1. How soils supply plant nutrients An Introduction to Soil Chemistry
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For many of us soils are a black box. We put things into the box and we get things out of the box, but we don’t have a very good idea of what happens inside the box. We put seed, fertilizer, and water into the soil and out from the soil comes the crops we are growing. But what exactly happens inside that black box we call soil? Farmers and scientists and have been studying that question for hundreds of years and continue to study it today. They have learned that many complex physical, biological, and chemical processes are carried out in soil. Lets open up that black box just a little and learn something about the chemistry of soils. Knowing something about soil chemistry will help us understand how soils supply plant nutrients.
Prepared by:
Richard Stehouwer
Department of Agronomy

2. Soil is the unconsolidated cover on the surface of the earth.
Soil is made up of
mineral particles,
organic particles,
air, and
water.
Soil is capable of supporting plant growth.
What is soil?
Before we get into soil chemistry, we need to back up a bit and think more generally about soils.
What is soil?
To a geologist soil is the decomposed surface of rocks.
To an engineer soil is the medium that must be strong enough to support a highway or a skyscraper or your house.
To scientists who study soil formation, soil is a natural body consisting of several layers and formed from weathered rocks over a period of thousands to millions of years.
Today we will consider soil from an agricultural perspective.
Soil is the unconsolidated material at the surface of the earth. (Unconsolidated simply means that it is granular material that is not cemented together like rock.)
Soil is made up of mineral and organic matter and contains both water and air.
Most importantly, soil is capable of supporting plant life. It’s the material that sustains not only the farmer’s livelihood, but that of the whole world.
It is from this perspective that we will now look more carefully at soil. First, we will consider what functions must be performed by soil used for crop production, and then we will look at how the soil accomplishes those functions.

3. Functions of agricultural soils
Anchor plant roots
Supply water to plant roots
Provide air for plant roots
Furnish nutrients for plant growth
Release water with low levels of nutrients
Soils used for crop production must perform five basic functions.
Soil must firmly anchor plant roots. It must be strong enough to hold crops and even large trees erect. Yet soil must be permeable enough to allow tiny root hairs to penetrate it.
Soil must retain rain that falls on it in order to continuously supply water to growing plants. Yet it must also allow excess water to drain. The soil must drain because it must also supply air, more specifically oxygen, to crop roots. Too much water means too little air and the crops suffocate.
Soil must supply nutrients for plant growth. To do so it must be store nutrients and then release them to the roots of growing crops.
But soil must not release those nutrients to draining water.
Soil is a truly remarkable material to be able to perform each of these tasks – tasks that sometimes seem to be in conflict with each other.
Our focus in this session will be on the last two functions of an agricultural soil.
How soil provides nutrients for plant growth, and
How nutrient laden soil can release water with low levels of nutrients.
In particular, we will consider the chemical characteristics of soil that allow it to perform these functions.

4. Soil Components The 4 parts of soil
About ½ of the soil volume is solid particles
About ½ of the soil volume is pore space
Lets review a couple of soil science basics.
Soil is made up of 4 parts: mineral matter, organic matter, water, and air.
Mineral matter and organic matter together form the solid part of soil. Soil air and soil water occupy the spaces between the solid particles. This space is the pore space.
A good agricultural soil will be about half solid particles and half pore space.
Most of the soil solids will be mineral matter that is made up of particles of sand, silt, and clay. A small part of the solids will be organic matter. Most agricultural soils have somewhere around 2 - 5% organic matter. Organic matter is mostly made up of decomposed plant litter and roots.
Conditions for root growth will be ideal when about half the pore space is filled with water and half is filled with air. When a soil becomes compacted the mineral particles are pressed more tightly together. When this happens the soil loses pore space, and so has less capacity to store water and air.

