A Gardener’s Introduction to Soil Biodiversity

Soil Biodiversity

As gardeners, we know that healthy soil is essential for growing healthy plants. We know that an abundance of earthworms is a sign of healthy soil and that they are vital for decomposition both in the garden and in compost bins. Earthworms are just part of soil biodiversity.

Living soil has interactions between different types of organisms, including bacteria, archaea, fungi, protozoans, nematodes, mites, insects, such as beetles, ants and termites, spiders, slugs, snails, mammals, birds, and even plant roots.

Encouraging a natural balance between all these organisms is not only essential to building up healthy soil, but it can also make gardening very easy because soil biodiversity will do most of the work for you. To appreciate just how valuable each type of organism is for us as gardeners, we need to know how each organism’s function contributes to the function of soil as a whole.

Here’s how some of these organisms contribute to creating healthy soil:

Plant roots

You may not have previously thought of plant roots as part of soil biodiversity, but considering that they spend all their time in the soil, it may not be surprising either.

When we think of plant roots, we usually think they only help attach the plant to the ground and absorb nutrients. Plant roots in healthy soil without artificial fertilizer are busy bartering for nutrients and water with bacteria, fungi, and other soil organisms while competing with them for the same. In fact, plants control interactions between soil organisms to a large degree.

  • Plant roots secrete carbons and proteins (exudates), which attract bacteria, archaea, and fungi (referred to as ‘smaller microbes’ below), which consume these exudate compounds.
  • In turn, larger microbes (nematodes and protozoa) are attracted to the rhizosphere, the area of soil close to the surface in which plant roots are found. These larger microbes consume the smaller microbes and excrete waste products, which contain nutrients that are in a form that plants can absorb and use.

Bacteria and Archaea

Bacteria are single-cell organisms that are numerous in soil. Although they are more well known as disease-causing agents, healthy soil should contain many thousands of beneficial bacteria. 

Like bacteria, archaea are also single-cell organisms that are primary decomposers. Archaea were identified relatively recently and we are just about beginning to know more about them.

  • Bacteria are primary decomposers. They consume organic matter, mainly young, green, fresh plant material that are full of sugars.
  • Bacteria are rather immobile. When they consume organic matter, nutrients are trapped within the bacteria itself and cannot be easily washed away.
  • Nitrifying bacteria are important for nitrogen fixation. They can convert ammonium produced by fungi (see below for a description) into nitrate.
  • Archaea also can convert atmospheric nitrogen into forms that can be taken up and used by plants. It is also thought that archaea may be more dominant than bacteria for nitrogen fixation in soils because they can be found deeper in the soil.
  • Bacteria and archaea produce a slime that can bind soil particles together.
  • Archaea are also found in the digestive tracts of animals, such as termites, that eat cellulose (the main component of plants and a very complex molecule) and break down cellulose already broken down by protozoa to help these organisms digest cellulose.


The most common types of fungi are mushrooms, yeasts, and mold, some of which are known to cause diseases. Mushrooms are only the fruiting bodies of fungi and comprise only a small part of the organism, while most other soil fungi are microscopic.

  • Fungi are most important as decomposers. Unlike bacteria, fungi can break down and digest lignin, a complex compound that contributes to the formation of wood and the bark of trees.
  • Fungi can also break down minerals that are normally not found in forms that plants can absorb into forms that are available to plants. An example is phosphorus.
  • Fungi secrete enzymes that break down organic matter before they consume it. Some of these enzymes may remain in the soil long after the death of the fungi and will continue to help digest organic matter.
  • Fungi help bacteria by breaking down complex organic matter into simpler forms that bacteria can then break down.
  • Mycorrhizal fungi form a symbiotic relationship with plant roots. The fungi look for nutrients and water and bring it to the plant, while the plant supplies the fungi with carbohydrates.
  • Fungi grow hyphae, which are thin thread-like structures rarely visible to the human eye, can hold soil particles together to form soil aggregates.
  • Fungal hyphae can travel through the soil several meters away or to the soil surface to locate new sources of nutrients and transport them to their origin, which is quite often a plant root.
  • The nutrients absorbed by the hyphae are then immobilized and cannot be washed off from the soil.
  • When fungi die, the network of tunnels leftover by hyphae that have penetrated the soil are ideal for bacteria to hide away from protozoa, which are too large to enter these tunnels.
  • Fungi also produce vitamins and antibiotics that kill soil pathogens and protect plants from these pathogens. Interestingly penicillin is one of these antibiotics that humans now rely on.

