Most soil organisms are inactive for long periods throughout their life. For example, only about 10-15% of the bacteria in a farm or garden soil are in their most active state at any one time. Their activity is related to soil conditions: if the conditions are not suitable, organisms are inactive. Since soil conditions are rarely suitable, organisms spend long periods being inactive. Often the conditions that suit one group of organisms are different to those that suit another group, so as the soil environment changes there is a succession of activity.
Activity is a physiological state where cellular functions allow the organism to grow and reproduce. In less active states, an organism can maintain a very low level of physiological function. When conditions become suitable for the organism to grow, rapid increases in activity occur. It is under these conditions that soil organisms colonise plant roots or organic matter, release enzymes into soil and move into their reproductive states.
It is not easy to tell from simple observation whether fungi or bacteria are in an active state. When hyphae are removed from the soil, they often look the same irrespective of whether they are alive or dead. Therefore, staining methods have been developed that indicate whether hyphae are alive or not. The methods detect the presence of molecules, such as enzymes, that are only present in living organisms. Fluorescein diacetate is a chemical that stains the components of the cell where specific enzymes are active. Using this approach, the activity of fungi in straw was monitored (Wessen and Berg 1986). The proportion of active hyphae, ie the hyphae with enzymes was high 170 days after the fungi colonised the straw, but after 200 days activity levels were declining and by 300 days, there was very little activity. This decline occurred as the fungi degraded most of the molecules in the straw that were accessible.
A novel technique has been developed to determine the proportion of living bacteria in a soil. The method is based on the observation that the chemical nalidixic acid prevents the normal division of bacterial cells. Usually, bacteria divide during their reproductive phase. Nalidixic acid prevents cell division but does not stop the cells from growing. Therefore, elongated cells are formed which grow more than twice the length of normal cells. The elongated cells are alive and the non-elongated cells are either alive but unable to grow in the soil extract or are dead.
This method was applied to a soil sample to estimate the proportion of living bacteria (Bottomley and Maggard 1990). About 70% of bacteria elongated in the presence of nalidixic acid in this study. The nalidixic acid method was also used to estimate the number of a specific group of bacteria (rhizobia). In this case, the proportion of rhizobial cells stained using the fluorescent antibody technique that elongated in the presence of nalidixic acid was estimated.
Another method for assessing the activity of organisms in soil is to measure the amount of CO2 released over several days. The process of CO2 release is called respiration. A highly active soil community usually respires more, releasing more CO2 than an inactive community. However, the abundance of microbial biomass in the soil and the amount of CO2 released is not always closely related. This is because the amount of CO2 released by soil organisms depends on factors that influence their activity. One factor that affects respiration is temperature. In soil, higher respiration occurs at higher temperatures.
The activity of enzymes produced by soil organisms can also be measured. As noted earlier, some enzymes are released into soil and remain active even after the organisms that produced them have died. Other enzymes are only active inside a living organism (see Winkler et al. 1996).
When organic material is added to a soil, the activity (measured as respiration, enzyme activity etc.) of many organisms increases rapidly. Once all the readily available material is degraded, activity returns to the original level. Heterotrophic organisms increase rapidly in number in response to the addition of suitable carbon substrates. Autotrophic organisms do not respond directly to the addition of organic matter because they do not use it as a source of energy and carbon. However, some autotrophic organisms, such as nitrifying bacteria, increase in number in response to the release of an inorganic molecule such as ammonium from organic matter. Therefore, addition of organic matter to soil can indirectly affect the activity of some organisms even if they do not use it as a source of energy or carbon
The abundance and activity of organisms in a soil can be related to the total mass of organic matter to give a baseline for measuring any changes with land management practices. For example, the ratio of the quantity of microbial biomass to the total organic matter in soil has been used to indicate the impact of management practices on soil carbon (Sparling 1992; Wardle and Ghani 1995).
Microbial biomass C (g per g soil)
Total organic matter C (g per g soil)
Another ratio takes into account the level of activity of the soil microbial biomass in relation to the size of the microbial biomass. This second ratio is called qCO2 or the respiratory quotient.
Respiration (g CO2 produced per g soil per hour)
Biomass of organisms (g biomass per g soil)
Although measures of this kind provide additional information about the activities of soil organisms, caution is required in interpreting them. For example, the qCO2 ratio increases or decreases as the soil environment changes. Further still, activity can be high even when there are only a few organisms, if there is severe stress on the organisms as might occur in a highly degraded soil environment, although this is not always so. However, it is difficult to find a single factor that reflects the functioning of the community of organisms in soil.
