Understanding Soil Processes

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Understanding Soil Processes

used with thanks from www.Petrik.com website: Written by Vaclav Petrik Snr. in the late 1980's and is based on the Petrik Approach to practical soil microbiology

Soil Fertility


Most of us will agree that the soil is the major natural resource available to humankind. Yet it is and has been abused by us to the point of self destruction. Many past civilizations have perished due to their abuse of the soil (like Mesopotamia and the Mayan civilization). Why didn't anyone stop the destruction? The soil destruction process takes time and the changes in each generation are "small" so no one cared and most of us still don't.
The soil in which we plant crops today has been self perpetuating for millions of years without man's help. It will continue to do so if we do not disturb its natural cycle.
In the soil there are nutrients and trace elements both of which plants require for growth. They are essential.
Soil moves continually in a natural cycle aided by oxygen, water, minerals and decomposing animal and plant matter. These elements create life in the soil, which is ongoing if not disturbed. We speak of healthy soil if it works well and nutrients continue to be available to the plant.
Good soil consists of 93% mineral and 7% bio organic substances. The bio organic parts are 85% humus,10% roots, and 5% edaphon.
Edaphon is itself a "world" of life and consists of microbes, fungi, bacteria, earthworms, micro fauna, and macro fauna as follows:
Some of the nutrients get lost naturally through leaching continually wet weather, melting snow, flooding or through denitrification. Also each cultivated plant takes nutrients from the soil, as soon as the crops are harvested. The substantial task of the farmer is to take care of returning nutrients taken from the soil through harvesting. The conventional farmer is using water soluble, mostly salty chemical fertilizers.
In contrast, the bio-organic farmer uses organic matter in the form of crop residues, and other wastes, and /or compost and BTR, in order to take of soil life, its proliferation and stimulation to highest effectivity.
With this treatment and approach, the bio farming system should bring out the following: Stronger nutrient accumulation and nitrogen fixation. Availability of soil nutrients to plants.


The natural life cycle of out fields must be kept functional through the addition of organic matter after the residues from the previous crop have been depleted in order to build new Bio-Organo-Mineral nutrition for our next crop. This action cannot be replaced with the water soluble salts or overdoses of chemical fertilizer which destroy soil life, not build it. During the growing season, as the plants fix carbon dioxide by photosynthesis, about 10-25% of this fixed carbon,finds its way back to the soil through the roots (root exudates) this is even if all residues including roots are removed. This is very important in bio-organic farming.
The production of humus is a complex process. In general cyclic substances like phenol groups and also other like organic acids and vitamins (humus is also related to crude oil) are polymerized with help of enzymes,like phenol oxidase. These cyclic compounds are both from plant parts(like lignin) and are also produced by the micro-organisms. Mostly fungi, actinomycetes (Streptomycets) seem to be responsible for humus formation. Aspergillus, Pisolithus, Rhizoctonia, Streptomycets are only but a few examples of micro-organisms actually capable of synthesizing cyclic(aromatic) compounds and form them into humus from non cyclic materials.
It is impossible for man to produce stable humus synthetically. Man can properly cultivate the field, supply organic matter and so encourage the development of stable humus in the soil. Soil with stable humus must always be protected to maintain the fertility and productivity of the soil.
The production and maintenance of stable humus in the soil should be the primary goal of every farmer. Good stewardship of the land is necessary to protect and maintain mankind's most important asset, fertile soil.
For nearly one hundred years soil science in most schools of higher learning (especially in agricultural colleges) has been primarily concerned with the physical and mechanical aspects of soil structure. Biological thinking has become a major concern only in the last few years.
The new approach considers not only the physical properties and mineral structure of the soil,but also the process by which organic matter is transformed into humus by micro-organisms.

Organic Transformation

Humification - the transformation of organic matter into humus, is a fascinating process. Organic materials such as manure or field wastes ,when disked into the upper three to six inches of topsoil, will undergo several changes. The humification process involves first catabolism , then anabolism. These are not truly correct terms as they are usually used for same functions within living organisms, but we may consider soil as one living organism.


