Soil Biology 1

by Sue Gebicki

soil from Black Sugarloaf
1. soil from Black Sugarloaf

2015 was the International Year of Soils designed to create awareness of the importance of healthy soil, the amount of damage that we have inflicted on soils around the world, and to teach how to maintain soils in good condition and prevent further loss.

Soil is one of nature's most complex ecosystems and one of the most diverse habitats on Earth. It contains an amazing number of different organisms, all interacting, contributing to global cycles and making a large proportion of life possible.

Soils are a product of physical, chemical and biological processes, and while there has been much research into the physical and chemical aspects of soils, there has been comparatively little research into soil biology and ecosystems. Although soils are home to over a quarter of all living species on earth, to date it is estimated that only 1% of soil bacteria and fungal species, 4% of mites, 15% of collembola, 1.3% of nematodes, and 7.5% of protozoa have been identified. To add to the difficulty of research, soil microbes can readily exchange genetic information leading to a very fast and ongoing diversification of microbes in natural environments (Monier et al., 2011). Furthermore processes within the soil are not the result of a single organism but of microbial communities which closely interact with each other (Aneja et al., 2006). Even the development of symbiotic interactions between plants and microbes are much more complex than described in textbooks as they include the involvement of a diverse number of ‘helper organisms’ which contribute to the process.

Actions of soil organisms and organic matter

Organisms in the soil act together in complicated relationships of predators, prey, parasites, decomposers and soil reorganisers, maintaining a healthy equilibrium which sustains soil fertility. These organisms:

Soil organisms

Soil contains organisms from every kingdoms of classification. A typical healthy soil may contain many species of invertebrates including several species of earthworms, 20–30 species of mites, 50–100 species of insects, tens of species of nematodes, hundreds of species of fungi and perhaps thousands of species of bacteria and actinomycetes.


Bacteria are the most numerous of soil organisms, with up to one billion per gram. They are generally about 1 micron in length or diameter and usually occur as single cells. Various bacteria contribute to soil health with the decomposition of organic compounds, nutrient cycling, humus production, soil aggregation, nitrogen fixation, plant growth formation and control of plant pathogens. Other bacteria, such as the denitrifying bacteria are anaerobic (active where oxygen is absent) and convert nitrate to nitrogen or nitrous oxide in saturated soils. Bacteria are found in highest numbers in the rhizosphere which is the area around the root zone. Plants exude carbon-rich materials to stimulate bacteria and in return benefit from a wide range of functions. Here they are presented according to their function:


Mycena austrororida
2. Mycena austrororida

Fungi grow long threads called hyphae that mass to form mycelium, which absorb nutrients from the roots they have colonised and surface organic matter. The hyphae are usually a few thousandths of a millimetre wide.

Fungi are important in the soil by performing services related to water dynamics, nutrient cycling and disease suppression. They are also important decomposers and their hyphae bring soil particles together into stable aggregates. Fungi can be grouped into broad categories:

Cortinarius metallicus
3. Cortinarius metallicus

As an interesting aside, scientists studying the evolution of fungi have found evidence that the end of the carboniferous age may have been brought about by the evolution of fungi able to digest lignin. Prior to that, much dead vegetation was decomposed at such a slow rate that it was possible for it to be buried by natural processes, and eventually physically and chemically acted on to produce the vast coal reserves that we dig up and burn today.


Protists and other similar single-celled organisms, several times larger than bacteria, have a nucleus and live in wet environments. About 1,500 of about 50,000 known species live in soils, more than a billion amoeba and up to several million ciliates have been found per square metre in the top 50 mm of some soils,. They have developed the ability to shut down their bodies and form a cyst when soils dry out to varying degrees.

The two main groups of soil protists are the ciliates and the flagellates. Along with the amoeba they play an important part in boosting the nitrogen available to plants as they feed primarily on soil bacteria, which are rich in nitrogen. The protists cannot absorb all the nitrogen, so excrete the excess as ammonium, which is readily used by plants. They also regulate populations of bacteria because their grazing stimulates the growth of bacteria which are an important food source for other soil organisms and help suppress disease by competing with or feeding on pathogens. One group of amoebae, the vampyrellids - so called as they attach to the surface of hyphae, generate enzymes that eat through the fungal cell wall then suck dry or engulf the cytoplasm inside the fungal cell - include root pathogens in their diet.

- Svoboda E, 'Below our Feet, a World of Hidden Life' Quanta Magazine June 16, 2015
- Waksman S A and Starkey R L, (1931) The Soil and the Microbe John Wiley and Sons
- McDonald D and Rodgers D, May 2010 Soils Alive: Understanding and Managing Soil Biology on Tasmanian Farms Department of Primary Industries, Parks, Water and Environment Tasmania
- Food and Agriculture Organization of the United Nations Soils and biodiversity
- Edmonds R, 'Forest Soils and Site Productivity - Soil Organisms and their Effects on Soils and Productivity' Soil Ecology and Forest Pathology pdf file
- Ingham E R, The Soil Biology Primer
- European Commission DG ENV Final Report February 2010 Soil Biodiversity: functions, threats and tools for policy makers
- Pettit R E, 'Organic Matter, Humus, Humate,.Humic Acid, Fulvic Acid and Humin: Their Importance in Soil Fertility and Plant Health' pdf file
- Soil Biology Basics: 2005 New South Wales Department of Primary Industries
- Jenkins A, 'Nematodes' in Reid G and Wong P, Soil Bacteria

soil 2
4. cow paddock soil
soil 3
5. plantation soil

All photos taken by Sarah Lloyd; soil photos taken with DSLR camera on stereo microscope.

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