Soil Macronutrients: History, Cycles and Impacts

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In this module, you’ll get an overview of some of the main macronutrients needed by plants that are now, many in synthetic form, used in industrial agriculture at a mass scale. You’ll explore their functions and how they occur in nature, and the history of human use and relationship with these nutrients in both industrial agriculture and agroecology. For each, you’ll also learn about the potential external effects on humans and the environment when using these nutrients in large quantities.

Nitrogen (N)


The earth’s atmosphere is 78% nitrogen (N₂) gas, but nitrogen in this form (N₂) cannot be easily utilized by plants. To be used by plants, atmospheric nitrogen must be ‘processed’ or ‘fixed’ into nitrate (NO₃⁻). Nitrogen is fixed (N₂ to NO₃⁻) by lightning strike, or by symbiotic bacteria which combine atmospheric nitrogen with hydrogen to produce ammonia, which is converted by the bacteria into other organic compounds like nitrate (NO₃⁻). Some of these bacteria are free-living (that is, they don’t need a host), whereas others, such as Rhizobium, are symbiotic and live in the root nodules of legumes (peas, alfalfa and locust trees). These symbiotic nitrogen-fixing bacteria form a mutualistic relationship with the plant, and produce ammonia, and in return, the bacteria receives carbohydrates from plants.

When a plant or animal dies or an animal expels waste, nitrogen in the form of ammonia (NH₃) is released. During decomposition, bacteria or fungi convert the ammonia (NH₃) to nitrates (NO₃⁻). Finally, bacteria transform nitrates back into inert N² gas, returning nitrogen back to the atmosphere.

Synthetic nitrogen fertilizer is nitrogen in the form of nitrates (NO₃⁻). Nitrates are very soluble in the soil. As a result, they can easily enter groundwater. Elevated nitrate in groundwater is a concern for drinking water use because nitrate can interfere with blood-oxygen levels in infants and cause methemoglobinemia or blue-baby syndrome.

Where groundwater recharges streams and other waterways, nitrate enriched groundwater can contribute to eutrophication, a process that leads to high algal population growth and decrease the availability of oxygen to other organisms. While not directly toxic to fish life, like ammonia, nitrate can have indirect effects on fish if it contributes to eutrophication. Nitrogen has contributed to severe eutrophication problems in some water bodies.

Nitrogen in Conventional Agricultural Systems

Nitrogen is limited in natural ecosystems by nitrogen-fixing bacteria and lightning. Traditional agricultural systems made use of different technologies to encourage nitrogen fixation, and to cycle nitrogen within their agroecosystems. Traditional agroecosystems are limited to the nitrogen available in their ecosystem. As you will see in this video, scientists figured out a way to make usable forms of nitrogen easily available for input into agriculture. Conventional agriculture relies on the availability of cheap, synthetic nitrogen fertilizers to increase productivity, but ignores the effects this has on the balance of the global nitrogen cycle.

Film 1: Synthetic Ammonia – Fritz Haber & Carl Bosch

The massive increase in crop yields over the last century were due to the increased bioavailability of nitrogen  in large part thanks to the Haber-Bosch process. After WWII, large industrial plants producing chemical weapons quickly and easily converted to producing synthetic fertilizers. These synthetic chemicals were promoted as part of the “Green Revolution Package”, and their application was quickly adopted. In 1940, 9 million tons of synthetic fertilizers were applied in the United States. This quickly rose to more than 47 million tons in 1980, and has continued to grow to beyond 170 million metric tons in 2007 (FAOSTAT 2012). Nitrogen fertilizers are produced en masse using fossil fuels. They are applied easily and uniformly to crops, in order to provide them ample nutrients to increase production. While they may increase crop production in the short-term, the abundance of synthetic fertilizers has lead to their overuse, allowing farmers to ignore long-term soil fertility and its maintenance. Additionally, since synthetic fertilizer is produced using petroleum, its cost is variable and puts growers at the mercy of the chemical companies who produce it.

