Soil Fertility: Module 2

Module 2. Principles and Concepts of Soil Fertility

Module Overview

As we explained in the introductory module, this course is focused on how to set up and implement an ISFM program. In the last module we introduced a suggested framework for doing this. Later on we will come back to this approach but would first like to make sure that everyone in the class has a common understanding of the important technical considerations that underlie the approach. These are related to soil and the key principles and concepts underlying soil fertility.

In this module we will cover some of the most important factors associated with soil fertility. We will talk about the important nutrients that plants require to grow and reproduce as well as the ways in which soils provide (or fail to provide) these nutrients. We will talk about how soil is formed, what it is made of and the role of the various soil components.

Lesson 2.1: Plant Nutrition

No course on soil fertility management would be complete without some discussion of the fundamental reason why we are so interested in managing soil fertility – providing adequate nutrition for plants. It is very important to understand the basic nutritional needs of plants before going on to discuss the best ways to provide these requirements.

All plants are dependent on a favorable combination of five environmental factors; light, heat, air, nutrients, and water.Since the dawn of agriculture, farmers have well understood this general concept. They sow their crops in locations with sufficient sunlight and at the time of the year when temperatures allow growth to maturity. They try to ensure adequate water availability either through irrigation or by predicting rainfall. As you may have learned in the historical overview of fertilizer use linked to in the last lesson, they have also been aware of the importance of nutritional supplements.

Through modern science, we now have a fairly sophisticated understanding of the nutrient requirements of plants. Science has identified some 20 nutrient elements that are essential for the growth and reproduction of plants. Plants obtain 3 of these elements – carbon, hydrogen, and oxygen – from the air and water. Although these elements are extremely important, (for most plants, 94 percent or more of their dry tissue is composed of these three elements) there is really not much that can be done to improve or manage their availability. The other elements combined represent less than 6 percent of the plant dry matter but crop production is frequently reduced and growth limited by a deficiency of one or more of these.

These essential elements are generally divided into two groups. Themacronutrients are nitrogen (N), phosphorus (P), potassium (K), sulfur (S), calcium (Ca), and magnesium (Mg). The second group of essential elements is calledmicronutrients (or sometimes ‘minor’ or ‘trace’ elements) because those elements are required in small (micro) amounts by plants. They include manganese (Mn), iron (Fe), boron (B), zinc (Zn), copper (Cu), molybdenum (Mo), chlorine (Cl), cobalt (Co), nickel (Ni), sodium (Na) and silicon (Si).

For additional information on these key elemental nutrients and their functions in plant growth, development and reproduction interested participants may want to access the following supplementary pages.

  • Macronutrients
  • Micronutrients

(N)-Nitrogen: Nitrogen is a constituent of all living cells and is a necessary part of all proteins, enzymes and metabolic processes involved in the synthesis and transfer of energy. Nitrogen is a structural part of chlorophyll which is responsible for photosynthesis. Photosynthesis is a process which involves combining the energy of light with water and carbon dioxide to form simple carbohydrates essential for plant growth. Other functions of N include stimulating plants into rapid, vigorous growth, increasing seed and fruit yield and improving the quality of leaf and forage crops. Too much can delay fruiting. Too little and yields are reduced, leaves yellow (reduced photosynthesis) and plant growth is stunted.

(P)-Phosphorus: Like N, phosphorus (P) is an essential part of the process of photosynthesis. It is readily translocated from older tissue to younger tissue, and as plants mature, most of the element moves into the seeds and/or fruits. P is important for overall growth and metabolism including utilization of starch and sugar, cell nucleus formation, cell division and multiplication, fat and albumin formation, cell organization, and transfer of heredity. When P is deficient, plants exhibit purple stems and leaves, retarded growth and maturity; poor flowering and fruiting. Too much can result in zinc deficiency.

