Homesteading · Observations · Soil care · Wildlife

An Introduction to the Soil Micro-Ecosystem

Soil Microorganisms microbes sample microscope
Soil sample under a microscope

To the majority of people soil is just soil – a sandy/clay substance in which plants grow and where little boys dirty their clothes, but to the savvy vegetable gardener, we know that the soil is the essential foundation from whence plants gain their nutrients. Without the correct balance of nutrients; plants grow poorly and become prone to attack from a variety of pests and diseases.

Yet, upon closer inspection– you would notice that the soil is alive! It is a habitat and hunting ground for many insects (beetles, flies and moths), arthropods (earthworms, spiders and minute lice) and crustaceans. These we notice easily and know well, but they are merely the top point of the soil trophic pyramid (or food chain). To understand the processes in the soil that leads to good plant health and nutrition we need to inspect soil much closer – as to say at the microscopic level!

Here is where most people throw up their arms in the air and wail as Soil Microbiology is just too ‘sciency’! Fear not! I will do a brief breakdown of the soil micro-ecosystem with many a picture and interesting fact that will provide you with a glimpse into the microscopic world of soil and how to use this to your food-growing advantage. Let us venture down the proverbial rabbit hole and into a world of fantastic creatures…

Firstly, we have to pinpoint where these microbes grow and multiply. The soil is an aggregate of different micro-environments (similar to those in your vegetable garden) depending on the amount of trapped air pockets (oxygen), water and the type of growth medium (nutrients). Here is a microscopic view of soil and where you would expect to find microbes.

Soil microenvironments Whisker Flowers micro-organisms health niche

Micro-organisms feed on four main nutrients, namely Carbon (supplied by growing and decaying plants), Nitrogen, Phosphorus and Sulphur. These elements are available in the soil as complex materials, which microbes process and release for plants and other soil life. The bulk of the soil microtrophic pyramid constitutes Archaea, Bacteria and Fungi.

  • Archaea are a primitive and ancestral organisms similar to Bacteria, but with restricted habitat in the soil. They specialise at thriving in conditions of extreme temperatures, acidity and salinity. They cannot out-compete soil bacteria and hence they have a low abundance in the soil.
  • Bacteria are single cellular organisms that are highly diverse and provide many ecosystem functions, such as photosynthesis, nutrient cycling, pest control through antibiotic production and some are even predatory!
  • Microfungi, such as moulds and mildews, create vast networks of mycelium (the fungal growing body) throughout the soil that assist with soil structure, nutrient – and water retention as well as providing symbiotic platforms between plants and fungi.


Soil Organism Ecosystem Role Biological Process Cool Example
Bacteria Nutrient cycling, pathogen control Carbon, nitrogen, phosphorus and sulphur cycles. Antibiotic production. Predatory activity Predator: Bdellovibrio bacterivorus, is a motile bacterium that attacks other bacteria, invades their cells and devours the contents. Subsequently, it releases multiple progeny after host cell destruction. It is currently being studied as a live antibiotic for humans!bdello_new
Fungi Decomposition, pathogenic Break up and release of complex organic material, some are parasitic on other fungi. Assist plants with acquiring phosphorus. Mycoparasite: Trichoderma spp., ensnare and consume other fungi as well as nematodes that live in the soil.
Archaea Nutrient cycling Nitrogen and methane cycles Extremist: Haloquadratum walsbyi, can endure hypersaline or halophilic environments that are almost rendered sterile with salt. They are one of a few microbes with square shaped cells!

The next organisms to join the soil tropic pyramid are Protists and Viruses. These groups provide more complex roles in the soil ecosystem, especially the protozoans that can be regarded as mini herbivores and predators of soil aggregates.