Ecological Effects of Synthetic Nitrogen Use

The use of the Haber-Bosch process, along with the nitrogen pollution emitted by vehicles and industrial plants, humans have more than doubled the annual transfer of nitrogen into biologically available forms. Nitrous oxide (N₂O) has risen in the atmosphere as a result of  agricultural fertilization, biomass burning, factory farming of animals and industrial sources. Nitrous oxide is responsible for the destruction of the ozone layer; it is also the third largest contributor to global warming.

Nitrogen leaching from agricultural systems also is a concern. Because of how easily available synthetic nitrogen is, it is often over-applied and highly mobile in water, it easily leaches out of irrigated systems. A large amount of nitrogen leaches into streams, lakes and rivers, leading to eutrophication. The following video explains some of the dangers associated with nitrogen leakage.

The following video shows the dangers of nutrient leaching:

Film 2: Nutrient Leaching

Nitrogen in Agroecosystems

Legumes/Cover Crop

Since nitrogen is fixed into usable forms by bacteria, one way to increase nitrogen in an ecosystem is to increase the soil bacteria. Many nitrogen-fixing bacteria are in symbiotic relationships with legumes. By planting legumes, you can increase the nitrogen available in your soil. Most of this nitrogen is fixed within the plant, so frequently legumes are planted in the winter as a cover crop as are incorporated into the soil before they go to bloom and invest the nitrogen into blossoms. This way, the maximum amount of nitrogen is in the plant material, and as it decays it is made available for the next crop planted in that soil.

Protecting Soil Ecology

Any steps that can be taken to protect soil ecosystems will conserve the bacteria responsible for nitrogen fixation. By reducing tillage and erosion, keeping soil covered by cover crops when they aren’t being cultivated, and maintaining proper moisture levels, you can protect and provided suitable habitat for soil bacteria. Green manures, which are fast-growing plants sown to cover bare soil, provide plant matter for decomposition as well as weed suppression. When turned back into the soil while still green, they can put important nutrients back into the soil.


Animal manures are high in available nitrogen, and provide a source of nitrogen in agroecosystems. Since animal production and vegetable production have largely become separated for efficiency in conventional agricultural systems, synthetic nitrogen is produced and used while animal waste festers in large lagoons. Occasionally animal waste is sprayed on conventional agriculture fields. However, this can lead to runoff in many cases, as plants cannot take up the nitrogen quickly enough. This leads to runoff, and is a short-term fix for nitrogen as it does little for long-term soil fertility management.

In contrast, rotational pasturing of animals is a long-term solution for soil solution. By rotating animal pasture and vegetable fields, manure has time to become integrated into the soil, and the same piece of land provides vegetables and protein. Since animals can be destructive, this practice only keeps animals on a given piece of land for a short amount of time before they are rotated to the next site, preventing erosion or over-tillage. For more on rotational grazing practices click here (optional).

Phosphorous (P)

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Retrieved from

The soil is the main abiotic reservoir for less mobile elements such as phosphorus, sulfur, potassium, calcium. Plant roots take up these elements, store them for a period of time as biomass, and decomposers eventually return them to the soil within the same ecosystem.

Phosphorus can be found in water, soil and sediments. Unlike other nutrients cycled on the global scale, phosphorus isn’t found in a gaseous state in the atmosphere. Phosphorus cycles slowly through water, soil and rock. This macronutrient is most commonly found in rock formations and ocean sediments as phosphate salts. Weathering releases phosphate salts from rocks, which dissolve into soil and absorbed by plants. Animals absorb phosphates by eating plants, or by eating animals that have consumed plants. When plants and animals die, phosphates in their tissues will return to the soils or oceans again when they decay. Eventually, phosphorus will end up part of sediments and rock formations, remaining there for millions of years, to be released again through weathering and further cycles.