(K)-Potassium: Potassium, unlike N and P, is not found in organic combination with plant tissues. Potassium plays an essential role in the metabolic processes of plants and is required in adequate amounts in several enzymatic reactions, particularly those involving the adenosine phosphates (ATP and ADP), which are the energy carriers in the metabolic processes of both plants and animals. Potassium also is essential in carbohydrate metabolism, a process by which energy is obtained from sugar. There is evidence that K also plays a role in photosynthesis and protein synthesis. K is involved in maintaining water balance and cold hardiness. Plants deficient in K exhibit spotted, curled or burnt looking leaves.

(S)-Sulfur: Sulfer is another element essential for chlorophyll and is a constituent of the amino acids cystine, cysteine, and methionine and, hence, proteins that contain these amino acids. It is found in vitamins, enzymes and coenzymes. Sulfur is also present in glycosides which give characteristic odors and flavors to many vegetables. In legumes, it is required for nodulation and N fixation. Deficient plants exhibit light green leaves.

(Mg)-Magnesium: Magnesium is part of the chlorophyll in all green plants and essential for photosynthesis. It also helps activate many plant enzymes needed for growth and the formation of fruits, nuts and seed germination. Magnesium is a relatively mobile element in the plant and can be readily translocated from older to younger plant parts in the event of a deficiency. Plants deficient in Mg may show yellowing between the veins of older leaves; chlorosis and drooping leaves.

(Ca)-Calcium: Calcium is an essential part of plant cell wall structure and provides for normal transport and retention of other elements as well as strength in the plant. It influences water movement; cell growth and division and is required for uptake of nitrogen and other minerals. Symptoms associated with Ca deficiency include stunting of new growth in stems, flowers and roots; black spots on leaves and fruit and yellow leaf margins.


Iron plays an important role in enzyme functions and is a catalyst for synthesis of chlorophyll. Plants deficient in Fe may exhibit pale leaves and/or yellowing of leaves and veins.

(Mn)-Manganese: Manganese is necessary for enzyme activity for photosynthesis, respiration, and nitrogen metabolism. When limiting the symptoms are similar to Fe deficiency with pale young leaves pale and green veins. Sometimes brown, black, or gray spots are observed next to veins.

(B)-Boron: The primarily function of Boron is in regulating the metabolism of carbohydrates in plants. It affects at least 16 functions including flowering, pollen germination, fruiting, cell division, water relationships, movement of hormones, cell wall formation, membrane integrity, calcium uptake and movement of sugars. When deficient, the terminal bud may die, causing rosette of thick, curled, brittle leaves or brown, discolored, cracked, fruits, tubers and roots.

(Zn)-Zinc: Zinc is essential for plant growth because it controls the synthesis of indoleacetic acid, which dramatically regulates plant growth. It is a functional part of enzymes including auxins (growth hormones), carbohydrate metabolism, protein synthesis and stem growth. Zinc deficient plants often show mottled leaves and irregular yellow areas.

(Cu)-Copper: Copper is necessary for nitrogen metabolism and an important component of many enzymes. It is believed that copper is part of the enzyme system that uses carbohydrates and proteins. Copper deficient plants may show die back of shoot tips and terminal leaves develop brown spots.

(Mo)- Molybdenum: Molybdenum is a structural part of the enzyme that reduces nitrates to ammonia. Without it, synthesis of proteins is blocked and plant growth ceases. This element is also required by nitrogen fixing bacteria. When molybdenum is deficient plants have pale leaves with rolled, cupped margins and seeds may not form. Plants may also show nitrogen deficiency symptoms when plants lack molybdenum.

(CI)-Chlorine: Chlorine is involved in osmosis (movement of water or solutes in cells) and important for maintaining ionic balance necessary to take up mineral elements. It also plays a role in photosynthesis. When limited, plans may show wilting, stubby roots, yellowing and bronzing.

(Co)-Cobalt: Cobalt is required by nitrogen fixing bacteria and lack of this element may cause plants to exhibit nitrogen deficiency symptoms.

(Ni)-Nickel: Nickel has only recently been recognized as an essential element. It is required for the urease enzyme to break down urea into usable nitrogen and for iron absorption.

(Na)-Sodium: Sodium is important for the regulation of osmotic (water movement) and ionic balance in plants.

