CAGAYAN STATE UNIVERSITY

Carig Campus
College of Engineering

CHEMISTRY FOR ENGINEERS

CHEM111

UNIT III
ENVIRONMENTAL CHEMISTRY: SOIL
Learning Objectives:
At the end of this unit, the students will be able to:
1. Understand the nature of soil formation and the general composition of soil;
2. Understand the mechanisms of ion exchange in soil;
3. Understand the factors that affect soil pH; and
4. Understand the basics of how to correct extreme soil pH conditions.
CONTENTS:
I. Nature and Importance of Soils
II. Ion-exchange and Soil pH

INTRODUCTION
Agriculture is a very important practice as it provides food and sustenance – the most basic
human need. But however important it may be to sustain the human population, it can also impact
the environment negatively by displacing local flora and fauna, through erosion, pesticide pollution
and many more. Agricultural processes also affect the soil, as well as the hydrosphere and the
atmosphere.
Soil is the most fundamental requirement for traditional methods of agriculture. It is made up
of complex biogeochemical components (minerals, organic matter) and is home to a wide range of
micro-organisms and animals.

Figure 4c.1.1 Traditional agriculture

Soil is a fragile resource and it can be lost or degraded to the point where it will no longer be
able to support vegetation. Desertification refers to the process associated with drought and loss
of fertility by which soil becomes unable to grow significant amounts of plant life. (Manahan, et al.)
This process has been accelerated by human behavior and is now a global problem.

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 A related problem is deforestation or the loss of forests. Deforestation not only leads to the
extinction of plant and animal species, but the loss of plant life can also cause the rapid deterioration
of soil quality through the loss of nutrients and through erosion.
In addition to these, the actual soil layer is only very thin compared to the underlying bedrock
of the earth’s lithosphere/crust, and yet it is still responsible for producing the sustenance needed
by most living things on the planet. And because soils are exposed to a lot of activity, it is the receptor
of a large quantity of pollutants. Fertilizers and pesticides, other soil additives, and even particulate
matter from the atmosphere and hydrosphere can settle in the soil. For this reason, the chemical, as
well as the physical and biological properties of soils are important things to study.

I. NATURE AND IMPORTANCE OF SOILS

Soil is a mixture of organic matter, weathered minerals, and pockets of moisture and air,
capable of supporting life. The organic matter is composed of plant and animal biomass in various
stages of decomposition while the mineral/inorganic matter is made up of small pieces of rocks that
have undergone physical and chemical processes over time.
The solid fraction of a soil capable of supporting life is approx. 5% organic matter and 95%
inorganic matter. Some soils only contain as little as 1% organic matter. The type of soil in any given
area is dependent on the nature of its parent rock material, the climate, the type of vegetation
present, as well as the time period over which it is formed. Soils are also open systems – they are
ever-changing and can exchange matter and energy with the atmosphere, the hydrosphere, and
the biosphere that it is in contact with.

Figure 4c.1.2 Soil components showing the three different phases it contains
Soils exhibit different distinctive layers, called horizons, at different depths. These are formed
from complex interactions during the weathering and erosion processes like biological decay and
deposition of minerals thru water runoff.

Figure 4c.1.3 The different soil horizons

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 The top layer of soil is called the A horizon or topsoil. It is usually several inches thick and is
the layer of maximum biological activity.
The B horizon or the subsoil is the layer which receives both organic material and clay and
mineral particles that have leached from the topsoil. The layer containing the parent rocks of the
soil material is called the C horizon.

