularly freshwater, ecosystems.
Phosphorus occurs in nature as the phosphate ion ($\ce{PO4^3-}$). In addition to $\ce{PO4^3-}$ runoff as a result of human activity, natural surface runoff occurs when it is leached from phosphate-containing rock by weathering, thus sending phosphates into rivers, lakes, and the ocean. This rock has its origins in the ocean. Phosphate-containing ocean sediments form primarily from the bodies of ocean organisms and from their excretions. However, volcanic ash, aerosols, and mineral dust may also be significant $\ce{PO4^3-}$ sources. This sediment then is moved to land over geologic time by the uplifting of Earth’s surface.
Phosphorus is also reciprocally exchanged between $\ce{PO4^3-}$ dissolved in the ocean and marine organisms. The movement of $\ce{PO4^3-}$ from the ocean to the land and through the soil is extremely slow, with average $\ce{PO4^3-}$ oceanic residence time between 20,000 and 100,000 years.
The $\ce{P}$ cycle is a relatively slow cycle, and it can take millions of years for $\ce{P}$ to move from one reservoir to another. The main reservoirs of $\ce{P}$ are rocks, sediments, soil, and living organisms. Most $\ce{P}$ in nature exists in the form of $\ce{PO4^3−}$.
```{figure} https://openstax.org/apps/archive/20230220.155442/resources/9562c1b0dad72fbb700154d03a689a5c00d2ddce
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In nature, phosphorus exists as the phosphate ion (PO43-). Weathering of rocks and volcanic activity releases phosphate into the soil, water, and air, where it becomes available to terrestrial food webs. Phosphate enters the oceans in surface runoff, groundwater flow, and river flow. Phosphate dissolved in ocean water cycles into marine food webs. Some phosphate from the marine food webs falls to the ocean floor, where it forms sediment.
Image source: [20.2 Biogeochemical Cycles - Concepts of Biology | OpenStax](https://openstax.org/books/concepts-biology/pages/20-2-biogeochemical-cycles)
```
Excess $\ce{P}$ and $\ce{N}$ that enter these ecosystems from fertilizer runoff and from sewage cause excessive growth of algae. The subsequent death and decay of these organisms depletes dissolved $\ce{O2}$, which leads to the death of aquatic organisms, such as shellfish and finfish. This process is responsible for dead zones in lakes and at the mouths of many major rivers and for massive fish kills, which often occur during the summer months.
```{figure} https://external-content.duckduckgo.com/iu/?u=http%3A%2F%2Fsvs.gsfc.nasa.gov%2Fvis%2Fa030000%2Fa030400%2Fa030479%2Fdead_zones_crops_particulate_carbon.png&f=1&nofb=1&ipt=c8b816c24b28dd7266ae900f0d7d7fb5fec0907bb2b849fe41d00c71be6e24ee&ipo=images
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The size and number of marine dead zones—areas where the deep water is so low in dissolved oxygen that sea creatures can’t survive—have grown explosively in the past half-century. Yellow circles on this map show the location of observed eutrophic zones. Red dots show where hypoxic zones have been observed. It’s no coincidence that dead zones occur downriver of places where land is intensively used for agriculture. Some of the fertilizer we apply to crops is washed into streams and rivers. Fertilizer-laden runoff triggers explosive planktonic algae growth in coastal areas. The algae die and rain down into deep waters, where their remains are like fertilizer for microbes. The microbes decompose the organic matter, using up the oxygen. Mass killing of fish and other sea life often results. Satellites can observe changes in the way the ocean surface reflects and absorbs sunlight when the water holds a lot of particles of organic matter. Darker blues in this image show higher concentrations of particulate organic matter, an indication of the overly fertile waters that can culminate in dead zones.
Image source: [Coastal Dead Zones (nasa.gov)](https://svs.gsfc.nasa.gov/30479)
```
A dead zone is an area in lakes and oceans near the mouths of rivers where large areas are periodically depleted of their normal flora and fauna; these zones can be caused by eutrophication, oil spills, dumping toxic chemicals, and other human activities. The number of dead zones has increased for several years, and more than 400 of these zones were present as of 2008. One of the worst dead zones is off the coast of the United States in the Gulf of Mexico: fertilizer runoff from the Mississippi River basin created a dead zone of over 8,463 square miles. Phosphate and nitrate runoff from fertilizers also negatively affect several lake and bay ecosystems including the Chesapeake Bay in the eastern United States.
## Nutrient Pollution
Nutrient pollution is the addition of excess nutrients, mainly nitrogen and phosphorus, into the water or air.
According to US EPA "nutrient pollution is one of America's most widespread, costly and challenging environmental problems.” ([Nutrient Pollution | US EPA](https://www.epa.gov/nutrientpollution))
Nitrogen and phosphorus are nutrients that are natural parts of aquatic ecosystems. Nitrogen is also the most abundant element in the air we breathe. Nitrogen and phosphorus support the growth of algae and aquatic plants, which provide food and habitat for fish, shellfish and smaller organisms that live in water.