(Si)-Silicon: Silicon is a major component of cell walls and helps to create a mechanical barrier to piercing – sucking insects and fungi. It enhances leaf presentation; improves heat and drought tolerance, and reduces transpiration. Deficiency symptoms include wilting, poor fruit and flower set and increased susceptibility to insects and disease.

Lesson 2.2: Soil Fertility

It is possible for plants to develop and mature quite well without soil if they are provided with suitable combinations of the five essential environmental factors; light, heat, air, nutrients, and water. This concept is the basis of “hydroponics” and it is not uncommon for plants to be grown commercially in production systems that do not involve soil.

However, soil is still the natural medium for the growth of plants and it is doubtful that soilless agriculture will ever be a cost effective alternative for the production of the bulk of the food and fiber needed. For at least the foreseeable future the world will continue to rely on soil for agriculture.

We’ve already learned that much of the world’s soils are becoming less fertile. But what exactly does soil fertility mean? Some define soil fertility simply as the capacity of the soil to supply nutrients to the plant and then only with macronutrients, usually nitrogen (N) and phosphorus (P) and sometimes potassium (K). Using this definition, a fertile soil is one that contains an adequate supply of all the nutrients required for the successful production of plant life.

This principle is probably best summed up by the “Law of the Minimum” propounded by Justus von Liebig in the mid-1800’s. This law states that if one of the nutritive elements is deficient or lacking, plant growth will be poor even when all the other elements are abundant. Any deficiency of a nutrient, no matter how small an amount is needed, will hold back plant development. If the deficient element is supplied, growth will be increased up to the point where the supply of that element is no longer the limiting factor. Increasing the supply beyond this point is not helpful, as some other element would then be in a minimum supply and become the limiting factor.

But, a nutrient rich soil is not necessarily a productive one. To be productive, soil must also provide a satisfactory environment for plant growth and the nutrients it contains must be available for use by the plants. In this course we take a broad view of soil fertility and see it as a complex of soil chemical, physical and biological factors that affect land potential and the degree to which a soil is productive. Fertile soil is characterized by ongoing complex interactions involving decomposition of rocks, organic matter, animals, and microbes to form inorganic nutrient ions in soil water. Roots absorb these mineral ions if they are readily available and not ‘tied up’ by other elements or by alkaline or acidic soils. Soil microbes play a critical role in ion uptake and in the cycles that permit nutrients to flow from the soil to the plant.  The microbiological community of the soil system around the roots breaks down the available organic material in the soil into a usable form that the plant root system can readily absorb.

In the following lessons, we will provide some basic specific information on these soil components and soil characteristics that influence and determine soil fertility.

Supplementary Reading

Lesson 2.2.1: Soil Formation and Taxonomy

Soil is a relatively thin layer of unconsolidated mineral and organic material on the immediate surface of the earth. Fertile soil contains approximately 25% of both air and water, about 5% organic matter and about 45% mineral matter. It is important to understand something about how soils are formed to determine the best use of available soils and how to manage their fertility.

In general, soil formation starts with rocks that are pushed to the surface of the earth by geological or climactic forces. These rocks then undergo weathering – the chemical alteration and physical breakdown of rock during exposure to the atmosphere, hydrosphere, and biosphere. Through the weathering process, eventually enough essential elements become available to support lichens and other lower forms of plant life. As continuing generations of lichens grow, die, and decay, they leave increasing amounts of organic matter. Naturally-occurring organic acids further hasten decay of the rock. An increasing build-up of organic matter and formation of fine rock fragments result in more water retention in the soil and more water available for use by larger numbers of plants and animals.

Four factors determine what type of soils are formed. These are Climate, Organisms, Topography and Parent Material.

Climate has two major components for soil formation. The first is the temperature. As the mean annual soil temperature increases, the weathering of the rocks and minerals in the soil will be faster. Along with temperature is the climate factor of precipitation or rainfall. In general, areas with more rainfall will have greater weathering and greater leaching.

