As climate variability, rising input costs and declining soil quality continue to challenge South African agriculture, the focus is shifting beyond conventional soil chemistry towards the living ecosystem beneath farmers’ feet.
While fertiliser programmes remain essential, experts say long-term productivity depends just as much on nurturing the billions of organisms that drive nutrient cycling, improve soil structure and build greater resilience against drought and extreme weather.
For many years, soil management has largely centred on correcting nutrient deficiencies and adjusting pH levels. However, research increasingly shows that healthy soils rely on far more than their chemical composition. Beneficial fungi, bacteria, nematodes and other microorganisms form an intricate soil food web that supports crop growth, recycles nutrients and helps protect plants against pests and diseases.
Sheila Storey, MSc (Agric) and consultant for Nemlab, says soil biology should now be regarded as equally important as soil chemistry in modern farming systems.
Soil is a living ecosystem
Storey explains that a balanced soil food web delivers a range of ecosystem services that directly benefit crop production.
“Provided the soil food web is balanced, it provides many ecosystem services. The most important of these is nutrient cycling,” she says.
One of the most significant contributors to nutrient availability is the activity of beneficial nematodes.
“Beneficial nematodes can provide between 9% and 30% of the nitrogen available to plants when the biology is balanced.”
Storey adds that beneficial fungi also play a critical role in making nutrients available to crops.
“Mycorrhizae exchange phosphorus, which the fungus has ‘mined’, in return for carbon that the plant provides. The carbon is then stored by the mycorrhizae in the soil.”
Beyond nutrient cycling, Storey says soil organisms perform several essential functions that cannot be replicated by fertilisers alone.
“Biology is responsible for breaking down organic matter. Microbes can also regulate pests and diseases.”
She says this biological activity creates healthier soils that function more efficiently while supporting sustainable production over the long term.
Keeping roots in the ground
One of the six key principles of soil health is maintaining living roots throughout the year.
Storey says plant roots continuously feed soil organisms through carbohydrates released into the surrounding soil.
“Roots 24/7 is one of the six principles of soil health. The plant roots provide food for the biology in the form of carbohydrates,” she says.
These root exudates sustain a diverse community of microorganisms that help drive nutrient cycling and improve soil structure.
She adds that diversity above ground directly influences diversity below ground.
“The greater the diversity of cover crops, the greater the diversity of exudates and so too the greater the diversity of soil biology. Above-ground diversity begets below-ground diversity.”
Rather than relying on a single cover crop species, Storey encourages producers to plant diverse mixtures wherever possible to encourage a more complex and resilient soil ecosystem.
The diversity of plant species creates a wider range of food sources for soil organisms, ultimately strengthening the biological processes that underpin soil health.
Why soil should never be left bare
Keeping the soil covered is another fundamental principle of healthy soil management.
Whether through mulch, crop residues or living cover crops, protecting the soil surface provides multiple benefits that extend well beyond reducing erosion.
“Mulching regulates soil temperatures, provides carbon and covers the soil. We always say, ‘Cover the soil to protect the biology beneath’.”
Storey explains that the carbon supplied through mulches contributes to the formation of humus.
“The carbon creates the humus which, in turn, acts like a sponge and increases water-holding capacity.”
This improved moisture retention becomes increasingly valuable as South African producers contend with prolonged dry spells, more frequent heatwaves and increasingly erratic rainfall patterns.
By moderating soil temperatures, mulch also creates a more stable environment for beneficial organisms that are sensitive to extreme heat and fluctuating moisture levels.
Legumes remain an important tool
Nitrogen-fixing crops continue to play an important role in building soil fertility, particularly when incorporated into cover crop programmes.
Storey says these crops naturally contribute nitrogen to the system, provided the correct symbiotic bacteria are present.
“Nitrogen-fixing crops provide nitrogen provided the associated bacteria are present.”
However, she cautions against viewing legumes as a complete replacement for synthetic fertilisers.
“On their own they cannot reduce the farmer’s reliance on synthetic fertilisers, but they can definitely cut the amount of nitrogen required.”
When combined with healthy biological activity and sound soil management practices, legumes can help reduce fertiliser requirements while supporting long-term soil fertility.
Beneficial nematodes outnumber harmful ones
Although many producers associate nematodes with crop damage, Storey says only a relatively small proportion of them are harmful.
“Harmful, or plant-parasitic, nematodes damage plant roots. The beneficial nematodes feed on different food sources. Bacterivores, fungivores, omnivores, predators and entomopathogenic nematodes all have a role to play in the soil food web,” she says.
Because different nematode groups respond to changing soil conditions, they provide valuable information about overall soil health.
“This makes these nematodes excellent bio-indicators of soil health through a nematode community profile.”
She says understanding the balance between beneficial and harmful nematodes gives farmers a clearer picture of how well their soils are functioning biologically.
Soil health requires a systems approach
Storey says soil health depends on consistently applying all six principles rather than focusing on individual practices. These include maintaining living roots throughout the year, promoting root diversity, keeping the soil covered, minimising chemical, physical and biological disturbance, incorporating livestock where appropriate to recycle nutrients and utilise cover crops, and adapting management according to the specific context of each farm, orchard or field.
“Cover crops provide living roots throughout the year, while mulches protect the soil surface and contribute organic carbon. Nitrogen-fixing species improve fertility, and beneficial soil organisms recycle nutrients, build soil structure and help suppress pests and diseases,” she says.
Together, these practices strengthen the soil food web, improve water movement through the soil profile and increase the system’s ability to withstand environmental stress.
Avoid expecting quick fixes
According to Storey, one of the most common mistakes farmers make is expecting soil health to improve through a single product or practice. Soil health will only be achieved by following the six soil health principles.
Another common mistake is planting only one cover crop species when a mix is required.
She also cautions against believing that commercially available microbial products alone can restore healthy soils.
“Believing that adding a microbe out of a container will improve soil health is another misconception. Most of these products are there to improve root health, but they don’t provide the complexity required for soil health,” she says.
Instead, Storey says farmers should focus on creating the conditions that naturally support diverse biological communities.
Looking beyond conventional soil tests
While laboratory soil analyses remain important for measuring nutrient levels, Storey says farmers need to monitor physical and biological indicators as well.
Among the simplest assessments are infiltration tests, observing the presence of small soil organisms such as springtails, physically feeling the soil structure and using a penetrometer to measure soil compaction.
“To refine the tests, use a laboratory such as Nemlab,” she says.
Monitoring these indicators over time provides valuable insight into whether soil health is improving beyond what conventional nutrient analyses reveal.
Greater resilience in a changing climate
Healthy soils are increasingly recognised as one of agriculture’s most effective defences against climate-related challenges.
Storey says soils with strong biological activity have better water infiltration, greater water-holding capacity and reduced run-off during heavy rainfall events.
“The soil is more resilient. With improved water-holding capacity and infiltration there is less run-off.”
She says cover crops also help stabilise soil temperatures while healthier soils often lead to lower production costs.
“Cover crops reduce and stabilise temperature. Input costs are decreased,” she explains.
These improvements become increasingly valuable as farmers face more variable rainfall patterns and rising production costs.
Where should farmers begin?
For producers looking to improve soil health this season, Storey recommends starting with a relatively simple but highly effective step:
- Start with two cover crops that will grow on the land or in the orchard;
- Cover crops provide roots 24/7, cover the soil and reduce disturbance;
- There is no universal formula for every farming operation as each situation, land or orchard is different.
