The diversity, abundance and activity of organisms in soil are constrained by the physical, chemical and biological characteristics of the environment. Most organisms can tolerate a range of soil conditions, but each usually has a set of conditions at which they function best. Some soil organisms tolerate a wide range of environmental conditions, while others live in very specific habitats in soil. Some soil organisms can tolerate extreme conditions including hot terrestrial environments, frozen soils, acidity, salinity and environments polluted by toxic substances. Most of the time, the majority of organisms in soil are inactive due to a major limitation in the environment (e.g. accessibility of carbon or water).
The types of organisms present in an area are determined by a combination of past land-use, chance introduction of organisms, and the tolerance of organisms of changes in soil conditions. Microorganisms rapidly adapt to changed conditions and their ability to exchange genetic material contributes to their tolerance of environmental stress.
Although the physical, biological and chemical environment plays a large role in determining which organisms occur where, the initial composition of a soil community is mostly a consequence of who arrived first. This chance introduction of soil organisms to a newly exposed land surface is most apparent on newly formed volcanic islands. An example of this is the intensively studied Surtsey Island in the northern Atlantic Ocean (Fridriksson 1975).
The observations of soil microorganisms during early stages of colonisation of Surtsey Island were:
(i) slow microbial colonisation; the air above the new island had a low density of microorganisms; organisms were mostly present where water had accumulated,
(ii) small numbers of Thiobacillus thiooxidans and Thiobacillus ferrooxidans appeared in hot areas; denitrifying bacteria, nitrifying bacteria,
(iii) fungi were present mainly in association with plants; transport of terrestrial microorganisms on feet of sea birds, attached to floating plant material or from air,
(iv) organisms present in sea water were ineffective colonisers of the land surfaces, and
(v) two species of lichens appeared after 10 years, being slow to colonise (Fridriksson 1975).
Researchers found that the microbial colonisation of the newly formed land surface required a tolerance of extreme physical and chemical conditions on the exposed larva. The abundance of organisms of course depended on the availability of nutrients.
Organisms reach new surfaces in air currents, attached to ocean birds and on plant debris washed onto shorelines. However, not long after the arrival of new organisms, their long-term survival will be determined by the environmental conditions present. Most will not survive, only a few hardy pioneers will flourish until the environment improves (more soil, more diverse above ground communities, etc). Nevertheless, the succession of microorganisms that colonise a newly exposed land demonstrates that soil organisms can disperse great distances, and that organisms can overcome extreme environmental conditions.
Most organisms play a minor role in soil biological processes. Therefore, studying organisms individually is not particularly useful for identifying appropriate soil management practices. Indeed, it is impossible to study every soil organism individually and it is not necessary to do so. Nevertheless, there are some organisms that can be studied separately because they are easy to identify and extract from soil, and their impact is obvious.
The most useful area of study is the investigation of the effects of disturbance on groups of organisms involved in similar processes such as the cycling of phosphorus from soil organic matter or the role of microorganisms in the uptake of manganese by plants. Genetically diverse organisms in soil are influenced by soil disturbance in different ways, which will have consequences for all biological processes.
In the past, it has been conventional practice to study the effects of soil management practices on the activity of soil organisms by investigating soil chemical or biochemical changes (e.g. increases or decreases of inorganic or organic nutrients, CO2 respired) rather than measure changes in the organisms themselves. Now that techniques for assessing soil biological activity associated with nutrient cycling processes are more advanced, there is greater emphasis on the organisms themselves, how they are affected by their environment, and what effect this has on biological processes.
However, most investigations of nitrification, a key biological process, investigate changes in soil inorganic nitrogen concentrations rather than changes in the activities of the organisms themselves. This is partly because nitrifying bacteria are very difficult to isolate and grow. Similarly, species of arbuscular mycorrhizal fungi cannot be grown in culture and are difficult to identify in roots. Therefore, most studies of arbuscular mycorrhizas simply report the total length of roots colonised rather than the quantity of root that is colonised by different species in the roots. This procedure is followed even though each fungus may function in a different way.
Although it is often difficult to study organisms individually in soil, such an approach can provide useful information, especially for organisms that have major and independent effects on plants, such as plant pathogens. For example, if groups of organisms such as nitrifying bacteria are studied as a whole, the fact that nitrification is a process that requires the participation of two distinct groups of bacteria (ammonium oxidising bacteria and nitrite oxidising bacteria) is overlooked. An understanding of the biology of each group could lead to better prediction of the conditions that favour or limit nitrification. In the same way, a study of arbuscular mycorrhizal fungi as if they are all identical would overlook the fact that these species differ in the way they function in soil.
The general objectives for studies of individual organisms are to understand (i) the biology of the organism, (ii) the factors (physical, chemical and biological) that influence each stage of the life cycle of the organism, and (iii) the difference between the short- and long-term impacts of the activity of the organism on soil and of the effect of the soil environment on the organism.
Research that includes investigations of individual soil organisms, as well as soil biological processes, allows an integrated approach to investigations of soil biological fertility.