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This topic contains seven questions:

Where are the organisms located in soil?
What are soil aggregates and soil pores?
What is a polysaccharide?
How could bacteria be involved in the formation of a soil aggegate?
How could fungal hyphae be involved in the formation of a soil aggregate?
How is microbial biomass measured?
What techniques are used for assessing soil organisms?

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Question 1: Where are the organisms located in soil?

Most organisms are in the top layers of soil, usually the top 2-3 centimetres, because this is usually where most of the organic matter is. Organisms occur to depths of several kilometres below the soil surface, but the types of organisms that occur this far down are not the same as those close to the surface. The organisms in soil are often commonly found close to root surfaces, in living roots, in dead roots, on soil particles, or amongst aggregates of soil particles.

Within the top layers of the soil, the earthworms and soil animals are able to travel through most parts of the soil. Fungi extend to cover soil particles and aggregates. They can form a mat of hyphae, which can extend centimetres or even metres in the soil. Fungi can also grow into soil aggregates and form a network of hyphae inside the aggregate. Bacteria tend to accumulate inside soil aggregates because they are less likely to be eaten by soil animals such as protozoa and mites in this environment. Bacteria can be carried down further into the soil in water that is percolating downwards.

Soils that are clayey often have many bacteria because these soils have lots of small pores (spaces) which protect the bacteria. Sandy soils with few aggregates are less suitable habitats for bacteria and fungi unless there is lots of organic matter, because in sands the bacteria have fewer small pores to live in.

Question 2: What are soil aggregates and soil pores?

Soil aggregates are clumps of soil particles that are held together by moist clay, organic matter (like roots), gums (from bacteria and fungi) and by fungal hyphae. The aggregates are relatively stable. Aggregates vary in size from about 2 thousandths of a millimetre across, up to about 2 millimetres across. Soil pores are the spaces between soil particles and between soil aggregates. They can be full of air or they can have water in them. Soils with lots of aggregates are called "well-aggregated" and this condition is thought to be very desirable, for a number of reasons. The aggregates are made up of particles of different sizes and some of these particles fit closely together. Some do not. This means that there are spaces of many different sizes in the soil and these spaces are essential for storing air, water, microbes, nutrients and organic matter.

Question 3: What is a polysaccharide?

A polysaccharide is an organic compound composed of many simple carbon compounds, identical to eachother, joined together in a long chain. They are released into the soil by microorganisms and roots. Polysaccharides are long and flexible and they can make points of contact with many soil particles. In this way they have been associated with the formation of aggregates in soil.

Question 4: How could bacteria be involved in the formation of a soil aggegate?

There are two ways that bacteria could be involved in the formation of soil aggragates. Firstly, bacteria produce polysaccharides which can make many points of contact with soil particles producing aggregates. Unlike the polysaccharides produced by plant roots, bacterial polysaccharides resist decomposition long enough to be involved in holding soil particles together in aggregates. Secondly, bacteria develop a small electrostatic charge which attracts to the electrostatic charge on clay surfaces, bringing together small aggregates of soil.

Question 5: How could fungal hyphae be involved in the formation of a soil aggregate?

Fungi grow in long thin strands called hyphae. The length of fungal hyphae in the soil has been found to be related to the amount of aggregates in the soil. Fungi help to form aggragates in the soil hen their hyphae enmesh soil particles and when they form cross links between soil particles. Mycorrhizal fungi and fungi that colonise fresh organic matter and are believed to be the most important for assisting aggregation.

Question 6: How is microbial biomass measured?

Microbial biomass is the whole mass of living organisms in soil. It can be estimated by measuring the amount of carbon, nitrogen, phosphorus or sulfur that is present in the microorganisms, small animals and algae in the soil. There are a number of different ways of measuring microbial biomass.

For example:

1. The fumigation-incubation technique. Two samples of soil are collected. One is not treated; this is called the untreated soil. The other sample is fumigated to kill all the organisms in it. Then living organisms are added back into the fumigated soil and the sample is left to incubate. During incubation, the living organisms degrade a proportion of the dead organisms. The difference in the amount of carbon dioxide released between the untreated soil sample and the treated soil is used to estimate the amount of respiration that has occurred during the degradation process. This is then used to estimate the amount of carbon degraded (only a proportion of the organisms will be degraded, so this is taken into account).

2. The fumigation-extraction method. Again, two soil samples are collected, one remains untreated and the other is fumigated to kill all the organisms. Then chemical tests are done on the fumigated soil to extract the ninhydrin positive compounds. Next, the carbon, nitrogen, or phosphorus that has been released from the dead microorganisms is measured.

3. The substrate-induced respiration method. Again two samples of soil are collected and one sample is left untreated. A source of energy (eg sugar) is added to the other sample, so that the organisms in the soil can be more active. When they are more active, they respire (breathe) more and so release more carbon dioxide into the soil. The amount of carbon dioxide released by the organisms in the treated soil is then compared to the untreated soil to calculate the probable mass of microorganisms in the soil.

4. Using ATP or enzyme activity. ATP is the name given to one of the molecules that carries energy inside living things. Enzymes are proteins that help reactions to go faster. The amounts of ATP and specific enzymes in soil indicate how many organisms are in that soil.

Question 7: What techniques are used for assessing soil organisms?

Soil organisms are identified by looking at their:

· Morphology (their structure and shape)

· Physiology (what happens inside them)

· Genetic characteristics (what sort of genes they have)

· Ecological characteristics (where they live, how they interact with other living things), and

· Molecular characteristics (whether they have particular parts of genes, or proteins or molecules)

Methods used to assess organisms include: · Molecular markers (DNA profiles) · Serological techniques · Protein and enzyme profiles · Embedding soil with resin · Rossi-Cholodny slides · Sieving, heating and floating to extract animals · Artificial media · MPNs (Most Probable Number technique) · Baiting techniques · FAME tests (Fatty Acid Methyl Ester assay) The type of method used to characterise the organisms in soil depends on how you want to use the information.

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