In this Equine Permaculture series, we ‘dig deeper into soils’ and explore what soils are, how soil is formed, the different types of soil and how they sustain life through the soil-food-web. 

We will also discuss the importance of soil tests – in the lab and DIY – and how to interpret soil test results, as we build up the story of how all this knowledge can assist your pasture management decisions and the health of your horses. 

Last month, we began the series by brushing up on some facts about soil. If you missed that article you can read it here. Now, let’s dig deeper to meet the organisms that live in the soil and sustain all life.

Soils are complex mixtures of minerals, water, air, organic matter, and numerous micro and macro-organisms that are the decaying remains of once-living things. Soil forms on the surface of land – it is the ‘skin of the Earth’. Soil supports plant life and is vital to life on Earth, yet it is the most overlooked, underrated and taken-for-granted partner in our attempt to grow plants.

If we want to grow healthy pastures, we must take care of our soils, but how much time have you spent – as a horse and property owner – getting to know your soils, compared to the time you spend planning and managing your pastures?

Soil biology

The variety of organisms that contribute to the soil-food-web is astonishing. They range in size from the smallest single cell bacteria, algae, fungi and protozoa, to the more complex nematodes and micro-arthropods, to the recognisable earthworms, insects, small vertebrates and plants.

As these organisms eat, grow, move through, die-off and decay in the soil, they create humus (the organic material in soil) and they contribute to clean water, moderated water flow, clean air and, very importantly, to growing healthy plants that can feed our horses.

The exchanges between these organisms form a ‘web of life’ in exactly the same way as the interactions between flora and fauna that biologists study above ground. What most people forget to realise is the above ground interactions would not survive without the below ground systems functioning.

Soil biology is understudied when compared to biology above ground, yet it is vital for the health of our pastures, gardens, shrub lands and forests. If pasture soil is healthy, there will be high numbers of beneficial bacteria and bacterial-feeding organisms.

If the soil has received heavy treatments of herbicides, chemical fertilizers, soil fungicides or fumigants that kill these organisms, many of these tiny critters die, and the balance between pathogens and beneficial organisms is upset, allowing opportunistic, disease-causing organisms to become problems; not to mention negatively affecting the growth and quality of your pasture.

There are many reasons why the soil-food-web is an integral part of landscape processes, for example:

  • Soil organisms decompose organic compounds (including manure, plant residue and pesticides), preventing them from entering water and becoming pollutants.
  • They sequester nitrogen and other nutrients that might otherwise enter groundwater, and they ‘fix’ nitrogen from the atmosphere, making it available to plants.
  • Many organisms improve soil aggregation and porosity, thus increasing infiltration, and reducing runoff and soil erosion.
  • Soil organisms prey on crop pests and are food for above- and below-ground animals.

The soil-food-web

The soil-food-web refers to the community of organisms that live the entire or part of their lives in the soil. A food web diagram shows a series of exchanges (represented by arrows) of energy and nutrients as one organism eats another (see Image A).

The ‘fuels’ of the food web are the primary producers; these are photsynthesizers – the first trophic level (first position in the food chain), such as plants, lichens, moss, photosynthetic bacteria and algae, that use the sun’s energy to convert carbon dioxide from the atmosphere into the carbohydrates that allow them to sustain themselves and grow.

Most of the soil organisms get their energy and carbon by consuming plants, other organisms and waste by-products (second to fifth trophic, or food chain levels). A few bacteria, called chemoautotrophs, get energy from nitrogen, sulphur or iron compounds, rather than carbon compounds or the sun.

As organisms decompose complex materials or consume other organisms, nutrients are converted from one form to another, and are made available to plants and to other soil organisms. This means all plants – grass, trees, shrubs, agricultural crops and so on – depend on the food web for their nutrition, and this is why I often highlight we do not feed pasture plants directly, we feed them through the soil organisms that make up the soil-food-web.

The role of soil organisms

Growing and reproducing are the primary activities of all living organisms. As individual plants and soil organisms work to survive, they make exchanges with each other.

By-products from growing roots and plant-residue feed soil organisms. In turn, soil organisms support plant health as they decompose organic matter, cycle nutrients, improve soil structure and control the populations of soil organisms, including crop and pasture pests.

Let’s have a closer look at some of the soil organisms that make up the soil-food-web and their functions.