A. WATER AND AIR IN SOIL

As shown in Figure 4c.1.2, water is part of the solid-liquid-gas system that makes up soil. Large
quantities of water are needed in the growth of plants as it is the basic medium that transports the
necessary nutrients and minerals from the solid soil, into the roots, and up to the leaves.
Water in the soil behaves like regular water in the atmosphere; it can dissolve a lot of chemical
species it meets. This aqueous portion of soil containing dissolved matter is called the soil
solution. The dissolved mineral matter occur largely as ions H+, Ca2+, Mg2+, K+, and Na+. Small amounts
of Fe2+, Mn2+, and Al3+ are also present. Once the necessary nutrients have been absorbed, the plants
release the excess water back into the atmosphere in a process called transpiration.
Another part of this three-phase system is air. A typical soil also has air-filled pores. In fact
most soils are roughly 35% air by volume.

When soil becomes waterlogged or oversaturated, its physical, chemical, and biological
properties all change drastically. In fact, most useful crops cannot grow in waterlogged soil. an
exception to this is rice.
Water in the soil is not always readily available to plants. This availability is dependent on
gravity as well as on capillary forces (see previous modules on properties of water): the larger the
water pocket in the soil, the easier it will be to be absorbed by roots and the easier it will also be to
drain away due to gravity. The availability of nutrients in water is also dependent on several factors:
concentration, solubility of nutrients, electrical potential, etc.
Different soil components also affect the amount of water in the soil. Soils with large amounts
of inorganic materials may not hold water well (sandy) or they may be prone to oversaturation (clay)
because of strong bonding forces. Soils with large amounts of organic material may also hold a lot of
water, but this water may not be readily available to plants because they are physically/chemically
bound into the organic matter.
An overabundance of decaying matter as well as water decreases the oxygen in soil. This is
because the microorganisms necessary for biodegradation consume oxygen. This causes the bond
holding the soil particles to break down, disrupting the soil structure. As well as consuming oxygen,
the decay process also increases the water and CO2 amounts in soil as shown in the formula:
{𝐶𝐻2 𝑂} + 𝑂2 → 𝐶𝑂2 + 𝐻2 𝑂
These soils then ‘suffocate’ the plants as there is very little oxygen in them which is needed
by plant roots.

Another chemical effect of waterlogging is pE reduction in the presence of bacteria.

Remember, in our previous discussions, we have established that changes in pE and pH determine
the type of active species dissolved in bodies of water. When the pE value drops, the redox condition
of the soil becomes much more reducing.
A good example of this is the reduction of iron and manganese. Manganese and iron oxides are
generally not soluble and are therefore unavailable to plants. But when they become reduced to
their soluble metal ions, plants can absorb them.
𝑀𝑛𝑂2 + 4𝐻 + + 2𝑒 − → 𝑀𝑛2+ + 2𝐻2 𝑂 𝑀𝑛4+ → 𝑀𝑛2+

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 𝐹𝑒2 𝑂3 + 6𝐻 + + 2𝑒 − → 2𝐹𝑒 2+ + 3𝐻2 𝑂 𝐹𝑒 3+ → 𝐹𝑒 2+
**Note that 𝐹𝑒 2+ and 𝑀𝑛2+ are toxic to plants at high amounts.

B. INORGANIC COMPONENTS
Inorganic components come from the weathering or breakdown of the parent rocks and
minerals. These components are colloidal in nature and are an important source of plan nutrients.
Inorganic soil colloids are also capable of detoxing soil by absorbing toxic substances which may
otherwise harm plants.
How easily the plant nutrients may be absorbed by plant roots depends on the ionic strengths
and structures of the soil’s inorganic components. The earth’s crust is abundant with oxygen, silicon,
iron, aluminum, calcium, sodium, and magnesium. Due to this, mineral components of the soil are
usually made up of these elements. Some common soil minerals are finely divided quartz (𝑆𝑖𝑂2 ),
orthoclasen (𝐾𝑎𝑙𝑆𝑖3 𝑂8 ), geothite (𝐹𝑒𝑂(𝑂𝐻)), magnetite (𝐹𝑒3 𝑂4 ), calcium and calcium magnesium
carbonates (𝐶𝑎𝐶𝑂3 , 𝐶𝑎𝐶𝑂3 ∙ 𝑀𝑔𝐶𝑂3 ), and oxides of manganese and titanium.

