Our Living Soil

Soil is at the bottom of the food chain, yet it is the cornerstone of life on Earth


Soil is linked to everything around us. It is Earth’s only non-renewable resource, and with a natural formation rate of approximately 6-8 cm of fertile soil over a period of 2 000 years, this is not surprising. Traditionally, soil has always been seen or treated as a “dead” medium in which our crops bury their roots only to keep them from falling over.

What very few people realise is that soils also filter out pollutants from water as the water trickles down to underground water tables, and that healthy soils can store up to 9 000 tons of water in a 0.4 hectare piece of land.

In order to feed a global population that increased from 1 billion people in 1800 to 6.5 billion in 2002, agricultural production has doubled four times between 1820 and 1975 across the globe. Consequently, our precious soils have been subjected to annual planting of the same crop on the same piece of land, continuous ploughing in combination with crop residue either being removed by cattle or burned after harvesting. These practices have left valuable topsoil bare and unprotected – vulnerable to being blown away by windstorms and washed away during rainstorms. Keeping in mind that 10 tons of topsoil spread evenly over 1 ha is only 2.35 mm thick, it is astounding to realise how much topsoil is actually lost; consequently, huge crop losses result because of unproductive soils.

The development of synthetic fertilizers, herbicides and pesticides during the 19th century brought about more intensive types of agriculture. This transformation may have rescued billions of people from starvation, but our soils have been reduced to a state of “fertilizer addiction” – being unable to function effectively without the addition of increasing levels of fertilizer. The constant decline in yields (despite increased fertilizer application) due to unproductive and nutrient-depleted soils, along with the subsequent increase in pollution, ecosystem decline, and dietary disorders in humans, make it clear that this type of agriculture has never been sustainable.

The soil’s living component

Every producer knows about the importance of the soil’s chemical and physical properties which are frequently analysed and adjusted in order to optimise annual crop production. What a lot of producers do not know, however, is that there is also a living component present in soil that plays a crucial role in the functioning of a soil ecosystem. As an unintended consequence, the above-mentioned continued application of chemical fertilizer destroys this living component that is responsible for soil fertility.

Your first contact with the soil’s living component was most likely when you enjoyed that “fresh earth” smell when the plough ripped through the earth in preparation for planting season. Have you ever wondered where that “earthy” smell comes from? That is the smell of a harmless chemical called geosmin, synthesised by a specific group of bacteria called actinomycetes – just a very small fraction of microscopic organisms responsible for crucial functions within the soil. This “earthy” smell is also evident after the first spring rains, because as rainwater enters the soil, the air between the soil particles is displaced by the water, thus releasing the air and geosmin.

On the other hand, you would almost certainly also have experienced the less enjoyable aspect of your soil when your crops started wilting or rotting or showing signs of stunted growth and the professionals at the co-op used words like “fungal infection”, “bacterial infection” or “nematode infestation” while hurriedly escorting you to the chemical section of the store to kill the “bad bugs”!

Functioning of the soil

An intricate relationship exists between the soil’s physical, chemical and biological properties. This relationship is not only exceptionally complicated, it is also extremely sensitive due to the finely tuned balance existing between the triad. Depending on the existing soil conditions, these relationships can be either positive or negative to plant and soil health.

As soon as this intricate relationship is disturbed through intensive tillage, monocropping, reckless use of agrochemicals, and overgrazing, the functioning of the soil’s ecosystem is impacted negatively. In these cases, the beneficial microorganisms are usually suppressed, while the pathogens then dominate the soils, resulting in high levels of plant diseases.

The functioning and health of a soil, which is usually reflected indirectly in the health of a crop, is greatly influenced by the availability of soil organic matter, the activity and biodiversity of soil (micro)organisms, as well as the flow of nutrients within the soil system. It is extremely important to keep in mind that this flow of nutrients is only possible because soil microorganisms do not function in isolation – they are intimately integrated with each other. These microorganisms are found in very high numbers in soil habitats, with bacteria reaching numbers of 100 million to 1 billion bacteria in a teaspoon of healthy soil, meaning that eight teaspoons of healthy soil may contain more bacteria than there are currently people on Earth! Indigenous soil microorganisms are present in unique microenvironments favouring their optimal survival and nutrient cycling.

With an increasing demand to grow more food on soils that have been mismanaged for millennia, it is clear that the responsibility lies with us to look after our soils. Since healthy soils form the foundation of food production in successful agriculture, unproductive soils can be rehabilitated through the adoption and implementation of more environmentally-friendly approaches promoted by the three main interlinked principles of Conservation Agriculture (CA): no or minimum soil disturbance, permanent soil mulch cover, and crop diversification.

The effect of CA practices on soil microorganisms

Soil microorganisms feed not only on decomposing plant material, but also on plant root exudates, i.e. chemicals secreted into the soil by roots. These exudates contain various amounts of different carboxylic acids, carbohydrates, amino acids, etc., depending on the type of plant, growth stage, and even the cultivar. Since soil microorganisms are very energy-efficient, different microorganisms will be attracted to different combinations of root exudate compounds that they are well-adapted to utilise rapidly. By implication, as the composition of the root exudates changes, so will the composition of the microbial community – thus influencing the diversity of the microbial community, and consequently the nutrient cycling process. Therefore, by planting a wider variety of crops as part of a rotation or intercropping system, a more diverse microbial community is stimulated to conduct more vital functions simultaneously in the soil ecosystem.