  • Protophyta include single cellular algae that contain chlorophyll (green plant pigment) and are capable of photosynthesis (production of carbon). Algae or phytoplankton are important photosynthesizers in aquatic environments, such as the oceans. Some algae live in soil, but the main carbon sources for soil microorganisms are carbon-based excretions from plant roots (AKA root exudates).
  • Amoebas are large protozoans, which are motile animal-like single celled organisms. They are higher in the soil microtrophic pyramid and can be symbionts, parasites as well as predators of algae, bacteria and other protozoans.
  • Viruses are organisms that cannot proliferate without a host. They infect their host cell, commandeering the cell’s biological processes in order to manufacture and assemble virus particles, finally causing the cell to die (lysis). Cell death releases large numbers progeny viruses into the environment to seek out new hosts. Viruses are diverse and can infect every living organism on planet Earth. You wonder why they exists, what is there contribution to life or the greater scheme of things? They provide an essential evolutionary role to their hosts; a type of natural selection. Hosts are kept on the tips of their toes so to speak by participating in an evolutionary arms-race with their associated virus(es). Each trying to out-wit the other by evolving superior biological mechanisms. Hosts evolve mechanisms that can recognise and destroy virus particles, whereas the virus strives to improve infection and to remain hidden within the host cell.
Soil Organism Ecosystem Role Biological Process Cool Example
Protist Carbon produces and pest control Carbon cycle, predators and parasites The Farmer: Dictyostelium discoideum, incorporates bacteria into its fruiting bodies that allow the next generation to ‘seed’ bacteria in new locations, which later become a food source.dictyostelium_fruiting_bodies
Viruses Pathogenic Cause microbial mortality (may be applied as pest control) and constitutes a type of natural selection Pandora’s Box: Pandoravirus, is the largest known virus and infects amoebas. Created by Digital Micrograph, Gatan Inc.
Primitive Agriculture

Now, let’s build the soil micro-trophic pyramid with the basic members of the microbial world. The photosynthesizers or primary producers of carbon are at the base of the pyramid. Afterwards primary carbon consumers come into play as herbivores, decomposers and nutrient cyclers. From our discussion so far we slot in predators, pathogens and parasites as secondary consumers. Hence, the pyramid will have three trophic levels:

Soil microbial trophic pyramid

Each of the organisms at the different trophic levels are essential for soil biodiversity, which leads to multiple and dynamic ecosystem functions as well as robust nutrient storage and release. The biological activity of these organisms ensures soil health by supplying nutrients and maintaining soil structure. Healthy soil leads to healthy plants and huge flavour-packed wholesome produce!

As you would notice: the Nutrient Cyclers are the most important players when comes to food production. They acquire nitrogen/phosphorus/sulphur from the soil or through their own biological processes, and exchange this for carbon derived from plants via the plant roots. This is a mutualistic relationship where both parties benefit by the presence of the other.

In order to promote the biodiversity of the soil in your vegetable garden that leads to healthy soil, strong plants and lovely produce – you will have to learn to work with Mother Nature and practise some benign neglect. No chemical pesticides, no synthetic fertilisers and no regimented rows of vegetables! You must let the vegetable garden grow a bit wild, leave mulch or vegetable debris on the soil to decompose through the workings of the microbial life. This releases nutrients to the plants and assists with water retention in the soil.  Also – NO TILLAGE OR BARREN SOILS! No working over the soil with a spade or double-digging! This destroys the microbial population. And finally, always have some type of plant cover in/on your garden soil, dead or alive, as this maintains your microbial population as well.

Whisker Flowers Vegetable Garden South Africa
Live a bit on the Wild side of vegetable gardening! My garden, Summer 2014/2015.

To complete the pyramid we move into the meso- and macro-worlds of the soil ecosystem. Each representing members larger in size and more complex in biology, and an entire article would have to be devoted to each.

I will list here more complementary articles pertaining to soil health and maintenance. These you will find at my blog:

  1. Economic Food Production: Vegetables Worth Growing
  2. Conservation Agriculture: Soil Health
  3. Integrated Organic Gardening: Sustainable Food
  4. Wild Vegetable Gardening: Planting Guide & Management


  1. Bdellovibrio bacterivorusReprinted with permission from G. O’Toole & D. Kadouri, Dartmouth Medical School MicrobeWiki
  2. Trichoderma: MicrobeWiki
  3. Haloquadratum walsbyiWikiPedia
  4. Dictyostelium Fruiting Bodies: By Bruno in Columbus – Own work, Public Domain, MicrobeWiki
  5. PandoravirusPandoravirus salinus, MicrobeWiki

This post was featured on Gardening Know How’s weekly guest post under my previous blog identity!


4 thoughts on “An Introduction to the Soil Micro-Ecosystem

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