Soil has traditionally been seen as a "dead" agricultural medium – something to keep crops upright. Soil physicochemical analyses were conducted to determine the application rate of chemical fertilizers to sustain/increase the season's yields. Soils were injudiciously ploughed, drenched in herbicides and pesticides, crop residues were burned, and fields were left bare and vulnerable to nature's elements, with precious fertile topsoil being blown away or carried off during wind and rainstorms. The vital role of soil microorganisms in agriculture have only recently gained popularity with South African farmers after they experimented with various agricultural practices in an effort to increase their yields and soil's health/fertility in a sustainable way. Before this paradigm shift, we never realized that only 6-8 cm of fertile soil was naturally formed over a period of 2000 years; that soil-life consisted of thousands of different insects, earthworms, mites, nematodes, fungi, yeasts, and single-cell organisms; that a teaspoon of fertile soil could contain a billion bacteria and almost 5,000 different species of bacteria per gram of soil.

After decades of collaboration between researchers and farmers, conservation agriculture (CA) was promoted as the most probable solution to sustainable agriculture. Conservation agriculture aims to improve/sustain productivity, increase profits and food security while preserving and enhancing the resource base and the environment. Long-term implementation of CA's three main principles, i.e. minimum soil disturbance, permanent organic soil cover, and crop diversification, will inevitably lead to healthier soil and sustainable agriculture.

Nematodes, fungi and bacteria are usually associated with large-scale yield-losses, but what we fail to realize in a healthy soil with its high microbial diversity and activity, is that beneficial and harmful organisms are present in a very fine balance. With this sensitive balance maintained, plant-pathogens are suppressed and/or out-competed by the indigenous soil life, and vital soil processes are optimally executed. This attribute is highly beneficial, especially when external forces, such as drought and diseases, disrupt soil processes performed by specific species. In the event of such an external force, these vital processes can immediately be re-initiated and maintained by other individual or groups of species, thus strengthening the soil's resilience and resistance to disruptive forces.

Due to the sensitive nature of soil microbial populations, they could be used as "early warning systems" or sentinel organisms to detect deterioration or improvement in soil quality – almost like the canaries that were historically carried into the coal mine tunnels by the miners to detect the collection of dangerous gases. If the canary was killed by the gases, it served as a warning to coal miners to exit the tunnels immediately. With the case of soil microbial populations, for example, when a soil's microbial diversity (the number of different microorganisms) decreases but the activity (how hard/fast they work) increases, or vice versa, it indicates a disturbance in the soil's balance and that the soil's health might be compromised. Such an imbalance typically occurs during injudicious ploughing and fertiliser application, extended fallow periods, or continuous monocropping.

Unfortunately, these "early warning systems" cannot be determined by conducting only a single analysis to provide a complete soil health status report. Below is a simplified diagram of how many analyses could actually be conducted on a single soil sample; each of these analyses providing an answer to a different question.

Thies JE. 2007a. Methods for studying the soil biota. In: Paul, EA (ed.), 3rd Ed. Soil Microbiology, Ecology and Biochemistry. Academic Press, Burlington, MA.

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