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1.3 Soil is a habitat for living organisms

What does soil look like from the inside?

Using your imagination is an important part of developing an appreciation of the environment that organisms living in the soil experience. If you cannot imagine what organisms experience in soil, it is difficult to appreciate the many ways in which they are influenced by their surroundings.

Novel techniques are available for looking directly into a soil to observe living organisms. For example, special video cameras can be used with time-lapse cameras to follow the growth of fungi or the movement of animals. Borescopes and mini-rhizotrons are two tools that can be used in this way. This technology provides an image of the habitat of soil organisms.

Why is soil such a diverse habitat?

The physical and chemical characteristics of a soil are different in different parts of the soil profile. Generally, the upper layers of a soil have more organic matter and roots than the lower layers. Other differences are related to the nature of the soil constituents, to weathering processes and to past land management practices. The origin of the soil determines the particle size distribution, which in turn affects the way the soil is packed, creating spaces and surfaces that are either accessible or inaccessible to soil organisms. The proportion of clay or sand influences the structural characteristics of soil and determines its response to management practices.

The structure of a soil is related to the extent to which particles are aggregated into relatively stable formations. Aggregates vary in size and the degree of soil aggregation dictates the number and size of the pores within it. The type and quantity of organic matter also influences the degree of soil aggregation. Soil structure determines the number and size of air spaces and influences the water holding capacity and drainage properties of the soil.

Roots can also alter the soil environment for living organisms and play an important role in supplying nutrients for organisms that live around them. Roots are dynamic structures, especially when young, releasing carbon compounds that can be readily used as an energy and carbon source by many soil organisms. However, over time roots change, and older roots have different surface properties and release different compounds to younger roots. As roots age, the outer layers of the root die, providing a source of organic material as well as a habitat for soil organisms.

It is important to consider the soil as a continually changing and complex environment for organisms. Part of this complexity arises because the organisms themselves contribute to the some of the changes that occur within the soil.

What environments do organisms experience in the soil?

The habitat available to a soil organism depends on its size: the soil environment of bacteria will be quite different to that of an earthworm. For a bacterium, important aspects of the soil environment include:

Microhabitat (structure)

• surfaces of soil particles; • pore spaces; • roots; • dead organic matter (plant, animal or microbial); • water films

Physical and chemical characteristics

• the charge of soil particles (positive or negative); • degree of aeration; • pH; • salinity; • temperature; • nutrients

Biological aspects

• other living organisms (including roots)

Bacteria are usually attached to the surfaces within soil pores or fragments of organic matter. They may attach themselves using flagella or fine hair-like fribrillae, although not all bacteria have these structures. Another method of attachment occurs through the production of polysaccharide gums that are released through the cell wall of some bacteria. Certain fungi also produce gums that actually help bacteria attach to soil particles.

Fungi experience a similar soil environment to that of bacteria, but the scale is greater. Fungi spread much further through the soil than do bacteria and will encounter a greater variety of soil environments. Also, bacteria have access to smaller pore spaces than most fungi. Protozoa and mites both feed on bacteria but only the protozoa are small enough to enter some soil pores. Mesofauna such as mites and collembola cannot enter smaller soil pores and therefore bacteria that occur there are protected. The smallest soil pores are inaccessible to bacteria and may contain organic matter that is protected from degradation.

While the soil environment obviously has a great effect on soil organisms they, in turn, may affect their physical environment. The breakdown of organic matter by soil organisms changes the structure of the soil, which leads to changes in the habitats available for soil organisms. The chemical environment of soil organisms can also be of their own making. Some bacteria and fungi initiate many of the biochemical reactions that occur in soil. The decomposition of leaves requires the enzyme cellulase, which is produced by soil organisms. The activity of cellulase changes with time, with the main peak in activity occurring soon after the addition organic matter, such as red maple leaves, to soil (Linkins et al. 1999).

This reflects the increased production of cellulase by soil organisms in response to organic matter. Cellulase enzymes occur within the organisms (endocellulase), but can also be excreted into the soil (exocellulase). Thus, the data reflect the greater cellulase activity during the early stages of decomposition.

Waste products excreted by soil organisms provide substances that can be degraded further by other organisms. Alternatively, the wastes may be toxic to some organisms and inhibit their growth.

Some organisms tolerate a wide range of conditions whereas others are adapted to a more limited environment. For example, cyanobacteria are rarer in acidic soils than in soils of pH 7 to 8. The abundance of bacteria is less in acidic soils than in soils of higher pH. Generally, there is not such a strong relationship between soil pH and fungi as there is between soil pH and bacteria, although individual fungi can have a marked pH preference.

Soil habitats differ greatly depending on land use. For a similar soil type within the same climate zone, a forest soil will generally have a greater diversity of habitats for soil organisms than a cultivated agricultural soil. These differences are primarily associated with a greater diversity of plant species and heterogeneity of the soil itself and the characteristics of organic matter produced in natural and agricultural ecosystems.