Our native soils are full of bacteria, both beneficial and pathogenic. A spoonful of ordinary backyard soil may contain billions of bacteria of thousands of different kinds, many of them specific to a region. In general, bacteria help water move through the soil more easily, they recycle organic matter and they help ward-off soil diseases.

There are many types of bacteria, but one of the most important groups you may have heard of is the nitrogen-fixing bacteria. These bacteria are especially found on the roots of leguminous plants and shrubs (for example clover, lucerne and acacias).

Nitrogen-fixing bacteria are capable of transforming atmospheric nitrogen into fixed nitrogen (inorganic compounds usable by plants). They dine on particles of humus (organic matter), creating a waste product called ‘bacteria manure’ that adds new forms of organic content to the soil.

Many plants absorb nutrients most efficiently through this bacterial waste product, so the more nitrogen-fixing bacteria in the soil, the better. This is why we often want to plant legumes in our pastures. Lucerne, for example, is one of those plants we like to have in pastures because, in symbiosis with Rhizobium bacteria, it can make athmospheric nitrogen more available to the plants and because it offers great feeding value to grazing animals.

Bacteria and bacteria’s waste products are also eaten by fellow soil dwellers of many kinds, so they feed other organisms in the soil, in addition to feeding our plants. Our pastures and gardens soils are typically dominated by beneficial bacteria.


Protozoa (single-cell organisms), comprised of three groups; (1) flagellates, (2) amoebae (both naked and testate), and (3) ciliated are important in maintaining plant-available nitrogen and mineralisation processes and, as bacterial-feeders, are important in controlling bacterial numbers and community structure in the soil.

The presence or absence of certain protozoa species is indicative of the presence of certain hazardous wastes and, therefore, can be a very useful indicator of certain types of environmental impacts.


Many horse owners assume fungi must be bad for the soil, but this is far from the truth. When most people think of fungi, they think of mushrooms. They also tend to think of fungi as plants.

A characteristic of plants is they inhale carbon dioxide (CO2) and exhale oxygen (O2). Fungi actually breathe in O2 and exhale CO2, just like humans. Interestingly, fungi have survived two mass extinctions over 65 million years and the only plants that also survived those extinctions are the ones that formed associations with fungi. This should highlight the health implications of not managing soil and all the life it contains correctly.

Fungi are vitally important to soil health and beneficial forms are found in virtually every kind of soil on earth. Like bacteria, fungi break down organic matter by digesting and excreting humus, followed by recycling nutrients through the soil-food-web.

Mycorrhizae are among the best known soil fungi. They attach themselves to the roots of plants and create a mesh of fine feeder ‘rootlets’ that act like pumps, pulling nutrients and water into the host plant’s root system. They have a symbiotic relationship because, in return, the plants exchange carbohydrates with the mycorrhizae fungi.

In effect, the fungi networks – chains of microscopic strands (mycelium) that have been recorded at lengths and depths of approximately 10 kilometres – increase the surface area of the roots and, thus, the plant’s ability to absorb nutrients.

For example, plants will send out chemical signals to fungi telling them they require magnesium – an element essential for plant growth. The fungi networks can search the surrounding areas and deliver the required magnesium to the plant in exchange for the food the fungi need: carbohydrates.

Healthy woodland soils are dominated by fungi, meaning there are more fungal creatures than bacteria in the soil. Whereas pasture soils tend to be dominated by bacteria.


Nematodes (non-segmented worms, such as parasitic worms), like fungi, are usually assumed to be pathogens, but beneficial nematodes abound in the soil. Nematodes are one of the most ecologically diverse groups of animals on Earth, existing in nearly every habitat.

Nematodes eat bacteria, fungi, algae, yeasts and microalgae (diatoms), and may feed on several small invertebrate animals, including other nematodes. In addition, they can be parasites of invertebrates, vertebrates (including horses and humans) and plants. Nematodes range in length from the tiniest marine nematode measuring just 82 μm (micrometres or 0.00082 of a centimetre) to the massive nine metre whale parasite, but most of the species found in soil are between 0.25mm and 5.5mm long.

Nematodes are recognised as a major consumer group in soils, generally grouped into four to five trophic categories based on their food preferences, the structure of the stoma (mouth) and oesophagus, and method of feeding.

Plant-feeding nematodes possess stylets (spear-like structures in the mouth) with a wide diversity of sizes and structure. They are the most extensively studied group of soil nematodes because of their ability to cause plant disease and reduce crop yield.