5. Soil Texture
The mineral part of soil consists of sand, silt, and clay particles
The amounts of each size particle determines the textural property of the soil
Coarse textured, loose (more sand, less clay)
Fine textured, heavy (more clay, less sand)
Loamy (more even mix of sand, silt and clay
1/100 in
Sand
0.1 – in
2 – 0.05 mm
Silt
0.002 – in mm
Clay
Less than in
Less than mm
Soil texture refers to the amount of various size mineral particles that are present in the soil.
Soil mineral particles are separated into sand, silt, and clay on the basis of the particle diameter. This diagram shows the size of sand, silt and clay relative to each other.
Sand is the largest and gives soil a gritty feel. Particles larger than 1/10 inch would be considered gravel. The sand particle in this diagram represents a fine sand particle – about 1/100 inch in diameter.
Silt is intermediate in size between sand and clay. Soil with a lot of silt has a floury feel. Sand and silt provide a skeleton for the soil. The main function of sand and silt in soil is to give strength. Sand and silt contribute very little to the capacity of soil to retain water and nutrients.
Clay is the smallest of the mineral particles, and makes soil sticky when wet. Clay particles are microscopic, so individual clay particles cannot be seen by the naked eye. The black dots in this diagram are representative of the largest clay particles. Relative to the size of the sand and silt in this diagram, the dots are larger than most clay particles.
The relative amounts of sand, silt, and clay give the soil its textural property. A loose, coarse textured soil has a lot of sand and less silt and clay. A fine textured soil is heavy and has a lot of clay and less sand. A loamy soil has a more even mix of all three.
When you scoop up a handful of good topsoil you see crumbs or granules of soil that are much larger than the individual particles shown in this diagram. That brings us to the topic of soil structure.

6. Soil Structure. The arrangement of sand, silt, and clay particles
Soil Structure The arrangement of sand, silt, and clay particles to form larger aggregates.
Organic matter is the glue that holds the aggregates together
Large pores (spaces) between aggregates are filled with air in a moist soil.
Small pores are filled with water in a moist soil. Even smaller pores inside the aggregates (not shown) are also filled with water.
Individual particles of clay, silt, and sand stick together into larger particles called aggregates. Aggregates can take on many shapes and sizes, but in a good topsoil they tend to be small crumb-like particles. Small aggregates, like those shown in this diagram tend to clump together into still larger aggregates. Soil structure refers to the arrangement of individual particles of sand, silt and clay into small aggregates, and the arrangement of small aggregates into larger aggregates.
Clay is important in soil structure because it is sticky and makes individual particles clump together. Aggregates, and the individual particles in them, are often coated with soil organic matter. The soil organic matter acts like a glue that strengthens the aggregates, and helps to hold them together.
The spaces between aggregates are called pores. These spaces are also an important part of the soil. They are not empty, but are filled either with water or with air. In a soaking wet soil (just after a rainfall or snowmelt), all the pores will be filled with water. As the soil drains due to the force of gravity, water in the larger pores moves downward to tile lines or groundwater. When the water drains out it is replaced by air. These drained, air-filled pores are shown in yellow in this diagram. Water in smaller pores is held more tightly by the soil and does not drain (blue areas in this diagram). Water will be lost from the smaller pores due to plant uptake of water and evaporation. In addition to the pores shown in this diagram, there are also very small, even microscopic pores within each of the aggregates. These are pores that occur between the individual particles of silt and clay that make up the soil aggregates. These very small pores will be filled with water in all but the driest soil.
1/10 inch

7. Supplying Plant Nutrients
Nutrients that plants obtain from the soil
Macronutrients:
(needed in large amounts)
Nitrogen (N)
Phosphorus (P)
Potassium (K)
Calcium (Ca)
Magnesium (Mg)
Sulfur (S)
Micronutrients:
(needed in small amounts)
Chlorine (Cl)
Cobalt (Co)
Copper (Cu)
Iron (Fe)
Manganese (Mn)
Molybdenum (Mo)
Nickel (Ni)
Zinc (Zn)
Plants require many different nutrients and almost all of these must be supplied by the soil. On the left hand side of this slide are the major nutrients needed by crops. These are also known as “macronutrients”. These are the nutrients that most of us are familiar with. Most of these, with the exception of sulfur, are routinely added to soil in commercial fertilizers, lime, and manure. These are called macronutrients because plants need large amounts of them to grow well.
On the right-hand side are nutrients that may not be as familiar. These are nutrients that plants must have in order to grow, but they are needed in very small amounts. In fact too much of some of these nutrients can be toxic to plants. These micronutrients usually do not need to be added to soils. Most soils are able to supply all that are needed for good crop growth.
Now on to some soil chemistry. Lets look at where these nutrients come from, how soil holds on to them, and how soil supplies them to crops.