This video talks about the phosphorous cycle:

Film 3: Phosphorous Cycle

Plants need phosphorus for most processes and reactions in plant cells. Phosphorus is essential for photosynthesis, and is an essential element in RNA of the nucleus and ribosomes. Phosphorus is essential for a number of catabolic enzymes in plants.

Phosphorus is not usually abundant in the soil, and it frequently appears in an insoluble form that isn’t available for use by plants.  Because the amount of phosphorus in the soil comes largely from the parent material, the concentration of phosphorus in the soil is all that is there, and over the long-term in an agricultural ecosystem, lack and removal of phosphorus will becoming a limiting factor to plant growth. The demand for phosphorus compared to its usually low concentration in the soil means that especially in regards to phosphorus, a closed-cycle sustainable system is nearly impossible. The few soils that have high amounts of phosphorus are either soils that have developed from parent materials high in phosphorus, or where phosphorus levels have built up over time in response to years of fertilization.

Plants take up soluble phosphorus through their roots, and incorporate it into their tissues. After death, it becomes part of the soil organic matter, is taken up by microorganisms, and reverts back to the soluble pool. The problem is that phosphorus can be fixed into a form that plants cannot use.

Only in a limited pH range is phosphorus easily available; even then, not a large percentage of the total phosphorus in the soil. However, there are important microorganisms in the soil that can convert insoluble phosphorus into a soluble form. These include various bacterial genera (Pseudomonas, Bradyrhizobium, Rhizobium, Bacillus) and fungi (Aspergillus niger). While the addition of these bacteria would make more phosphorus available in the soil solution, it would more quickly reduce the long-term stores of phosphorus in the soil.

In industrial agriculture, phosphate is applied as part of a synthetic fertilizer regime. Conventional phosphorous fertilizer is first mined, often from a Morocco-occupied territory in the Western Sahara, then it undergoes a chemical process involving an acid treatment to convert the phosphorus into a usable form. It is possible that with the addition of phosphorus-solubilizing microorganisms and untreated rock phosphate, soil phosphorus could be provided for a long period.

Article 1: Be persuasive. Be brave. Be arrested (if necessary)

Jeremy Grantham | Nature

Article 2: You Need Phosphorous to Live – And We’re Running Out

Tom Philpott | Mother Jones, March/April 2013

Sources of Phosphorus in Agroecosystems

Nightsoil or Human Manure

Nightsoil or Human Manure

For thousands of years, China’s farmers have used human manure, or “nightsoil”, as fertilizer (King, 1911). In this example from the Tai Lake Region, nightsoil is collected and stored in large ceramic tanks or water-tight slate-lined or concrete pits. Manure and urine are collected in buckets within the household, or deposited directly in the storage tanks, which are usually located in the animal stall and toilet area of the household. Occasionally urine is collected and applied separately. It is common to mix pig manure with nightsoil in storage, as pig stalls are connected to storage tanks via a sluice, to facilitate collection of pig manure and urine.

Nightsoil or Human Manure2

Prior to intensive use of synthetic fertilizers, nightsoil was an important fertilizer for nearly all crops, including rice and wheat. Now, nightsoil is applied mostly to small-scale vegetable plots and other rainfed household crops. The primary reason for this change is that nightsoil is

applied in liquid form, so that it is much heavier than chemical fertilizers. As vegetables and rainfed crop fields are usually nearer to the household than paddy fields, nightsoil use is now concentrated in these areas. Another reason for preferential use of nightsoil on horticultural crops is that it is believed to enhance the productivity and flavor of these crops, especially Bok Choy.

Case study on how to prevent phosphorus leaching from an agroecosystem: Crop Rotations Case Study with Sugar Cane and rice

READ MORE- Humanure Is No Laughing Matter

Potassium (K)


Potassium mostly cycles within a soil or specific ecosystem. Potassium moves back and forth between plants and soil solution. It’s source is from the weathering of soil parent material.  The primary source of potassium in soil solution is the weathering of parent rocks. Within an acidic soil, potassium may be tightly bound in insoluble minerals (micas and feldspars), slowly available when associated with 2:1 type minerals, moderately available when associated with clay and humus colloids, and easily available when in soil solution.  The small amount of potassium dissolved in soil solution as an ion is highly leachable, although losses of potassium from runoff and erosion is not a significant problem in forests, compared to some elements.

