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Soil microbiology: the fascinating world within the soil

Soil microbiology


Soil microbiology is the study of all organisms, microbial and faunal (animal) that spend a significant amount of their lifecycle within the soil.  This is a relatively new (or relatively unstudied) science, so we are only in the early stages of developing an understanding of soil microbiology and its effects on horticultural ecosystems.  However, what is known is that soil organisms break down organic matter* to make nutrients available for uptake by plants and other organisms and the nutrients that are stored within the bodies of soil organisms prevents the loss of nutrients from the soil by leaching. So it can be shown that the decomposition of organic matter by soil organisms has a significant influence (positive) on

  • Soil structure (eg. humus content)
  • Soil fertility
  • Plant growth
  • (Organic) carbon storage

*Organic matter: carbon-based compounds that have come from the remains of organisms such as plants and animals.

The interconnectedness of the living communities that exist within the soil is complex and we don’t properly know how they interact. However, there is an understanding of the roles individual types of organisms play in the soil ‘Food Web’ and of these, the ones of particular interest to horticulturalists are:

  • Earthworms
  • Nematodes
  • Protozoa
  • Fungi
  • Bacteria
  • Some arthropods


Earthworms (detritivores) ingest soil detritus (organic matter) and decompose it. Bacteria present in the worm’s digestive tract and in the soil break down this decomposed matter further to expose nutrients in a water-soluble form.

Bacteria are single-cell organisms and the most numerous form of microbe in the soil with populations ranging from 100 million to 3 billion in 1 gram of soil.

Bacteria are capable of very rapid reproduction by cell division.  In favourable conditions, one bacteria is capable of producing 16 million or more other bacteria in 24 hours.

Bacteria tend to live close to plant roots in the film of water that surrounds soil particles.  Bacteria that are beneficial to the decomposition of organic matter require aerobic conditions (the presence of oxygen) in moist* soil and are most active when there is an abundance of food in the form of carbohydrates and other micronutrients from organic matter.

*The soil must be moist rather than wet as excess water in the soil displaces the oxygen.

Anaerobic conditions (absence of oxygen) in the soil are hostile to beneficial bacteria and will generate the presence of non-beneficial bacteria.  This type of bacteria leads to the putrefaction of dead organic matter and the resulting production of methane, a potent greenhouse gas.  However, in hostile conditions, beneficial bacteria will enter a dormancy phase and become active when favourable conditions are once again present.

The important functions of soil bacteria:

Diagram: US Environmental Protection Agency

  • Nitrification – Bacteria are able to transform Ammonium (NH4+), produced by the decomposition of proteins, into Nitrates (NO3), a salt that is water soluble.
  • Nitrogen fixation – Atmospheric nitrogen (N2) is a relatively non-reactive molecule that is metabolically useless to all but a few microorganisms. Biological nitrogen fixation is the process where certain types of free-living bacteria in the soil convert atmospheric nitrogen into ammonia (NH3) which can be easily metabolized by most organisms. These nitrogen-fixing bacteria tend to have a symbiotic relationship with leguminous plants such as peas and beans where they live in colonies in the nodules they form on the roots of these plants.
  • Actinobacteria
    Actinobacteria in soil break down organic matter in soil into simpler, water-soluble compounds so they can be taken up by plants. In this role they provide a similar function to fungi and similar to fungi, colonies of actinobacteria grow extensive mycelia, long branch-like hyphae that are similar to the root system of a plant but significantly smaller. (Each hyphae has a diameter that measured in micrometres).
    Some soil actinobacteria develop colonies in close proximity to the plant’s roots.  In this symbiotic relationship, the actinobacteria fix nitrogen for the plants, in exchange for which the plants feed them saccharides* they produce and push down into the soil via their roots.
    Besides their roles to break down organic matter and nitrogen fixing, there is still much we don’t know about actinobacteria.  However, studies are now uncovering other important roles they play within the soil such as soil buffering** and providing a source of antibiotics that helps the plants fight of diseases from soil-based pathogens and impurities.*Saccharides: a simple form of carbohydrate produced by the plant
    **Buffering: keeping the pH of the soil constant despite changes in the acid or base conditions in the soil.


A gram of soil can contain up to 1 million fungi, some of which are visible in the form of moulds that form on or near the surface of the soil.  There are numerous types of fungi but not all are beneficial to plants.  Horticulturists are all too aware of fungi that are parasitic to the host plant, causing disease, such as misshapen or miscoloured leaves and fruit and dead foliage.  However, there is also an extensive range of fungi species that have a beneficial relationship with plants and it’s these that are of particular interest to ecological horticulturists.

  • Mycorrhizal fungi
    Fungi that are able to form symbiotic relationships with plants are known as Mycorrhizae (from myco meaning fungal and rhiza meaning root).
    The mycelia of these mycorrhizae attach themselves to the external surfaces of the roots and fine root hairs or incorporate themselves into the internal root structure.  The mycorrhizae will source nutrients the plant requires but cannot itself obtain (ie. certain nutrients may not be located within the reach of the plant’s root system).  The mycorrhizae’s mycelia are much smaller in diameter than a plant’s finest root hairs and as such, they can penetrate more easily through soil to where the nutrients are located.  In exchange for these nutrients, the plants supplies the mycorrhizal fungi with carbohydrates (saccharides) that it pushes down its root system (similar to how the plants supply actinobacteria).Extensive mycorrhizal networks have been found in native forests where the fungi has formed a fine mesh in the soil that connecting the root systems of the plants and trees into a single ‘network’.  In this network, the symbiotic relationship between the fungi and the plants extends beyond the basic supply of nutrients.  Where young trees are growing under the canopy of the forest, they will not be able to access the amount of light required to sufficiently photosynthesise (create the carbohydrates the plant requires to form new cells and grow).  An awareness of the needs of these young plants seems to be present in the mycorrhizal network that will then source and supply the nutrients these young plants require, often from other more mature trees in the forest.

Ask Malcolm

Malcolm has years of experience in horticulture and gardening and not only has an extensive knowledge of plants, including their propagation but also has experienced and overcome practically every issue that could confront the home gardener.

We would like to make Malcolm’s experience available to answer your questions related to your gardens or horticulture in general. Please send your questions with as much information about the issue you have, including photos (if that’s possible) to: malcolm@resurrectiongardens.com.au

Any questions and their answers that have broad appeal, we will publish on this website on the ‘Ask Malcom’ page.