Fungal-feeding nematodes have slender stylets, but are often difficult to categorise and have been included with plant-feeders in many ecological studies.

Bacterial feeding nematodes are a diverse group, and usually have a simple stoma in the form of a cylindrical or triangular tube, terminating in a teeth valve-like apparatus.

Predatory nematodes are usually large species with equally large ‘mouths’ and powerful ‘teeth’.

Omnivores (ones that eat other organisms and plants) are sometimes considered as a fifth category in the food chain of soil nematodes. They can fit into one of the categories listed above, but also ingest other food sources.

As an example, some bacterial feeders may also eat protozoa and/or algae, and some stylet-bearing nematodes may pierce and suck algae, as well as fungi and/or higher plants. Stages of animal parasitic nematodes, such as hookworms, may also be found in soils, but generally are not common in most soil samples.

Nematodes and protozoa function as regulators of mineralisation processes in soil. For example, bacterial- and fungal-feeding nematodes release a large percentage of nitrogen when feeding on their prey groups and are, thus, responsible for much of the plant-available nitrogen in the majority of soils.

Nematode-feeding also favours certain species of bacteria, fungi and nematodes and, thereby, influences soil structure, carbon utilisation rates and the types of substrates present in soil.


These critters are recyclers that feed on bacteria, fungi and earthworms, as well as plant particles. They include micro-arthropods – very small organisms, like mites – and larger organisms, like sow bugs, springtails, spiders and centipedes.

The micro-arthropods stay put in the soil, consuming debris, and making nitrogen and other nutrients more readily available to plants and other soil biota. Arthropods also control the population levels of other organisms in the soil, keeping things balanced naturally.


Of all the members of the soil-food-web, earthworms need the least introduction. Most people become familiar with these soft, slimy invertebrates at a young age.

Earthworms are hermaphrodites, meaning they exhibit both male and female characteristics. They are major decomposers of dead and decomposing organic matter, and derive their nutrition from the bacteria and fungi that grow upon these materials. They fragment organic matter and make major contributions to recycling the nutrients contained within.

Earthworms occur in most temperate soils and many tropical soils. They are divided into 23 families, more than 700 genera and more than 7,000 species. They range from an inch to two yards in length and are found seasonally at all depths in the soil.

The fuel of the food web

Organic matter is comprised of different types of compounds – some more useful to organisms than others. In general, soil organic matter is made of roughly equal parts humus and active organic matter.

  • Active organic matter is the portion available to soil organisms.
  • Bacteria tend to use simpler organic compounds, such as root exudates or fresh plant residue.
  • Fungi tend to use more complex compounds, such as fibrous plant residues, wood and soil humus.

As mentioned before, bacteria dominated soils are typically pastures, whereas fungi dominated soils are usually woodlands and forests.

Intensive cultivation of soil triggers spurts of activity among bacteria and other organisms that consume organic matter (convert it to CO2), depleting the active fraction first. Practices that build soil organic matter (reduced tillage and regular additions of organic material – by spreading mulch and compost) will raise the proportion of active organic matter long before increases in total organic matter can be measured.

As soil organic matter levels rise, soil organisms play a role in its conversion to humus – a relatively stable form of carbon that remains sequestered in soils for decades or even centuries.

Soil organic matter is the depot for the energy and nutrients used by plants and other organisms. Bacteria, fungi and other soil dwellers transform and release nutrients from organic matter. These micro-shredders, immature oribatid mites, skeletonise plant leaves. This starts the nutrient cycling of carbon, nitrogen and other elements, such as minerals, ultimately feeding our pasture plants!

Habitat of soil organisms

The organisms of the food web are not evenly distributed through the soil. Each species and group exists where they can find appropriate space, nutrients and moisture. They occur wherever organic matter occurs – mostly in the top few inches of soil, although microbes have been found as deep as 16km in oil wells. Soil organisms are concentrated in several areas, including:

  • On the surface of soil aggregates. Biological activity, in particular that of aerobic (requiring oxygen) bacteria and fungi, is greater near the surfaces of soil aggregates than within aggregates (lacking oxygen). Within large aggregates, processes that do not require oxygen, such as denitrification, can occur. Many aggregates are actually the faecal pellets of earthworms and other invertebrates.
  • In litter. Fungi are common decomposers of plant litter because litter has large amounts of complex, hard-to-decompose carbon, such as lignin. Fungal hyphae (fine filaments) can ‘channel’ nitrogen from the underlying soil to the litter layer. Bacteria cannot transport nitrogen over distances, giving fungi an advantage in litter decomposition, particularly when litter is not mixed into the soil profile.