But when too much nitrogen and phosphorus enter the environment - usually from a wide range of human activities - the air and water can become polluted. Nutrient pollution has impacted many streams, rivers, lakes, bays and coastal waters for the past several decades, resulting in serious environmental and human health issues, and impacting the economy.
Too much nitrogen and phosphorus in the water causes algae to grow faster than ecosystems can handle. Significant increases in algae harm water quality, food resources and habitats, and decrease the oxygen that fish and other aquatic life need to survive. Large growths of algae are called algal blooms and they can severely reduce or eliminate oxygen in the water, leading to illnesses in fish and the death of large numbers of fish. Some algal blooms are harmful to humans because they produce elevated toxins and bacterial growth that can make people sick if they come into contact with polluted water, consume tainted fish or shellfish, or drink contaminated water.
Nutrient pollution in ground water - which millions of people in the United States use as their drinking water source - can be harmful, even at low levels. Infants are vulnerable to a nitrogen-based compound called nitrates in drinking water. Excess nitrogen in the atmosphere can produce pollutants such as ammonia and ozone, which can impair our ability to breathe, limit visibility and alter plant growth. When excess nitrogen comes back to earth from the atmosphere, it can harm the health of forests, soils and waterways.
The primary sources of excess nitrogen and phosphorus are:
- [Agriculture](https://www.epa.gov/nutrientpollution/sources-and-solutions-agriculture): The nitrogen and phosphorus in animal manure and chemical fertilizers are necessary to grow crops. However, when these nutrients are not fully utilized by plants they can be lost from the farm fields and negatively impact air and downstream water quality.
- [Stormwater](https://www.epa.gov/nutrientpollution/sources-and-solutions-stormwater): When precipitation falls on our cities and towns it runs across hard surfaces - like rooftops, sidewalks and roads - and carries pollutants, including nitrogen and phosphorus, into local waterways.
- [Wastewater](https://www.epa.gov/nutrientpollution/sources-and-solutions-wastewater): Our sewer and septic systems are responsible for treating large quantities of waste, and these systems do not always operate properly or remove enough nitrogen and phosphorus before discharging into waterways.
- [Fossil Fuels](https://www.epa.gov/nutrientpollution/sources-and-solutions-fossil-fuels): Electric power generation, industry, transportation and agriculture have increased the amount of nitrogen in the air through use of fossil fuels.
- [In and Around the Home](https://www.epa.gov/nutrientpollution/sources-and-solutions-and-around-home): Fertilizers, yard and pet waste and certain soaps and detergents contain nitrogen and phosphorus, and can contribute to nutrient pollution if not properly used or disposed. The amount of hard surfaces and type of landscaping can also increase the runoff of nitrogen and phosphorus during wet weather.
The presence of excess nutrients in air and water can affect human health, the environment and the economy. Federal, state and local governments spend billions of dollars per year to minimize these effects.
- [Human health effects](https://www.epa.gov/nutrientpollution/effects-human-health)
- [Environmental effects](https://www.epa.gov/nutrientpollution/effects-environment)
- [Economic effects](https://www.epa.gov/nutrientpollution/effects-economy)
```{admonition} Phosphorus Pollution
Read the following article: [Phosphorus control is critical to mitigating eutrophication (pnas.org)](https://www.pnas.org/doi/pdf/10.1073/pnas.0806112105)
Answer the following questions:
1. What is the main point the author is trying to make?
2. How did researchers determine the cause of eutrophication? What did they find?
3. How are marine environments different than freshwater systems with respect to nutrients and eutrophication?
4. What activities do the authors suggest that could control both N and P inputs into aquatic systems?
5. What impacts on the critical zone does nitrogen have other than eutrophication?
6. Create a concept map of the pathways
```
## Readings and resources for this section
1. [Cronan, Soil Biogeochemistry | SpringerLink](https://link.springer.com/chapter/10.1007/978-3-319-66444-6_2)
2. [Cronan, Biogeochemical Models | SpringerLink](https://link.springer.com/chapter/10.1007/978-3-319-66444-6_11)
3. [Chapin et al, Principles of Terrestrial Ecosystem Ecology | SpringerLink](https://link.springer.com/book/10.1007/978-1-4419-9504-9)
4. [20.2 Biogeochemical Cycles - Concepts of Biology | OpenStax](https://openstax.org/books/concepts-biology/pages/20-2-biogeochemical-cycles)
5. [Nutrient Pollution | US EPA](https://www.epa.gov/nutrientpollution)
6. [The Culprit Behind Dead Zones and the Threat to Our Water Supply — ProPublica](https://www.propublica.org/article/phosphorus-the-culprit-behind-dead-zones-threat-to-water-supply)