8. Where do plant nutrients come from?
Decaying plant litter
Breakdown of soil minerals
Addition by humans
Commercial fertilizer
Manure
Lime
Other
Nutrients are added to the soil from several sources. The main sources of nutrients for agricultural soils are:
Nutrients that are recycled to the soil from decaying plant litter,
Minerals in soil that gradually dissolve and release nutrients, and
Nutrients added by humans in the form of fertilizers, manure, limestone, and other materials such as sewage sludge, compost, leaves, and food processing wastes.
The smoke stack shown here is another source of nutrients for soils. Interestingly a lot of sulfur used to be supplied to soils from this source, especially combustion of coal. We are now cleaning up our air and much less sulfur is falling onto our soils. We may eventually see a need for more sulfur fertilization.
Lets look a little more closely at each of these nutrient sources.

9. Recycling plant nutrients
Nutrient cycling is an extremely important function of soils.
Living plants contain all the nutrients essential for plant growth. When crops are harvested some of those nutrients are removed, but many remain behind in plant litter.
When the litter falls onto the soil or is plowed under, those nutrients are returned to the soil. Some of the nutrients in plant litter dissolve into the soil water like salt would. Most of the nutrients in plant litter are bound up in complex organic molecules and are not available to plants. The litter must first be broken down, or decomposed, by soil microbes. The ferocious looking critters in this cartoon are meant to be soil microbes. These are actually microscopic organisms and cannot be seen with the naked eye. Nor do they look anything like this under the microscope.
Hungry soil microbes, mainly bacteria and fungi, use the carbon in the litter for food. They consume some of the nutrients in the litter and release what they don’t need into the soil water. The feeding of soil microbes turns fresh plant litter into stable soil organic matter. When the microbes die the nutrients in their bodies are also released to the soil water and are available for plants to take them up again. K

10. Breakdown of soil minerals
Water
Acid Zn Ca
Another source of nutrients, especially micronutrients, is from the slow breakdown of soil minerals.
As soils age and weather, the rocks that were originally present gradually break apart and dissolve, just like a sugar cube dissolves in a cup of coffee. Only instead of taking a few seconds, this process takes millions of years in soil.
As plant litter decomposes, organic acids are produced. These acids, as well as other sources of acidity and water in the soil, attack soil minerals and gradually they are dissolved. These minerals contain nutrients such as calcium, magnesium, potassium and most of the micronutrient elements. These are released into the soil water and are available for uptake by plant roots. K Ni Cu Mg

11. Nutrient additions by humans
Commercial fertilizers
Nutrients are in a form that is available to plants
Dissolve quickly and nutrients go into soil water
Lime
Dissolves slowly as it neutralizes soil acidity
Releases calcium and magnesium
Organic nutrient sources
Manure, compost, sewage sludge
Decay and nutrient release is similar to crop litter
Farmers routinely add nutrients to soils to boost crop yields. Commercial chemical fertilizers like urea, ammonium nitrate, triple super phosphate, and muriate of potash are designed to be in a form that plants can take up and use. Most fertilizers are also designed to be very soluble, that is they quickly dissolve and release nutrients into the soil water.
Lime is added to “sweeten” the soil as the old timers used to say. Lime increases soil pH by neutralizing acidity in the soil. As it reacts the lime dissolves and releases calcium and magnesium into the soil water.
Farmers also add organic nutrient sources such as manures, composts, sewage sludge and others. These materials are similar to plant litter in that many of the nutrients are not available to crops. The materials must first be decomposed by soil microbes. As they decompose the nutrients are released into soil water.
Notice that with each of these various nutrient sources I have repeated the phrase “nutrients are released into the soil water.” So we have all these nutrients moving into the soil water. What happens to them now?