Organisms include animals living in the soil that contribute to soil development by their mixing activities. The mixing of the soil by organisms is called bioturbation. Humans also influence the soil with their activities of agriculture, urbanization, grazing, and forestry.

Topography as a soil forming factor is related to the soil’s position on the landscape elevation, direction and depth to the water table. Topography will have a great deal to do with the soils character as different topographic locations vary in respect to water runoff, erosion, leaching and temperature.

Parent material refers to the primary material from which the soil is formed. The type of soil that forms depends on the type of rocks available, the minerals in rocks, and how minerals react to temperature, pressure, and erosive forces. Soil parent material could be bedrock, organic material, an old soil surface, or a deposit from water, wind, glaciers, volcanoes, or material moving down a slope.

The length of time required for a soil to form depends on the intensity of the other active soil forming factors of climate and organisms, and how topography and parent material modify their affect.

Each of the world’s soils is assigned to one of twelve taxonomic soil orders, largely on the basis of soil properties that result from the five soil forming factors acting on the parent material over time.

Lesson 2.2.2: Soil Organic Matter (SOM)

Soil organic matter is defined as the soil fraction derived from materials of plant and animal origin. It includes these residues in various stages of decomposition, soil organisms, and their synthesized by-products. Since soil organic matter is derived mainly from plant residues, it contains all of the essential plant nutrients. Accumulated organic matter, therefore, is a storehouse of plant nutrients. Upon decomposition, the nutrients are released in a plant-available form. The stable organic fraction (humus) adsorbs and holds nutrients in a plant available form.

While there is not yet a consensus on exactly how to measure soil quality, there is little disagreement that organic matter content gives soils many of their desirable properties. Organic matter is important to soil structure and tilth. It provides energy for soil microorganisms, improves water infiltration and water holding capacity, reduces erosion potential and is an important element in the nutrient and carbon cycles. Organic matter is the adhesive of the soil, binding together the soil components into stable aggregates. It is widely considered to be the single most important indicator of soil quality and productivity

Soil organic matter plays a critical role in soil processes and is a key element of integrated soil management (ISFM). Almost all ISFM technologies are SOM dependent for their full success. Furthermore, SOM content can be used to set critical values that can help to make decisions when implementing ISFM programs. The SOM and ISFM relation is tricky, SOM build up is ISFM dependent and ISFM efficacy is SOM dependent.

Supplementary Reading

Lesson 2.2.3: Soil Organisms

Soil organisms are an important component of soil organic matter. Although soil is often considered (and treated as) a lifeless substance, it is not. Healthy soils teem with life, and would not exist without the organisms inhabiting it. Under a 1-meter-square soil surface, more than 10,000 bacterial and fungal types may be found, as well as 100 to 1,000 species of soil animals, such as protozoa, nematodes, mites, collembola, and earthworms. These organisms form an integral part of the soil, as they contribute to the development of soil structure, the dynamics of organic matter, and the availability of nutrients for plant growth.

One of the most important functions of soil microorganisms is the decomposition of organic matter and decomposition is performed by a variety of soil bacteria and fungi. A particularly important product of decomposition is humus (humic acid) which has a great influence on soil chemistry (cation exchange capacity) and water retention. Other products formed when organic matter is decomposed include carbon dioxide and nitrogen and other essential plant nutrients are released and made available to growing crops and other micro-organisms.

A particularly important soil organism is Rhizobium. This is a genus of soil bacteria that is responsible for symbiotic nitrogen fixation in legume plants. These organisms penetrate plant roots causing the formation of small nodules on the roots. They then live in symbiotic relation with the host plant.

Lesson 2.2.4: Soil Texture

Soil texture is arguably the single most important physical property of the soil in terms of soil fertility. This is because it affects and is related to several other soil properties such as soil structure, aeration, water holding capacity, nutrient storage and water movement.

Soil texture is dependent on the mixture of the different particle size separates (soil separates) and refers to the relative proportions of the various size groups of individual particles or grains in a soil. From largest to smallest the soil separates are:

  • Stones and cobbles are bigger than 64 mm (diameter)
  • Gravel is from 2 mm to 64 mm
  • Sand is from .05 to 2 mm
  • Silt is from .002 to .05 mm
  • Clay is less than .002 mm.