Apart from the decomposition of plant material, various microorganisms have the ability to produce chemical compounds, such as antibiotics and other anti-microbial chemicals, to suppress or decrease the proliferation of pathogens and favouring beneficial microorganisms, while others produce chemical compounds to stimulate plant root growth, solubilise phosphorous and potassium, and fix nitrogen from the atmosphere into the soil. Unfortunately, monocropping (monoculture) has the opposite effect. Since the same crop is planted annually on the same piece of land, the microbial communities lose their diversity and become highly specialised due to the continuous supply of the same food sources. As a result, some of the microorganisms with the ability to produce the anti-microbial compounds might disappear, creating the perfect environment for pathogens to thrive without having to compete with other microorganisms for the same food supply. Through crop rotation, this disease cycle can be broken, since the food source that the pathogen was used to is suddenly absent and replaced by a totally different food source that the pathogen is not adapted to, and it is suppressed – either by anti-microbial compounds produced by the new set of microorganisms that are encouraged by the new food source, or the pathogens are simply out-competed.

Soil structure can also be improved by planting different crops with different root systems that “break up” the soil structure as they grow through the various soil layers. Root exudates are consequently transferred to the deeper soil layers, thus increasing soil fertility by attracting soil microorganisms to increase nutrient cycling. The topsoil is subsequently kept cool by sustaining a soil surface cover with mulch, thus reducing evaporation to a minimum.

Under these favourable conditions, the growth of fungi (mainly) and bacteria responsible for decomposition, is stimulated. As plant material is shredded into smaller fragments by ants, termites and other insects, the shredded fragments are then carried into the deeper layers of the soil profile by the same insects, as well as by earthworms. Fungi and bacteria are mainly responsible for decomposition of plant material, thus breaking the complex molecules, which are locked inside the plant material, into smaller, simple elements that can be more easily utilised by microorganisms as a food source. In this way, the soil microbial communities are responsible for the mineralisation process in soil ecosystems by unlocking the nutrients in organic matter and releasing them into the soil in plant-accessible forms.

It is thus obvious that the soil ecosystem is finely integrated and working harmoniously to ensure the optimal functioning of this “underground factory”. Unfortunately, by ploughing the soil, this whole “factory” is significantly disrupted. With this physical process of overturning the soil, the microorganisms working optimally in the deeper soil layers under conditions of limited oxygen and sunlight, are suddenly exposed to conditions of abundant oxygen and sunlight. Similarly, microorganisms functioning optimally in the topsoil under conditions of sufficient oxygen and sunlight, suddenly have to survive under conditions of limited oxygen and sunlight. In the human world, it is similar to taking experienced fishermen who are used to spending days on a boat on the wide open waters of the ocean, and forcing them to become farmers who have to work daily with lots of soil and dust and very little water. Fungi, which are responsible for decomposition of plant material after harvesting, are destroyed during tillage, thus slowing the decomposition process. Earthworm tunnels, which allow oxygen and nutrients to flow into the deeper soil layers, are also destroyed, and functioning microbial communities are completely disrupted. Consequently, it is going to take some time for the microorganisms to re-organise themselves to function optimally again.

How is soil health or fertility determined?

For decades, soil physical-chemical analyses have been used to determine the health or fertility status of soils. Although this practice is not incorrect, it makes sense to also look at more sensitive indicators such as the soil microorganisms, due to their extreme sensitivity to any disruptions or changes in the soil environment.

When we, as humans, feel unwell, is it not true that we would like the doctor to test our most vital signs first to look for something wrong? We don’t want them to test our bone density if we have the flu – they should test our temperature and heart rate first, since these are more sensitive indicators of flu infections. When doctors are uncertain of the nature of the illness, they cannot conduct only a single test to determine the nature of the illness; they have to conduct a whole set of tests or analyses.

The same applies to soil microbial tests or analyses:

it is impossible to determine the health or fertility status of a soil by conducting a single analysis. It is strongly recommended that soil samples are sent to a microbiology laboratory two or three times a season over a period of at least five years for microbial analyses. Since a healthy soil is characterised by a high diversity of soil microorganisms that are actively busy cycling nutrients, soil microbial analyses will determine the changes in diversity and activity of soil microbial communities over time, providing an indication of improving or declining soil fertility. Frequent analyses of samples collected over an extended period of time will minimise the influence of seasonal fluctuations on microbial data, and enable the soil microbiologist to attain a more complete understanding of the effect that the various agricultural practices might have on soil microorganisms as indicators of soil fertility and health.

The Soil Microbiology Laboratory at the Agricultural Research Council - Plant Protection Research Institute (ARC-PPRI) in Pretoria is adequately equipped with facilities and knowledge to analyse soil microbial communities as indicators of soil health due to their sensitivity to changes in the soil environment. These services are available to anyone concerned about their soils. We have all been appointed as curators of our soils so let us own that responsibility, because without healthy soils, there can be no farmers, no agriculture and no life!

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