However, bacteria are abundant in the green litter of younger plants, which is higher in nitrogen and simpler carbon compounds than the litter of older plants. Bacteria and fungi are able to access a larger surface area of plant residue after shredder organisms’, such as earthworms, leaf-eating insects, millipedes and other arthropods, turn litter into smaller chunks.

Interestingly, by adding different type of green (nitrogen) litter versus older (carbon) litter to your compost or manure pile, you can create more bacterial- or fungi-dominated compost. Bacterial-dominated compost is preferred for pastures as mentioned earlier.

  • Around roots. The rhizosphere is the narrow region of soil directly around roots. It is swarming with bacteria that feed on discarded plant cells, and the proteins and sugars released by roots. The protozoa and nematodes that graze on bacteria are also concentrated near roots. Thus, much of the nutrient cycling and disease suppression needed by plants occurs immediately near roots.
  • On humus. Fungi are common here. Much of the organic matter in the soil has already been decomposed many times by bacteria and fungi, and/or passed through the guts of earthworms or arthropods. The resulting humic compounds are complex and have little available nitrogen. Only fungi make some of the enzymes needed to degrade the complex compounds in humus.
  • In spaces between soil aggregates. Those arthropods and nematodes that cannot burrow through soil instead move in the pores between soil aggregates. Organisms that are sensitive to dehydration, such as protozoa and many nematodes, live in water-filled pores.

When are soil organisms active?

The activity of soil organisms follows seasonal patterns, as well as daily patterns. In temperate systems, the greatest activity occurs in late Spring when temperature and moisture conditions are optimal for growth.

In tropical systems, this is more during the Summer months (wet-season). However, certain species are most active in the Winter, others during dry periods and still others in flooded conditions.

Not all organisms are active at a particular time. Even during periods of high activity, only a fraction of the organisms are busily eating, breathing and altering their environment. The remaining portion is barely active or even dormant within the soil.

Many different organisms are active at different times and interact with one another, in addition to interacting with plants and the soil. The combined result is a number of beneficial functions, including nutrient cycling, moderated water flow and pest control.

So… How does the soil-food-web impact my pasture?

The living component of soil, the food web, is complex and has different compositions in different ecosystems. Management of our pastures benefits from and affects the soil-food-web.

When practising pasture management, it is not the vegetation that is replenished, but the soil. The best means to achieve this is to replicate naturally-occurring nutrient cycles: we need to feed the soil through a process of breaking down organic matter with soil microorganisms, bacteria and fungi.

In a natural system, many species of plants and animals play a role in these processes. However, on farming land, it is the owner or manager’s responsibility to oversee the animals and return waste (via compost or mulch) to the soil and plants.

Permaculture is concerned with the restoration and development of soil as a priority, because healthy soil produces healthy plants and grasses – which help produce healthy horses!

One of the most difficult aspects of teaching people about working with natural systems and improving pasture health is that permaculture is a way of thinking. It is not a product, it is not something that can be bought off the shelf from the local rural supplier, spread, sprayed or watered.

The difference is, once natural health has been allowed to return through interaction in the soil-food-web, natural balance can be restored. Natural systems are the only science recognised by nature. All over the world, when natural systems are disregarded, the land suffers and, in the long-term, attracts high input costs, such as herbicides, chemical fertilisers, and so on.

However, this not to say we can use certain human tools, and agricultural and biological manufactured products, but we need to be aware there is no one solution or fix to our soil, weed or pasture problems, but rather, we need to adopt an integrated whole-system approach to our management.

One of such tools is conducting soil tests, which offers us a reference (current status of our soil) and allows us to monitor our outcomes of our farming practices. These soil tests should not only provide us with a nutrient/mineral profile, but also with an indication of our soil carbon and soil biology, often-overlooked aspects!

Thus, in the next part of this series, we will discuss the importance of soil tests – in the lab and DIY – and how to interpret these soil test results.

Further reading:

  1. Soil Biology Primer – Natural Resources Conservation Services (United States Department of Agriculture) –
  2. Soil Health, Soil Biology, Soil borne Diseases and Sustainable Agriculture. A Guide. By G. Stirling et al. 2016. CSIRO Publication, QLD, Australia.

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