An overview of the processes that soil organisms are involved in is presented here as an introduction to the diversity of activities of soil organisms. In Parts 2 and 3 of this book, each activity is covered in more detail. Biological processes occur concurrently or sequentially in soil; they are not isolated occurrences.
Soil organisms are involved in important processes such as:
• soil formation and aggregation
• organic matter breakdown
• degradation of toxic substances
• transformation of inorganic molecules
• beneficial associations with plants
• development and prevention of plant disease
Each of these processes is discussed briefly below.
Some microorganisms contribute to the formation of soil, which develops from the erosion of parent rock. The influence of lichens on rock surfaces provides a good example of a microbial contribution to soil formation. Lichens release acidic molecules that slowly dissolve the rock surface. These processes are very slow.
Lichens can also participate in stabilising soil surfaces. This occurs when communities of soil organisms including lichens, algae and other microorganisms form a crust on the soil surface that protects the soil from water and wind erosion.
Once soils have formed, microorganisms continue to play important roles in binding soil particles. Hyphae create a loose weft that aggregates larger particles. Some hyphae and bacteria also produce polysaccharide gums that assist in aggregation of finer soil particles. Earthworms ingest soil, including the microorganisms within it, and additional soil binding processes occur as a result.
Heterotrophic microorganisms, which get their energy from other organic material, are the most abundant of all soil microorganisms. They are involved in the breakdown and subsequent cycling of nutrients contained in organic matter (Waid 1984). Therefore, they are most active when there is a supply of organic matter to colonise. At any one point in time, most of the organic material in the soil has already been degraded to some extent. Once organic matter has been partially degraded it is difficult for the soil microorganisms to further degrade it. Therefore, organic matter remains for long periods in the soil despite the presence of soil organisms.
Different soil types have characteristic threshold quantities of microorganisms that they can sustain. The number of organisms returns to a threshold level. This happens because (i) the parts of the organic matter that are easily accessible physically and chemically degrade quickly, (ii) microorganisms are eaten by soil animals (e.g. nematodes and amoebae), and (iii) unprotected microorganisms may become desiccated and die.
Biodegradation is a familiar concept. An important example of this process involves the transformation of pesticides by heterotrophic and autotrophic organisms in the soil. During biodegradation the microorganisms may acquire energy or carbon from degrading the chemicals and they can also release complexes of enzymes into the soil. It is interesting to note that there are similarities between the enzymatic processes involved in degradation of toxic substances and the degradation of some of the complex structural components of plants, such as wood.
Autotrophic microorganisms are not directly involved in the breakdown of organic material in soil. Rather, they are important in altering the chemical structure of inorganic compounds (i.e. those that do not contain carbon) from one state to another. For example, autotrophic nitrifying bacteria convert ammonium to nitrite and subsequently to nitrate. Nitrifying bacteria have extensive membrane surfaces within their cells that are important for these transformations (Brock et al. 1979).
Various soil organisms form either specific or less specific associations with roots and interact with plants in their uptake of nutrients from soil. Some organisms live in loose associations on the surface of roots or in the vicinity of the roots (the rhizosphere). Others form symbiotic associations and assist in the uptake of phosphorus (e.g. arbuscular mycorrhizal fungi). Root nodule bacteria and plants form highly specific associations that lead to nitrogen fixation.
An important group of soil microorganisms that attract considerable attention are those microorganisms which cause plant diseases. These organisms include bacteria, fungi and soil animals such as nematodes that can become serious plant pathogens under some conditions. Many plant pathogens are highly specific to particular plant species but others cause disease in different plant species that may not even be closely related. In addition, soils contain organisms that are naturally able to limit the proliferation of pathogenic organisms when soil conditions are suitable for their growth and activity. This process of disease prevention of one microorganism by another is called ‘biological control’.
• The activities of soil organisms are varied and have important links to many soil processes.
• Heterotrophic organisms obtain their energy and carbon from organic matter.
• Autotrophic organisms transform inorganic molecules to obtain their energy.
• It is not easy to tell whether bacteria and fungi isolated from soil are alive or dead.
• The release of CO2, enzyme activity within organisms and growth and reproduction are forms of microbial activity.
• The total amount of CO2 released by organisms in soil is not necessarily related to the abundance of organisms.
• Individual organisms in a harsh environment may respire at a higher rate than those in less severe conditions.