12. The soil solution Soil water is a complex solution that contains
Many types of nutrients
Other trace elements
Complex organic molecules
Nutrients in the soil solution can be readily taken up by plant roots
If nutrients remained in solution they could all be quickly lost from the soil. N
Obviously, the soil water is far from pure water. Soil water is really a complex solution that contains all the nutrients we have been talking about. It also contains other trace elements and complex organic molecules that come from plant litter, manure, and soil microbes. If pesticides are sprayed over the surface of the soil, the soil solution will also contain some of those chemicals.
When nutrients, trace elements, and other chemicals are in the soil solution they can be readily taken up by plant roots. In fact they must be in soil solution to be taken up by plants.
But, if all of these nutrients and other chemicals simply stayed in the soil solution they would also be quickly lost from the soil. Every time very much rain fell on the soil all the nutrients and other chemicals would be flushed out of the soil in runoff, in drainage water flowing out tile lines, and flowing down into groundwater.
We know some nutrients and chemicals are lost from soil in this way. But, the vast majority stay in the soil. How does the soil hold them? P K Zn Ni Ca Mg Cu

13. Adsorption + -
Adsorption refers to the ability of an object to attract and hold particles on its surface.
Solid particles in soil have the ability to adsorb
Water
Nutrients and other chemicals
The most important adsorbers in soil are
Clays
Organic matter
Adsorption is the most important process in soil for holding nutrients and other chemicals. Adsorption refers to the ability of a solid surface to attract and hold other materials on its surface. Metal filings attracted to and sticking on the surface of a magnet illustrate the process of adsorption. Particles that are held by adsorption can also be released again. The process of adsorption is reversible.
Absorption is a somewhat different process in which one material is drawn into anther material, like water soaking into a sponge.
Solid particles in soil have the ability to adsorb water, nutrients, and other chemicals.
The most important particles in soil for adsorption are clays and organic matter. Lets first look at nutrient adsorption on clays, and then at adsorption on organic matter.

14. Surface area of clay
¼ cup
¼ cup of clay has more surface area than a football field
The large surface area of clay allows it to
Adsorb a lot of water
Retain nutrients
Stick to other soil particles
One of the features of clay and organic matter that makes them such good adsorbers is that despite their microscopic size, they have extremely large surface area.
Many of the clays in Pennsylvania soils are layer clays. That is they are shaped like sheets of paper. Because of their thin, sheet-like shape a small quantity of clay has a huge surface area. The amount of clay you could hold in a 1/4 cup measure has more surface area than a football field.
This huge amount of surface area means that a small amount of clay can adsorb and hold a lot of water. A small amount of clay can adsorb a lot of plant nutrients and other chemicals.
As I mentioned earlier, clay particles tend to stick to each other and to other soil particles (as well as your boots when the soil is wet). Their thin, sheet-like shape is what gives clay the ability to do this.

15. Properties of Soil Clays
Clay particles are stacked in layers like sheets of paper.
Each clay sheet is slightly separated from those on either side.
Each sheet has negative charges on it.
Negative charges have to be balanced by positive charges called cations.
There are many different types of clays in Pennsylvania soils. Many of these clays are known as layered clays and have a structure similar to what is shown in this diagram. They are built up of several sheets stacked together. Each sheet is slightly separated from the ones on either side of it. It is this structure that gives layer clays such a high surface area for just a little bit of clay. Every surface of these clay sheets will hold a film of water. Some of that water is available for plant roots to use. This structure of clays is what provides soils with much of their ability to store water for plant growth. Notice the size of the clay particle. We are talking about extremely small things here.
Each clay sheet is made up of crystals containing oxygen, silicon, and aluminum. When the clay sheets form, aluminum will often go into the crystal where silicon normally would be. This causes a negative electrical charge on the clay surface. This substitution of aluminum for silicon happens over and over in every clay sheet. Thus every clay sheet has many negative charges on every surface.
Nature cannot tolerate an unbalanced system, so these negative charges must be balanced by positive charges. Just as the negative pole of a magnet attracts the positive pole of another magnet, these negatively charged clays attract positive charges.
The amount of negative charge on the clay that can hold positive charges (cations) is called the “Cation Exchange Capacity” or CEC for short
Where do these positive charges (cations) come from?
1/20,000 in