C. ORGANIC MATTER IN SOIL

Organic matter in soil serves as a food source for microorganisms and it largely determines the
productivity of a soil despite typically composing only less than 5% of the whole soil matter. This
matter can also influence ion exchange and even the weathering/breakdown of mineral matter.

• Some fungi in soil produce citric acid and other chelating agents. These can react with
silicate minerals which can cause potassium and other metal ions to be released into the
soil for plant use.
• The strong chelating agent 2-ketogluconic acid is produced by some soil bacteria. It makes
minerals more soluble and contributes to their weathering. It can release phosphate ions
from insoluble phosphate compounds.
• Soil fungi release oxalate ion (C2O42-) as a metabolism byproduct. It exists in soil as calcium
salts whewellite and weddellite. In water, oxalates help dissolve minerals more,
accelerating the typical weathering process thru oxalate complexation. The reaction can
be shown below:
3𝐻 + + 𝑀(𝑂𝐻)3 (𝑠) + 2𝐶𝑎𝐶2 𝑂4 (𝑠) → 𝑀(𝐶2 𝑂4 )2− 2+
(𝑎𝑞) + 2𝐶𝑎 (𝑎𝑞) + 3𝐻2 𝑂, where M

represents metals aluminum or iron

The amount of organic matter that accumulates in soil is affected by oxygen availability and
temperature. The rate of biodegradation is higher when there is abundant oxygen and at higher
temperatures. Therefore, at colder climates and colder places, organic matter tends to build up in
soil rather than break down and decay. The same is true in waterlogged soils because large amounts
of water in the soil makes it difficult for biodegradable material to have access to oxygen.

Table 4C.1.1 The organic compounds present in soil

Compound type Composition Significance
Humus Hard to degrade residue from plant Most abundant organic component in
decay; largely made up of C, H, and soil; improves soil tecturel reservoir of
O fixed N and nutrients
Fats, resins, waxes Lipids that are extractable by Can adverseley affect soil physical
organic solvents properties since it repels water; maybe
phytotoxic

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 Saccharides Cellulose, starches, hemi-cellulose, Major food source of microorganisms;
gums helps stabillize soil aggregates
N-containing Nitrogen bound to humus, amino Provide nitrogen for soil fertility
organics acids and amino sugars, other N-
containing compounds
Phosphorus Phosphate esters, inositol Sources of plant phosphate
compounds phosphates (phytic acid),
phospholipids

Looking at Table 4C.1.1, we can see that soil humus is the most abundant organic matter in
soil. Humus is made up of the residue left after bacteria and fungi biodegrade plant matter. It is
made up of soluble components (humic and fulvic acids) as well as an insoluble component (humin).
Plant material is mostly made up of cellulose which is relatively quick to degrade and lignin which
takes a longer time to break down. This is because lignin has a higher carbon content arranged in
aromatic rings joined together by alkyl chains and methoxyl and hydroxyl groups.
Humification is the process by which humus is formed. Soil humus has similar properties as
lignin, its parent source, but it has more carboxylic acid groups. When plant biomass is transformed
into humus there is an observed increase in the nitrogen-carbon ratio. In humification,
microorganisms convert organic carbon into CO2 while incorporating bound nitrogen into the
byproducts of the decay process. The N:C ratio is approximately 1/100 in fresh plant matter; it
rises to 1/10 after humification.