Plants do not require potassium to build their structure, or to make enzymes and proteins. Instead, potassium is needed to maintain the proper chemical environment for metabolic reactions to take place. Potassium must be present for the formation of proteins, starches, sugars, as well as for their transport in the plant. Potassium has been linked to cell division and growth, and cell permeability, turgidity, and hydration. With proper potassium supplies, plants show better resistance to disease and environmental stress.

Ecological Effects of Synthetic Applications Potassium

Potassium has no known deleterious effect on the quality of natural and drinking waters and it does not induce eutrophication in rivers and lakes. Under regular agricultural practices, small amounts of potassium ions is leached into deeper soil layers and finally reaching the aquifers, which presents no ecological threat; K in drinking water and/or food is no hazard for human health provided renal function is normal. A diet high in K has no harmful effect and is recommended for people suffering from hypertension (RT 22, 2001, IPI).

In many of IPI field experiments worldwide, it is shown that with adequate supply of potassium and better nitrogen management, nitrogen use efficiency significantly increases, and consequently the disposed N to the environment is reduced (RT 22, 2001, IPI).

Calcium (Ca)

Calcium is important for plant growth and nutrition, especially the formation of cell walls. Additionally, calcium helps maintain the chemical balance in the soil, reduces soil salinity and improves water penetration.

Calcium is found in most soil minerals, but often isn’t in a form that makes it available for plants to use. That why while many soils may contain high levels of calcium, often in the form of calcium carbonate, crops may show a calcium deficiency.

Calcium is a cation, meaning it is positively charged ion. If the concentration of other positively charged cations, like magnesium, ammonium, iron, aluminum and especially potassium are high, the uptake of calcium by plants will be reduced, as the plants will absorb these cations as well as calcium.

Magnesium (Mg)

Magnesium is essential for photosynthesis- it is involved with the synthesis of chlorophyll, which is what makes leaves look green.

In soil, magnesium is naturally present. However, the pH of the soil determines how much magnesium is in a form available for uptake. In low pH soils, the solubility of magnesium decreases and it becomes less available. In high pH soils, magnesium has a tendency to leach, and other cations like manganese and aluminum become available, meaning the plant will take up less magnesium.

Sulfur (S)

Sulfur is used in the formation of amino acids, proteins and oils. It is necessary for the formation of chlorophyll. Sulfur promotes the formation of nitrogen-fixing nodules in legumes, and is a structural component of two amino acids that form proteins.

Decomposition of organic matter contributes S to the soil, so temperature and moisture affect the release of S. Sulfur is most likely to be deficient in soils with low organic matter levels, coarse (sandy) textures with good drainage, and high rainfall. Some crops, especially high-yielding forage crops such as alfalfa remove more S than other grain crops.


Iron, copper, zinc, manganese, molybdenum, boron and chlorine are the micronutrients or the “trace” elements in soil. Each is essential for plant growth, but in extremely small quantities. Micronutrient deficiencies are widespread. Around 51% of world cereal soils are deficient in zinc and 30% of cultivated soils globally are deficient in iron. Steady growth of crop yields during recent decades (in particular through the Green Revolution) compounded the problem by progressively depleting soil micronutrient pools.

In general, farmers only apply micronutrients when crops show deficiency symptoms, while micronutrient deficiencies decrease yields before symptoms appear. Some common farming practices (such as using lime as an additive for acid soils) contribute to widespread occurrence of micronutrient deficiencies in crops by decreasing the availability of the micronutrients present in the soil. Also, extensive use of glyphosate is increasingly suspected to impair micronutrient uptake by crops, especially with regard to manganese, iron and zinc.