The soil food web is how nature has been feeding nutrients to plants since the dawn of time. Farmers should be harnessing rather than working against this system.

The soil food web is a concept that might seem foreign to many mainstream farmers, and yet it is how nature has been feeding nutrients to plants for billions of years. Dr Mary Cole, a celebrated academic, plant pathologist and soil microbiologist, has dedicated much of her career to helping farmers restore a healthy and functioning soil food web on their properties. She is the founder of AgPath, a small soil biology company providing laboratory testing in many fields of fungal and microbial pathology and farming consulting services in agriculture.

Here is what Dr Cole recommends that farmers should know about this complex and fascinating system, and how it can be harnessed to build natural fertility and resilience. Farmers who are utilising the soil food web methods are seeing increases in their productivity and profits as well as improving the health of their land and the quality of their produce.

The soil food web and nutrient cycling

When plants photosynthesise, they combine carbon dioxide from the atmosphere and sunlight energy to produce simple sugars and carbohydrates. They use these sugars and carbohydrates to grow, build their own tissues and produce things that humans harvest, like starches.

But sugars and carbohydrates are not the only nutrients that plants need to survive and thrive. They require a wide array of micro and macro nutrients including nitrogen, phosphorus, potassium, iron and sodium. Fortunately for plants, there's a rich source of these nutrients right beneath their roots in soil parent material (rocks, pebbles, sand, silt and clay) and organic matter.

On a molecular level, the parent material comprises crystalline structures that contain atoms of minerals. However, the minerals are not available to the plant while they're bound up in these structures. In order for plants to be able to utilise nutrients from the parent material and organic matter, the soil food web must be in balance and a process called nutrient cycling must take place.

When plants need these nutrients, they 'invest' some of the simple sugars and carbohydrates they produce during photosynthesis into the soil through their roots. These root 'exudates' attract and feed two important microorganisms, bacteria and fungi, which then rapidly grow and reproduce at the root zone. This is an example of carbon sequestration, as CO2 is taken from the atmosphere and delivered into the soil, where bacteria and fungi use this food source to reproduce, building their bodies predominantly from carbon.

At the root zone, the growing population of bacteria and fungi, or 'decomposers', release enzymes that break down the crystalline structures of the parent material, releasing the nutrients bound up within. They essentially mine and consume these nutrients from the parent material as well as from decomposing organic matter.

The next step of nutrient cycling is where 'predator' microorganisms come in. Protozoa and nematodes are attracted to the root zone and consume the bacteria and fungi (and the nutrients within them). The waste left behind by these predator microorganisms contains an abundance of these minerals and nutrients in plant-available form, which are easily absorbed into the plant roots.

Thus, the plant gets a return on its investment of simple sugars and carbohydrates, in the form of essential macro and micronutrients. In other words, plants will give up some of their precious resources because, through these symbiotic relationships, they later gain nutrition. It is a cooperative and collaborative community and without a healthy and balanced soil food web, this nutrient cycling isn't possible and plant health suffers as a result.

Key microorganisms in the soil food web:

There are four key groups of microorganisms in a healthy and functioning soil food web, each with a specific and important role.


Bacteria are a type of decomposer organism. In order to survive, they feed off organic matter and extract and retain soil nutrients within their biomass. They also feed on the exudates released by plant roots, colonising at the root zone and forming an essential part of the nutrient cycling system.

Bacteria contribute greatly to soil structure by forming microaggregates. They bind particles of clay, sand and silt around themselves as protection from predator organisms. These aggregates become like building blocks for improved soil structure, which leads to better water infiltration and soil water-holding capacity.

Bacteria also cover plant surfaces both above and below the soil, forming a layer that protects plant tissue from disease, pests and harmful fungi. While individual bacteria organisms are very small, they make up the largest number of any soil microorganism.