16. Cation Retention on Soil Clays
Calcium, +2
Magnesium, +2
Potassium, +1
Ammonium, +1
Sodium, +1
Many important plant nutrients and many other trace elements in soil are in the form of cations, that means they are positively charged. Calcium and magnesium for example have a positive 2 charge and can balance 2 negative charges. Potassium and ammonium (a form of nitrogen) each have a positive 1 charge and can each balance one negative charge.
As this diagram shows, the positively charged cations in the soil solution are attracted to the negatively charged clay surface. The cations stick to the clay surface just like iron file shavings would stick to a magnet. Cations held this way are not likely to leach from the soil, but can still be released for plant uptake. The cations (or nutrients) that are on the clay surface can be exchanged with other cations that are in the soil solution.
In some clays potassium and ammonium can be held very tightly between sheets and are “fixed” or not likely to be released.
Copper, +2
Aluminum, +3
Hydrogen, +1

17. Cation Retention on Organic Matter
Hydrogen
Nutrients
Increasing pH
increases cation
exchange capacity
of organic matter
Stable soil organic matter is made up of large complex organic molecules that are resistant to further attack from soil microbes. Pieces of soil organic matter appear like coiled, twisted strands. This material coats particles of silt and clay and helps to hold clay and silt together in soil aggregates. The coiled structure also gives organic matter a very large surface area.
Soil organic matter is also like a sponge. It can soak up large amounts of water and store it for plants to use.
Soil organic matter has a very high cation exchange capacity. Unlike many layer clays, the cation exchage capacity of organic matter changes as soil pH changes. As soil pH decreases (becomes more acid) more and more hydrogen cations stick to organic matter. At low pH this hydrogen is held very tightly and will not exchange with nutrients or other elements. As soil pH increases the hydrogen is held less strongly and readily exchanges with other nutrient and trace element cations like calcium, magnesium, potassium, and sodium. These cations will also exchange with each other at near neutral pH.
Low pH, 4 - 5
(acidic soil)
Neutral pH, 7
(“sweet” soil)

18. Cation Exchange Capacity
Cation exchange capacity (CEC) is the total amount of cations that a soil can retain
The higher the soil CEC the greater ability it has to store plant nutrients
Soil CEC increases as
The amount of clay increases
The amount of organic matter increases
The soil pH increases
Together, clays and organic matter account for most of the cation exchange capacity of the soil.
Cation exchange capacity refers to the total amount of cations that a soil can retain.
The higher the exchange capacity, the better the soil is able to retain plant nutrients and other elements. The exact cation exchange capacity of soil depends on:
what type and how much clay it has,
how much organic matter it has, and
what its pH is.

19. Negatively Charged Nutrients (Anions)
Some very important plant nutrients are anions.
Soils are able to retain some of these nutrient anions.
Retention of nutrient anions varies from one anion to another 1- 2- 2- 1-
Nitrate
Phosphate
Sulfate
Chloride
Although most plant nutrients and other trace elements are cations (positively charged) some very important ones are anions. Anions are negatively charged. Nutrient that are anions include major ones such as nitrate (nitrogen source), phosphate, and sulfate, and some trace nutrients such as chloride, borhydrate (boron), and molybdate (molybdenum).
We just learned that most soil clays and organic matter carry negative charges. Since like charges repel each other (like the negative poles of two magnets), you would expect soil particles to repel these nutrients and keep them in the soil solution. This is sometimes, but not always, the case.
Retention of these anions in soil varies greatly from one anion to another.
Lets look at some examples.

20. Phosphate retention in soil
1. Formation of a new solid material +
Aluminum phosphate
solid
Phosphate
Aluminum
2. Anion exchange
Phosphate is an example of a nutrient anion that soils retain very strongly. There are three ways by which phosphate is held in soils.
Phosphate in commercial fertilizers is very soluble, but once in the soil it will react with cations in the soil solution to form a new solid material or mineral. Such reactions occur with aluminum, iron, and manganese.
Some soil clays do have some positive charges on their surfaces, most often at the edges of layer sheets. Anions such as phosphate can be attracted to these positive charges. + 2-
Phosphate +