Texture is used to define a range of soil classes. It is important that participants in this class understand these terms as they will be used in future lessons. The table below lists the recognized soil textural classes and their makeup.

Soil Classes

% Sand

% Silt

% Clay






























40 +







40 +

40 +




40 +

In talking about texture it is important to note that the term “clay” is used in two different ways when describing soils. The term “clay” is a description of particle size and is also used to identify a particular kind of silicate mineral found in soils – a chemical recombination of the base elements of silicon, aluminum, and oxygen into a silicate clay mineral.

Lesson 2.2.5: Soil Structure

Soil structure refers to the arrangement of particles in a soil and how the individual soil particles clump or bind together. Structure is very important because the arrangement of soil particles plays the biggest role in determining the size and shape of the pores that conduct air and water. It also affects the plant’s ability to send its roots through the soil. Soil scientists have developed a classification systems to describe soil structure that involves 5 major structural classes – granular, blocky, platy, prismatic and structureless.

For more information on soil structure, participants should refer to the supplementary resources listed below.

Lesson 2.2.6: Soil pH

Another important soil property that affects soil fertility and the availability of nutrients is soil pH, a measure of the acidity or alkalinity of the soil. This property also has considerable effect on microbial activity. Soil pH is defined as the negative logarithm of the hydrogen ion concentration. The pH scale goes from 0 to 14 with pH 7 as the neutral point. As the amount of hydrogen ions in the soil increases the soil pH decreases thus becoming more acidic.

Soil pH has a great effect on the solubility of minerals or nutrients. Most of the essential plant nutrients are obtained from the soil and are not available to the plant unless dissolved in the soil solution. Most minerals and nutrients are more soluble or available in acid soils than in neutral or slightly alkaline soils. If the pH isn’t close to what a plant requires, some nutrients, such as phosphorus, calcium and magnesium, can’t be dissolved in water. And, if the nutrients aren’t dissolved, the plant can’t absorb them. The plants won’t grow or produce to their full potential.

Soil pH also influences plant growth by its effect on the activity of beneficial microorganisms. Bacteria that decompose soil organic matter are hindered in strongly acidic soils. This prevents organic matter from breaking down, resulting in an accumulation of organic matter and the tie up of nutrients, particularly nitrogen, that are held in the organic matter.

For more on soil pH, participants should review the supplementary resources below.

Supplementary Reading

Lesson 2.2.7: Cation Exchange Capacity (CEC)

Cation exchange capacity(CEC) is the ability of the soil to hold onto nutrients and prevent them from leaching beyond the roots. The more cation exchange capacity a soil has, the more likely the soil will have a higher fertility level. This is because cations retained electrostatically are easily exchangeable with other cations in the soil solution and are thus readily available for plant uptake. When combined with other measures of soil fertility, CEC is a good indicator of soil quality and productivity. Knowledge of this phenomenon is basic to understanding how much and how frequently lime and fertilizers should be applied for optimum crop production.

Cation exchange capacity (CEC) is the amount of negative charge in soil that is available to bind positively charged ions (cations). Essential plant nutrients, potassium (K+), calcium (Ca2+), magnesium (Mg2+), and ammonium (NH4+) and detrimental elements, sodium (Na+), hydrogen (H+), and aluminum (Al+3) are cations. Cation exchange capacity buffers fluctuations in nutrient availability and soil pH.

Clay and organic matter are the main sources of CEC. The more clay and organic matter (humus) a soil contains, the higher its cation exchange capacity. These materials act as centers of activity around which chemical reactions and nutrient exchanges occur. The individual particles of each are characterized by extremely small size, large surface area per unit weight, and the presence of surface charges to which ions and water are attracted. This explains why sandy soils, which contain low percentages of clay and organic matter, have low exchange capacities and require more frequent applications of lime and fertilizer than soils containing more clay and organic matter.