II. ION-EXCHANGE AND SOIL PH

Soils facilitate the exchange of cations and anions. This exchange of ions, also called non-
specific adsorption, occurs in both the organic and the mineral portions of the soil. This ability of
the soil or any sediment to exchange cations is called the cation-exchange capacity (CEC). It is
defined as the number of milliequivalents (meq) of monovalent cations that can be exchanged
per 100 g of soil (dry weight basis). The CEC of each soil is different as it is a function of pE, pH,
and other factors.
The organic matter in soil exchange cations due to the presence of basic functional groups,
most notably the carboxylate group (RCOO-). For example, humus has a very high CEC value. The CEC
of peat can range from 300–400 meq/100 g. In soils with normal levels of organic matter, the overall
CEC values are around 10–30 meq/100 g.
As an example of cation exchange in the inorganic portion of soil, clay minerals exchange
cations. This exchange occurs due to the presence of negatively charged sites on the surfaces of the
soil solids.
The process of cation exchange enables minerals like potassium, calcium, magnesium, and
essential trace-level metals to be made available to plants. When the metal ions are absorbed by
roots, hydrogen ions are exchanged for the metal ions. This exchange, in addition to the leaching of
metal ions from the soil by water with carbonic acid, can make soils acidic as shown in the reaction
by producing H+ ions in the soil:
𝑆𝑜𝑖𝑙}𝐶𝑎2+ + 2𝐶𝑂2 + 2𝐻2 𝑂 → 𝑆𝑜𝑖𝑙}(𝐻 + )2 + 𝐶𝑎2+ (𝑟𝑜𝑜𝑡) + 2𝐻𝐶𝑂3 −
Soil also acts as a buffer and resists changes in pH. The buffering capacity depends on the
type of soil.

Production of Mineral Acid in Soil

If a soil contains pyrite, this pyrite can be oxidized to form acid-sulfate soils called “cat clays”
upon exposure to oxygen:

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 7
𝐹𝑒𝑆2 (𝑝𝑦𝑟𝑖𝑡𝑒) + 𝑂2 + 𝐻2 𝑂 → 𝐹𝑒 2+ + 2𝐻 + + 2𝑆𝑂42−
2
Cat clay soils can be very acidic, reaching pH values as low as 3.0. Soils that have been
reclaimed from marshlands and used in citrus plantations can become very acidic which is
detrimental to plant growth. In addition, when 𝐹𝑒𝑆2 reacts with acids, it releases 𝐻2 𝑆 which is very
toxic to plant roots.
The test for potential acid-sulfate formation in soils is a peroxide test. This involves oxidizing
FeS2 in the soil with 30% 𝐻2 𝑂2 solution then testing the result for acidity and the presence of sulfate:
15
𝐹𝑒𝑆2 + 𝐻2 𝑂2 → 𝐹𝑒 3+ + 𝐻 + + 2𝑆𝑂42− + 7𝐻2 𝑂
2
If the pH is below 3.0 and there are appreciable levels of sulfate then it means that the soil
has high potential in becoming an acid-sulfate soil. If the pH is above 3.0, this means that there is
little FeS2 in the soil, or there is sufficient 𝐶𝑎𝐶𝑂3 is in the soil to neutralize the 𝐻2 𝑆𝑂4 and acidic
𝐹𝑒 3+.
Pyrite-containing mine spoils (residue left over from mining) also form soils that are similar to
acid-sulfate soils of marine origin. These soils also have high acidity and toxic 𝐻2 𝑆. but they also
contain significant amounts of Al (III) or 𝐴𝑙 3+ which is very toxic to plants when liberated from the
soil.