The first stage in the break down process is important to be started by fungi, these make the debris "pre-digested" for many animals in the macro and mesofauna. Many of these animals lack needed enzymes for the start of the decomposition process (springtails, millipeds, earthworms, etc.) The debris is fragmented into smaller parts and chemical changes occur in breaking up of cellulose, chitin, etc.
Most plant parts already contain fungi within(seed,leafs,stems all are inhabited by fungi): these are going to start the decomposition process. Many fungi residing within seeds are known and seeds (or plant parts )carry only certain fungi, that will actually start the decomposition process (sometimes they also carry pathogens.)
If bacteria start the decomposition process instead of fungi, this may happen because of several reasons, the one most common would be water logging (too moist), the process turns to putrefaction. During this stage toxic substances are produced (methane, formaldehyde, hydrogen sulphide, phosphine) which are harmful to soil and retard the growth of plants.
Please do not misunderstand bacteria and fungi are decomposing all at the same time,we mean predominance of one over the other not that the other is not involved at all.
The excrements of the neso and macro fauna are a very suitable medium for growth of bacteria, algae, and nematodes. These multiply rapidly and again draw the mesofauna, as it feeds on the bacteria. Many new animals are involved in this stage, some are the same as in the first decomposition.
Slowly the materials are broken into smaller parts, at the same time many are again combined and used for building hormones, enzymes, proteins for the rapidly multiplying microfuna. Antibiotics are produced to secure an area for growth, form other micro-organisms.
Carbon dioxide is evolved back to the atmosphere and only about 20-30% of carbon originally found in the plant parts makes it to humic complexes.In case of carbohydrates as starting point the carbon percentage that makes it to humus is less than 20%. If the starting point is lignin, tannins, or other phenolic groupings (mostly found in wood and leaves) the percentage may reach 75%.
Mineralisation is the process of freeing minerals from organic molecules (carbon bonds). During humification there are two possible end products for atoms within the starting molecules. Minerals may either be build up stable humus or be in free form, carbon either tied within humus or evolve in form of carbon dioxide. The following is a summarizing table where atoms end up after humification:
All minerals within organic compounds
80% freed up and 20% in humus
Carbon from carbohydrates
80% evolves as carbon dioxide and 20% goes to humus formation.
Carbon from lignin, aromatic type amino acids (tyrosine, tryptophan...) and like compounds (fats, hydrocarbons like waxes,...)
25% evolves as carbon dioxide and 75% goes to humus formation
will remain to 50% in humic form.
The micro, meso, and macro fauna is so closely interwoven that one could say, if areas have small amounts of earthworms, beetles, etc. the microbial population will be small.


The second half of soil metabolism anabolism now begins, starting with the synthesis of soil plasma. It is in this process of plasmolysis that the catabolised organic matter becomes plasma building material for new plant life. This is the least understood of all the processes that go on in the soil.
Soil plasma is the liquid portion of the soil. It contains proteins, salts, degraded organic compounds and water. It is like the liquid part of the blood which, although without corpuscles , is much more than water.
Soil plasma is that substance in the soil that can spin catabolised remnants of former life into vital threads that are woven together into the fabric of new life through the processes of anabolism.
In the anabolism process the plasma is transformed into stable humus. This plasma also contains the decomposed cell walls of organic residues and has become a spongy, gelatinous substance that bonds the surface of the clay crystals together. In this manner, clusters of clay crystals form aggregates that are resistant to being broken apart. This gives the soil the ideal structure farmers refer to as tilth. The combination of plasma and clay forms what is known as stable humus.
The presence of stable humus allows air, water and essential mineral nutrients to be held in the aggregates. The chemical nutrients are in the form of ions atoms carrying positive or negative electrical charges . In science, they are referred to as swarm ions.
The spongier the soil the more pores or open spaces are within it. Like Swiss cheese reduced to an infinitesimal scale, each of these holes or pores has an inner surface that is coated with plasma. The greater the porosity of the soil the more capacity it has to accumulate and hold air, water and nutrients and prevent them from being washed away.
Consequently, we can imagine that a loss of this porosity with all its inner surfaces represents a catastrophe to the soil. With the loss of stable humus, the mineral particles of the soil come together almost like concrete. The porosity is lost and with it the ability of the soil to retain air, water and nutrients. As this capacity diminishes , the fertility of the soil is reduced and productivity declines.
When we have stable humus,we have all the ideal conditions we are seeking for our soils. We have the inner protected porosity, the glued together clay crystals coated with plasma containing the decomposed organic matter holding air, water and chemical nutrients swarm ions.
In this ideal environment the third phase of stable humus, plant feeder roots develop. It is here the dormant power and original resource of soil fertility comes to life. This is the secret of rebuilding the energy and fertility of "Mother Earth".
Here the living matter, which was originally buried in the soil to decay, celebrates the birth of new life; the re-births of organic matter for germinating and growing plants
Stable humus, the so desired, ideal stage of fertile soil, could be considered the connecting link or connector of life. Here decomposition ends the last stage of death:and new life begins. Through this process,we can understand the fertility of the soil depends on the ability of Nature to create living,organic order from inorganic disorder.
Many farmers are imprisoned in a way of thinking that is only concerned with levels of chemical fertilizers and must be re-educated to begin considering the biological processes occurring within the soil. Balanced soil fertility is a condition which cannot be measured by chemical or physical tests. The farmer who strives to maintain the bio-organo-mineral complex in correct balance in his fields can achieve the highest agricultural production levels as a result of these biological processes.
Today's popular chemical tests of soil do not tell anything about the decisive life processes. They are merely a yardstick of the mineral content of the soil and do not help farmers in knowing how to treat the fields for future productivity and healthy corps. The whole process misses the basic point that the true purpose of agriculture is to recycle life to capture the life factor from decomposing organic material and channel it into new growing plants. It is only by doing this that vital healthier life can be maintained in plant, animal and man.
When the farmer decides to begin a biologically balanced fertility program, soil analyses show minimal values of nutrient reserves and indicate that large amount of fertilizers should be applied to meet the needs of the crop. However, after a few years of successful biological farming, analyses can show high residual levels of available nutrients, although the farmer has not used any chemical fertilizers during that time.
The absurdity of conventional chemical thinking is revealed in the mistaken notion that larger quantities of nutrients will continue to result from the aid of chemical fertilizers. But the truth is ,that by the activity of microbes, the nutrients are biologically enriched, accumulate in the pores of the soil aggregates as swarm ions, and will become available to the growing plants. The farmer who implements the balanced fertility program can achieve needed levels of nutrients in the soil in a less expensive way, can achieve the highest possible yields, and a higher quality harvest. By using the wrong fertilizers, excessive chemicals and heavy machinery we are destroying our soil, our fields, our farms and our future.
Plants supplied with this kind of nutrient require less water. This assures the biological farmer a significant saving of water in the production of crops, an especially important consideration in arid zones and in dry seasons elsewhere.
We cannot outwit Nature. Nature does not allow a wasting or loss of living matter in the restless process of mineralisation the procedure for impregnating the soil solution with the mineral elements required for plant growth. In the final stage of decomposition the remnants of plasma still contain the essential elements of the life processes. These remnants are then transformed into soil plasma in the process of producing stable humus.
Stable humus is the crucial centre, the focal point of the life cycle. Adhering to farming practices that assure the production of stable humus thus becomes the farmer's main objective.

