A brief introduction to soil biology

One week has, rather predictably, not been enough to do justice to the subject of soils. Nonetheless, I hope I have been able to trigger an interest among some of you and have inspired you to find out more. I will certainly return to the subject in the (near) future but this post is the last in what has been a very enjoyable series to put together.

The subject for today – soil biology.

E coli Ag Res Mag

By this I mean not only the earthworms and larger arthropods that are visible to the naked eye but the microscopic community that can be found within the soil – the fungi, protists, bacteria – and the smaller nematodes, arthropods, springtails and mites.

Please bear with me as one blog post is (again) barely enough space to cover the subject. It is intended as an introduction only and I will try and return to the subject, looking at each in more detail.

For now though…

There are billions of organisms to be found within a spadeful of soil and once you start looking under the electron microscope it comes to life. You are given a small insight into this gloriously complex, ‘otherworldly’ place. And, it is beautiful.


Traditionally, soil organisms have been divided (in terms of taxonomy) into micro, meso and macrobiota.

  • Micro – all organisms less than 200 micrometres (1 millionth of a metre) – bacteria, protozoa, fungi, algae
  • Mesobiota – 2mm-1cm – nematodes, springtails, mites
  • Macrobiota – over 1cm – earthworms, slugs, snails, insects

Let’s take a brief look at some of these organisms…



  • They are unicellular, prokaryotic (lacks a membrane bound nucleus) organisms usually 0.5 -1 micrometre in length.
  • They consume the various exudates (sugars, carbons, carbohydrates) of the roots.
  • Many have a thick mucilaginous film around them that protect them from shifts in pH.
  • They are rod shaped, round or wavy.

Eubacteria (true bacteria, actinomycetes and cyanobacteria, prokaryotes

  • One gram of soil may contain up to 1 billion bacterial cells.



  • A group of bacteria that have features similar to fungi – like the ability to produce thread like extensions 10-15 micrometres long.
  • Their mycelium is made up of very fine hyphae less than 1 micrometre in diameter.
  • They will often decompose materials like lignin (the woody part of plants).
  • They grow well in anaerobic conditions.

Cyanobacteria – also known as blue-green algae


  • They can use atmospheric carbon to photosynthesise.
  • They can fix atmospheric nitrogen, making them important in early soil formations.

Bacteria and the nitrogen cycle


Nitrogen is released from decaying plants in the form of ammonia.

Ammonia in the soil is converted into nitrite by certain soil bacteria that live in symbiosis with leguminous plants. These are known as Nitrosomonas. The nitrite is taken by another group of bacteria – the Nitrospira – and converted into nitrate (nitrification).

Nitrogen is also fixed by free living bacteria known as Azotobacter and Clostridium – they require considerable quantities of decaying plant residues as a source of energy and work under anaerobic conditions.

Certain bacteria occasionally intervene (denitrifying bacteria) and convert ammonia into free nitrogen gas.



  • Bacteria don’t thrive when pH is below neutral. Then, decay is carried out chiefly by fungi.
  • In terms of tissue, fungi are the most dominant group of soil organisms (70% of total microbial weight – although most of it is dead).
  • They are made up of eukaryotic cells (have a nucleus and cell membrane) that form fine threads known as hyphae (2—10micrometres in length).
  • They play an important role in breaking down lignin.
  • Fungi will break down organic matter on the surface.
  • Certain fungi, known as mycorrhizal fungi have a peculiar mutually beneficial relationship with plants. Mycrorrihizae extend the nutrient and water supply for plants. In return the plants provide carbon and sugars. Up to 90% of plants have this relationship although only a small proportion have been studied.


An umbrella term consisting of three groups –

  • flagellates (less than 5 micrometres long)
  • amoebas (5-10 micrometres long and
  • ciliates (less than 20 micrometres).

Protozoa eat bacteria and organic debris (but prefer bacteria).

They are distinguished by the way they move:

  • Flagellates use a whip like motion.
  • Ciliates move with bristles like hair.
  • Amoeboe move by protruding their protoplasm and moving the rest of the cell behind it.


  • They will eat a wide range of organisms – plants, algae, bacteria, nematodes. Very important in the soil food chain. Some are herbivorous and some carnivorous.
  • About half are free living and the other parasites of other organisms.
  • Some are several cm in length but most are 0.2 – 0.5mm.

Macrofauna (anything bigger than 1cm)

The principal impact of the macrofauna (earthworms, millipedes, centipedes, ants, termites) is to mix the soil (bioturbation). This has a significant effect on soil formation. The burrows of earthworms aerate the soil, andincrease the stability of soil aggregates, assuring ready infiltration of water and improving drainage.

Earthworms create ‘casts’ which have higher available nitrogen, phosphorus, potassium, and calcium contents than surrounding soil.

Earthworms are fascinating (Darwin was particularly fascinated by them).

  • Though eyeless, they respond to the intensity and duration of light.
  • They have no hearing, but are sensitive to vibrations.
  • Their sense of smell is feeble.
  • They swallow leaves and other organic matter and break it down, making it easier for the other soil organisms to break down the material further.
  • In very acid soils, earthworms are almost entirely absent, such as coniferous forest.
  • Darwin calculated that there were 53,767 earthworms recycling away per acre.
  • He also estimated they turn over 50 tonnes of soil per hectare per year (enough to produce an extra 0.5 cm of topsoil).
  • There are 27 species in Britain but only a few secrete on the surface.

Soil organisms require organic matter, a relatively stable pH, ample pore space and relative saturation. We should question whether we are really doing enough to support this ecosystem?

I hope this has further inspired you to look more at soils and see them not just as a resource but a highly complex habitat.

In future, I will look at how practices such as cultivation impact on the soil and soil organisms.

For now though, have a great weekend!



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