21. Phosphate retention in soil
3. Adsorption on oxide surfaces
Phosphate anions -
Each held by two
chemical bonds to the
iron oxide surface
3. Finally, most soils contain minerals known as aluminum oxides and iron oxides. Iron oxides give many of our soils their reddish color. Iron oxides sometimes coat other layer clay particles, or they may be present as clay sized particles. Phosphate is held strongly by these oxide surfaces. Phosphate reacts chemically with the oxide surface and often will be held strongly by a double chemical bond.
Iron oxide surface

22. Nitrate (NO3-) retention in soils
Unlike phosphate, nitrate is very weakly held by soils
Nitrate does not react to form new solids
Nitrate is not held by oxide surfaces
NO3-
At the opposite extreme from phosphate is nitrate. Nitrate is a very important form of nitrogen and is readily taken up by plants. Nitrate, however, is very weakly held by soils. Unlike phosphate it is very soluble and does not react with with other elements in soils to form new solids. Nitrate also is not held by iron and aluminum oxide clay surfaces. The only way nitrate is held in soils is by anion adsorption. Nitrate is held very weakly by anion adsorption and most Pennsylvania soils have very little anion adsorption capacity.
Therefore nitrate tends to remain in the soil solution. Any nitrate that is not taken up by plants can very easily be leached from the soil as water moves downward through the soil. The nitrate can then move into tile lines and into streams, or downward into groundwater. To prevent nitrate pollution of surface or groundwater it is important to carefully manage nitrogen applications to crops.
Nitrogen in manures and in commercial fertilizers is readily converted to nitrate.
If nitrate is not taken up by plants it is very likely to be lost from the soil

23. Moving nutrients from soil to plants
Nutrients in soil solution
Plant
Root
At any given time, the vast majority of nutrients and trace elements in soil are adsorbed onto the surface of clays and organic matter. Some, however, remain in the soil solution (soil water). These nutrients in solution can move back and forth between the soil surface and the soil solution. This is called ion exchange.
When plant roots penetrate into the soil, they begin to remove nutrients from the soil solution to meet their nutrient needs. As plants remove nutrients from the soil solution they often exude other elements into the soil solution. The plant uptake of nutrients disrupts the balance between nutrient ions in the solution and nutrient ions on the soil surface is. To get back into balance, nutrients move from the soil surface out into solution and are then available for root uptake.
Adsorption of nutrients, trace elements and other chemicals onto soil surfaces keeps them in the soil, usually in available forms, and limits how much could be lost in drainage water or runoff from the surface.
Nutrients on soil clay and organic matter

24. Excessive Nutrient Loading
Nutrients in soil solution X
Plant
Root
When excessive amounts of nutrients are added to soil, the capacity of the soil to adsorb them may be exceeded. Nutrients then cannot move from the soil solution onto soil particles. Nutrient concentrations then build up in the soil solution. In this diagram the orange balls represent nitrate and the light green balls represent phosphate.
With increased nutrients in the soil solution there is increased likelihood that nutrients could be lost in runoff water or drainage water.
Nutrients on soil clay and organic matter
Nutrient loss in drainage water

25. The black box is open
Soil consists of mineral and organic matter, air and water
Soils are able to adsorb nutrients and other chemicals
The most important adsorbers are clay and organic matter
Adsorbed nutrients are available to plants
Adsorbed nutrients are not prone to loss in drainage water
Soil adsorption capacity can be exceeded leading to greater nutrient loss
We have opened the black box of soil chemistry, at least a little bit. Lets quickly review some of the key things we saw in that black box.
Soils consist of 4 parts: mineral and organic matter that are the solid parts of the soil, and air and water that occupy the pore space in soil.
Soils are able to adsorb nutrients and other chemicals. Adsorption means the ability to hold nutrients on solid surfaces and keep them out of the soil solution.
The most important adsorbers in soil are clay and organic matter. These materials have very high surface area and carry electrical charge
Adsorbed nutrients are available to plants. They are held on solid surfaces and can be exchanged for other cations in the soil solution.
Adsorbed nutrients are not prone to loss in drainage water. Adsorption greatly reduces the amounts of nutrients and other chemicals that are in the soil solution. Only chemicals in the soil solution will be lost in drainage from soil.
Soil adsorption capacity can be exceeded leading to greater nutrient loss. Once the soil has adsorbed everything it can hold, adding more nutrients will increase the amount in the soil solution and the amount that could be lost in drainage.