Soil Fertility

Over 130 years ago (1855) Justus von Liebig's discovery that plants are fed by water soluble substances started a revolution in agriculture. However this revolution went in a different direction far from the original thinking of von Liebig.
Von Liebig's discovery reads:
"Plants take up water soluble nutrients"
This discoveries became internationally understood, but unfortunately, a single word has been added to the Liebig statement and his sentence and the meaning changed as follows:
"Plants take up water soluble nutrients only"
There is a great difference between his original statement and his interpretation by the addition of the single word "only". The single addition changed the truth of his discovery. First to recognize the important misunderstanding was von Liebig himself. However, the huge agro-chemical industry built their fort based on the word "only".
Science neglected his best discoveries and findings which are as follows:
  • Man must regard nature as one unit, a whole and everything that occurs in nature works together as knots in a net
  • Diseases of plants are diseases of the soil.
  • We must treat the prime origin of the disease, not the symptom
  • It is important to understand that if the soil is living and healthy, the plants will be strong and healthy with natural resistance against disease. This opinion is the basic pillar of organic biological farming. Fertilizer facilities prospered and became firmly established as the bass of a huge, new agro-industry.
    Ammonia taken up by plants is utilized directly, but nitrates have to be converted to ammonia within the plant to be utilized. In addition the production of ammonia from nitrates within plants is only on a as needed basis; therefore if soil is high in nitrates that are taken up by the plant in higher amounts than needed they will not be formed into ammonia, but will sty in nitrate form and this is toxic to animals ( carcinogenic compounds may be easily created under certain cooking conditions.)
    Liebig actually discovered that plants take up solutes, these are dissolved substances. Well dissolved substances is a very broad statement, it does not mean in water only. Many things can be dissolved in substances other than water yet are not water soluble. The actual meaning of solutes in the biological sense is that the molecules are in fluid state, independent of each other, there may or may not be other substances present (solubilising agents , like water) The word dissolved means broken up into molecules, or ions in salts. This is what the agro-chemical changed "Only ions are taken up" But ions are not the only solutes, nor does the wording solutes necessarily imply a solubilising agents(like water) is present. The molecules only have to be disassociated to be solutes.
    Good soil is a world of working microbes. One gram of soil can contain over ten million bacteria. "Around the roots of a healthy growing plant a dense coating of microbes may contain a population of from 100 to 200 billion microbes. The life span of a single microbe in this environment is approximately one half hour.
    Microbes live in colonies and are very mobile. In their rapid life cycle from creation to death they develop tremendous metabolic activity and steadily improve the structure of the soil.
    Some microbes excrete antibiotics. They metabolize phosphorus and iron bonds which are difficult to dilute efficiently without this microbial activity. The earthy odour of the soil is due to them. They create two thirds of the soil carbons, attack cellulose and mineralize nutrients.
    We have another important grouping of life in the soil. These are mites, nematodes, centipeds,worms,and insects. All preying on or eating plant and animal residues, eating each other, producing dung and other excrements. As death they leave important waste. They work on stages in the formation of humus in the soil.