Ants and Termites

Although ants and termites are both insects, they are not closely related but they perform similar functions for soil health.

  • Ants and termites shred organic matter on the soil surface, making it easier for fungi and bacteria to decompose it.
  • Ants and termites build tunnels deep in the soil or mounds by bringing soil to the surface. This action mixes the soil.
  • These tunnels also allow air, water, and even other animals to move through the soil.
  • The tunneling action also makes it easier for roots to grow through the soil.
  • When ants and termites move through these tunnels, they often bring with them shredded organic matter that may have been colonized by bacteria, inadvertently transporting the bacteria, which are otherwise immobile.

Despite their many benefits, ants may encourage and protect certain pests in your vegetable garden but on the other hand may also be indicators of the presence of these pests.


As gardeners, we are all familiar with earthworms and know that their presence indicates healthy soil. We also use earthworms to quickly make vermicompost, but do we really know the value contributions earthworms make?

Earthworms eat many of the microscopic organisms found in the soil including bacteria and fungi, as well as organic matter. Inside the earthworm, all food is crushed using sand and rock particles, broken down into tiny particles, and moistened with saliva.

Then, bacteria living in the intestines of the earthworm digest the organic matter. The nutrients are absorbed by the earthworm but any organic matter that has not been fully digested is excreted. This waste matter is what is known as vermicastings and is an ideal soil amendment.

  • Earthworm castings are rich in organic matter and nutrients.
  • The castings contain tiny particles that can be easily broken down by microbes to release nutrients.
  • The castings also contain microbes that are enclosed and protected.
  • The burrowing action of the worms allows roots to penetrate the soil easily and provides the roots with nutrients and microbes.
  • Like ants and termites, earthworms also mix the soil and bring organic matter and microbes from the surface of the soil deep into their burrows.
  • The burrowing action of the earthworms also increases the porosity and water holding capacity of the soil, because air and water can easily pass through these burrows.

Slugs and Snails

Although many gardeners regard slugs and snails as garden pests, in balanced healthy soil, their numbers will be naturally controlled. These slow-moving creatures definitely do provide more benefits than the harm you may see them causing to your herbs.

  • Apart from fresh leaves, snails and slugs also consume fungi and decaying organic matter while foraging underground in the soil.
  • They are able to grind the organic matter into very small particles and some can even digest cellulose. This action speeds up decomposition and breaks down organic matter so that other smaller soil organisms can easily digest it.
  • Snails and slugs produce slime on which they glide. When they travel beneath the surface of the soil, their slime binds soil particles together.
  • Like ants, termites, and earthworms their movement into the soil allows air, water, and roots to easily travel through the soil.

Learn how to organically keep slugs and snails away from your vegetable garden.

In healthy soil that is high in biodiversity, all organisms function together to break organic matter into nutrients step-by-step, which can then be channeled back to plants. This process allows for nutrients to be recycled, without any loss or the need for additional nutrients to be added. The mechanical action of most of these organisms also helps air and soil to move through the soil and makes it easier for plant roots to penetrate the soil.

A Gardener’s Introduction to Soil Biodiversity

8 thoughts on “A Gardener’s Introduction to Soil Biodiversity

  1. A really helpful blog, we are first time proper veg growers, had a taste of it in 2020 and loved it so developed an allotment in my garden to hopefully be self sufficient veg wise in 2021.

    1. Thank you! That’s brilliant that you’ve started growing your own vegetables this year. All the best for your vegetable gardening in 2021!

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