The size of soil pores, and therefore the habitat available to bacteria etc, depends on soil structure. For example, soils with high levels of clay have a greater proportion of small pores less than 0.2 Ám in diameter than loams on sandy soils (Hassink et al. 1993). The very small pores are too small for bacteria to enter, providing protection to organic matter.

Soils with a higher number of small, but not too small, pores (e.g. 0.2 to 6 Ám in diameter) have more bacteria than do those with fewer pores in this size category. This is because bacteria survive best within aggregates of soil rather than on the surfaces of soil particles outside aggregates. Bacteria exposed on surfaces are likely to be eaten by soil animals such as mites and springtails (collembola) or damaged by extreme cycles of wetting and drying. Therefore, a clayey soil would be expected to have a greater number of bacteria than a sandy soil under similar land use. For one of the soils studied by Hassink et al. (1993), there was a close relationship between the biomass of bacteria and the percentage of the pore volume in soil that was in the size class 0.2 to 1.2 Ám.

Bacteria and fungi commonly occur within aggregates of soil, although they are not distributed evenly in all size fractions of soil aggregates. Most bacteria in this study were present in soil aggregates that ranged from 2 to 20 Ám in diameter.

The number of soil organisms varies greatly between the surface and very deep layers in the soil profile. The main reason for this is because the supply of plant organic matter that is essential for many soil organisms is almost absent lower in the soil profile. However, it needs to be remembered that organisms do occur at great depths within the regolith, even though their numbers are much reduced compared with communities at the soil surface.

How does land use alter the habitat of soil organisms?

Soil disturbance has major effects on soil habitat diversity. Disturbance changes the physical uniformity of soil and in natural ecosystems, it changes the diversity of plant species growing in the soil. Disturbances are not the same and they can have different impacts in different soil types.

Two examples of the effects of disturbance in different soil environments are:

• severe soil disturbance due to cultivation tends to create a more homogeneous soil environment than does disturbance of a forest during a process such as logging.

• the higher diversity of plant species in a natural forest creates more habitats in soil than does a more uniform plant community (such as a crop grown in monoculture).

When soil conditions are altered in any way, the number of organisms changes and the relative abundance of different types of organisms in the soil changes as well. A change in environment may favour one group of organisms so that its abundance increases, while the number of other organisms decreases either because the conditions are less favourable or because of the increased influence the organisms that have become dominant. An example of this is the change in soil organisms following the addition of nitrogen and straw to soil (Russell 1973). Adding nitrogen increased the length of hyphae, the number of bacteria and the number of amoebae. The thickness of the hyphae also increased when nitrogen was added. The change in thickness of hyphae is likely to have occurred because the increased nitrogen favours species of fungi with thicker hyphae.

Liming a soil by the addition of calcium carbonate can also change the number of bacteria and fungi present (Russell 1973), although the response is not always predictable. In this case, the outcome depended on the soil characteristics and the types of organisms present. In one soil, the addition of calcium carbonate increased the number of bacteria but decreased the abundance of fungi. In contrast, the addition of calcium carbonate to a second soil decreased the abundance of bacteria and had little effect on the abundance of fungi.

Do organisms live deep in the regolith?

Living organisms are not restricted to the surface layers of soil. Bacteria are the most common organisms at depth, and they even occur at more than 1 kilometre below the earth's surface. These bacteria cannot rely on sources of plant organic matter to meet their need for carbon and energy. One possible source of carbon for organisms deep in the regolith in some regions is oil. Microbial activity in oil wells, including their role in the corrosion of drilling rigs, has been well documented indicating that they are able to live and thrive using oil as an energy source.

Bacteria living at a great depth in the regolith have to be able to survive in environments with low levels of all nutrients. But they appear to be uniquely adapted: they are small (most are less than 1 Ám in size), generally have low rates of respiration and can exist in a physiologically stressed state.

We know relatively little about the biology of organisms that occur deep in the soil. It is difficult to study deep soil organisms. This is because their surroundings are often greatly altered during the investigation from what they normally experience and few deep soil bacteria will grow on artificial media. For example, deep soil organisms may experience increased or even toxic levels of oxygen when they are brought into the laboratory. To gain accurate information about the biology of organisms that occur deep down in the soil the experimental conditions need to resemble as closely as possible the conditions normally experienced by such organisms. If these requirements are not met, the experimental results may not represent what actually occurs at depth in the regolith. This is important for studies of all soil organisms and explains why investigations of organisms in artificial media need to be scrutinised carefully before conclusions can be drawn about the function of the same organisms in field soil.

Summary Points (1.3)

• Soil is a diverse habitat.

• Soil type dictates the number and characteristics of the microsites where soil organisms live.

• The diverse community of soil organisms is dynamic and interacts with both physical and chemical components of the soil habitat.

• The habitats in soil are changed by land management practices.

• Organisms at great depth below the soil surface are mainly bacteria that do not depend on the presence of plant organic matter for their energy and carbon supply.

• Organisms can proliferate deep in the regolith in association with isolated sources of carbon, such as oil deposits.

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