Similar to bacteria, soil fungi are decomposer organisms. They, too, feed on organic matter and extract nutrients from the soil's parent material. These nutrients get bound up in the fungi biomass until the plants require them, and aren't leached. When exudates are released from plant roots, fungi gather and grow prolifically at the root zone. They are then consumed by fungal-feeding nematodes and fungal-feeding arthropods and earthworms, and their nutrients are cycled through the food web system.

As fungi grow, they form networks with their hyphae (long branching filamentous structures) forming macroaggregates within the soil. In healthy soil, there are generally fewer fungi than bacteria, but due to their larger size, fungi have greater total biomass. Fungi thrive in soils that are disturbed minimally, as they take longer to reproduce than bacteria.


Protozoa are predator microorganisms that consume primarily bacteria. They perform an important role in the soil nutrient cycling system as their waste material contains essential nutrients in plant-available forms.

The number and diversity of protozoa can tell soil scientists a lot about the health and condition of a soil sample. For example, when there are a good number of flagellates and amoebae protozoa, the soil is well-oxygenated, or aerobic, which is essential for all soil life. If there is an excess of ciliates, on the other hand, it can indicate that there are anaerobic conditions, which can lead to poor soils, susceptible to disease. Protozoa are also one of the first microorganisms to disappear with an excess of synthetic and commercial fertilisation.


Nematodes are another predator microorganism that play an important ecological role in nutrient cycling and the soil food web. They consume bacteria, fungi and even each other, excreting nutrients in plant-available forms in their waste.

There are five groups of nematodes that can occur in soils: plant parasites, bacterial feeders, fungal feeders, omnivores and predators. Looking at the numbers of each group in a soil sample is a good way of getting a picture of the condition of the soil.

For example, a predominance of fungal-feeding nematodes indicates that the food web is dominated by fungi, and the process of nutrient cycling within the sample area will be occurring at a slower rate.

What happens when microbial activity is lost?

When humans first discovered the world of life beneath the surface of the soil they assumed that this microscopic biology was made up predominantly of diseases, pests and problem organisms. Some farmers still think like this.

Unfortunately, ignorance or disregard for the soil microbiome is causing large-scale ecosystem degradation and loss of productivity for many farmers. Synthetic fertilizers begin a collapse in soil biology by suppressing nitrogen-fixing bacteria and enhancing all the microorganisms that feed on nitrogen. This then increases the decomposition of organic matter and humus. As the organic matter is rapidly used up, the soil structure is altered and the whole system falls out of balance. Similarly, pesticides and fungicides destroy not just the organisms they target but also the beneficial organisms that allow for nutrient cycling and natural fertility.

When the soil food web system falls out of balance, the microorganisms that protect plants from pathogens are inhibited, and plants become more susceptible to diseases and pests. Subsequently, production costs are increased as more synthetic pesticides, and herbicides, are required and so the cycle continues. Additionally, as the soil microbiome is destroyed, the soil loses structure, thereby reducing water-holding capacity and drought resilience, as well as increasing topsoil erosion. Finally, crops decline due to the reduced functionality of fertilisers, as microbes are not as prevalent in the soil and therefore convert less of these nutrients into plant-available forms.

While the use of synthetic inputs often yields immediate visual benefits, they lose their effectiveness season over season, ultimately putting farmers into a cycle of increasingly expensive input reliance with diminishing returns leading to loss of our precious natural resources.

Restoring the soil food web

Fortunately, with the right biological inputs and management practices, the soil food web can be restored relatively quickly depending on the climate, soil type and the starting condition and previous history of the land. We worked with Dr Mary Cole to develop this in-depth guide on how to restore your soil food web.

Among the management practices and biological inputs listed in the guide, Dr Mary Cole emphasises the importance of fostering a love for the land and soil. "We are simply one incredibly insignificant species on this planet but we've been given the ability to be able to manipulate our environment. Plants and animals do that all of the time, but they don't do it destructively."

"Go out and stand on your land and say: how can I make this better tomorrow? It's a relationship with the land. It's not about making a profit from its destruction, but about working with it to make the planet better each day as well as earning an income. Most of all, it's got to come from the heart."