Adjustment of Soil Acidity

Soil pH is one of the most important physico-chemical properties of soils. It affects plant growth
as well as the behavior of ionic contaminants. Similar to the principles of aquatic chemistry, soil pH
is also a measure of the H+ ion concentration in the soil solution found in the water pockets in the
soil. These hydrogen cations are in equilibrium with the negatively charged surfaces of the solid soil
particles.
The range of pH values for soils is quite large, from 4 to 8.5. In extreme cases, some soils
may have pH values of 2 (very acidic) to (10.5) very basic. Water content and the frequency of rainfall
can affect the acidity of soils. Soils in humid/wet regions generally have a pH of 5 to 7, while soils
in arid/dry regions have a pH between 7 and 9. This shows that moisture in soils tend to make it
more acidic.
Most bacteria cannot tolerate acidic environments so if one needs to promote a healthy level
of biodegradation, the soil pH should be maintained at near neutral values (pH values between 6 and
8). Most plants also grow best in near neutral pH soils.
Acidic soil pH can be corrected thru liming (addition of lime). The chemical reaction that
occurs when soil is limed is shown below:
𝑆𝑜𝑖𝑙}(𝐻 + )2 + 𝐶𝑎𝐶𝑂3 → 𝑆𝑜𝑖𝑙}𝐶𝑎2+ + 𝐶𝑂2 + 𝐻2 𝑂
Basic (alkaline) soils, which is more common in areas of low rainfall, can be treated with
aluminum sulfate or iron sulfate which release acids on hydrolysis (addition of water):
2𝐹𝑒 3+ + 3𝑆𝑂42− + 6𝐻2 𝑂 → 2𝐹𝑒(𝑂𝐻)3 (𝑠) + 6𝐻 + + 3𝑆𝑂42−
2𝐴𝑙 3+ + 3𝑆𝑂42− + 6𝐻2 𝑂 → 2𝐴𝑙(𝑂𝐻)3 (𝑠) + 6𝐻 + + 3𝑆𝑂42−
Elemental sulfur may also be used to treat alkaline soils although it is rarely practiced at present.
This sulfur is oxidized (thru bacterial actions) to form sulfuric acid.
3
𝑆 + 𝑂2 + 𝐻2 𝑂 → 2𝐻 + + 𝑆𝑂42−
2
Ion Exchange Equilibria in Soil
The different cations in soil have different responses to each other. How they can displace
each other is usually determined by something called an exchange constant. An atom with a lower

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oxidation number in the clay will be substituted with one that has a higher oxidation number (except
for H+). The commonly quoted order of cation replaceability is:
𝐿𝑖 + = 𝑁𝑎+ > 𝐾 + = 𝑁𝐻4+ > 𝑅𝑏+ > 𝐶𝑠 + > 𝑀𝑔2+ > 𝑆𝑟 2+ = 𝐵𝑟 2+ > 𝐿𝑎3+ = 𝐻 + (𝐴𝑙 3+ ) > 𝑇ℎ4+
For example, magnesium will displace aluminum, and lithium will displace all other cations in soil.

To illustrate:
Soil that is flooded with seawater will have most of its exchange sites occupied by Na+
(from the NaCl in the water). If this soil is to be reclaimed and made fertile again for
farming, the Na+ ions must be replaced with other nutrient cations like 𝐾 + :
𝑺𝒐𝒊𝒍} 𝑵𝒂+ + 𝑲+ ↔ 𝑺𝒐𝒊𝒍} 𝑲+ + 𝑵𝒂+
The exchange constant, Kc, expresses the relative tendency of soil to retain K+ and Na+
and can be described by:
𝑁𝐾 [𝑁𝑎+ ]
𝐾𝑐 =
𝑁𝑁𝑎 [𝐾 + ]
Where 𝑁𝐾 and 𝑁𝐴𝑙 are the fractions of 𝐾 + and 𝑁𝑎+ in the soil (values of 𝑁𝑖 will range from 1
to zero), while [𝐾 + ] and [𝑁𝑎+ ] are the concentrations of 𝐾 + and 𝑁𝑎+ in the soil solution.

The exchange of anions by soil is not as clearly defined as the exchange of cations. Most soils
have much smaller capacities for anion exchange compared to cation exchange. Anion adsorption
occurs when positive charges in the solid soil attract anions.
Some ions such as orthophosphate species are strongly adsorbed/retained by soil. Meanwhile,
chloride and nitrate ions are very weakly adsorbed/retained by the soil. We term the process as
adsorption because the exchange only happens at the surfaces of the soil minerals (adsorption can
be visualized as ‘surface absorption’).
At low pH (acidic environments), metal oxide surfaces have a net positive charge which enables
them to attract and hold anions. At higher pH values (basic environments), the metal oxide surface
has a net negative charge due to the formation of OH- ions on the surface. In such cases, it is still
possible for anions such as HPO42- to displace the hydroxide ion:

SUMMARY
• Soil is organic matter + weathered minerals + moisture & air pockets, capable of supporting life.
• Soils exhibit different distinctive layers, called horizons: the topmost layer is called A horizon
or topsoil; the B horizon or subsoil is the next layer; the layer containing the parent rocks of
the soil material is called the C horizon.
• WATER IN SOIL: The aqueous portion of soil containing dissolved matter is called the soil
solution.
• AIR IN SOIL: A typical soil also has air-filled pores and is ~35% air by volume.
• Inorganic components of the soil come from the parent rocks and minerals. These components
are an important source of plan nutrients.
• Organic matter in soil serves as a food source for microorganisms and largely determines the
productivity of a soil. Organic soil matter is made up of the following:

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 Humus - Hard to degrade residue from N-containing organics – N in humus,
plant decay (C, H, O) amino acids and sugars, etc.
Saccharides – cellulose, starches, and Phosphorus compounds – phosphate
gums compounds and phospholipids
Fats, resins, waxes - lipids
• Soil humus is the most abundant organic matter in soil. It is made up of soluble components
(humic and fulvic acids) as well as an insoluble component (humin). Humification is the process
by which humus is formed. The N:C ratio is approximately 1/100 in fresh plant matter; it rises
to 1/10 after humification.
• Soils facilitate the exchange of ions (non-specific adsorption). The ability of the soil/sediment
to exchange cations is called the cation-exchange capacity (CEC). It is the miliequivalents of
cations exchanged per 100g dry soil. Units = meq/100g.
• Soil pH is a measure of H+ ion concentration in the soil solution. 4 < Soil pH < 8.5. Moisture in
soils generally make it more acidic.
• Acidic soil pH can be corrected thru liming (addition of lime). Basic (alkaline) soils can be
treated with aluminum sulfate or iron sulfate, or elemental sulfur.
• In cation exchange, the commonly quoted order of cation replaceability is:
𝐿𝑖 + = 𝑁𝑎+ > 𝐾 + = 𝑁𝐻4+ > 𝑅𝑏 + > 𝐶𝑠 + > 𝑀𝑔2+ > 𝑆𝑟 2+ = 𝐵𝑟 2+ > 𝐿𝑎3+ = 𝐻 + (𝐴𝑙 3+ ) > 𝑇ℎ4+
• Most soils have much smaller capacities for anion exchange compared to cation exchange. Anion
adsorption occurs when positive charges in the solid soil attract anions, or when OH- ions in the
solid soil are replaced by other anions.
Self-Assessment 21:
1. Soils exhibit distinctive layers with increasing depth called ________________.
2. In addition to solid mineral and organic matter and water, roughly 35% of the volume of typical
soil is composed of ________________.
3. Most of soil organic matter is composed of ________________, which consists of a base-soluble
fraction called ________________ and an insoluble fraction called ________________.
4. Essential plant micronutrients include: ________________.
5. What temperature and moisture conditions favor the buildup of organic matter in soils?
6. Why do you think plants grown on either excessively acidic or excessively basic soils may suffer
from calcium deficiency?
7. To prepare a rich potting soil, a greenhouse operator mixed 75% “normal” soil with 25% peat.
Estimate the CEC in meq/100 g of the product. CECsoil = 10-30 meq/100g; CECpeat = 300-400
meq/100g.

References:
1. Andrews, et. al. An Introduction to Environmental Chemistry, 2nd Ed. Blackwell Science Ltd.
2004.
2. Harrison, Roy. Principles of Environmental Chemistry. The Royal Society of Chemistry.
Cambridge. 2007.
3. Manahan, Stanley. Fundamentals of Environmental Chemistry, 2nd Ed. Boca Raton: CRC Press
LLC. 2001.

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