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7.1 Microbial indicators of the biological state of soil

Biological indicators could be useful in predicting how land management practices are affecting long-term productivity and soil loss. Ideally, such indicators should be able to notify land managers of a deviation from desirable soil conditions. However, at this stage, a simple biological indicator similar to that of soil pH does not exist for the complex living component of soil.

In fact, no universal indicators have been identified to describe soils with well-developed biological fertility. Biological indicators of the state of a soil will vary locally and indicators need to be developed for each soil type and climate region. In addition, soil biological activity is dynamic. Soil organisms change in abundance and activity due to seasonal cycles in temperature, moisture and plant growth. Therefore, measures taken at one time may be different to measures taken at another time and the time of sampling is just as important as what is sampled. The best time of year to sample soil is not likely to be the same for every indicator of biological activity and every environment. Furthermore, the depth at which samples are taken needs to be relevant to the types of organisms that need to be collected. The heterogeneity of organisms in soil also means that a large number of samples are necessary to reduce variability of the factors measured, although, this variability is itself an important characteristic of soil.

Although there are difficulties in assessing biological indicators, the search for suitable indicators provides a valuable means of exploring the impact of land use that may not otherwise be immediately obvious. The fact that soil organisms are sensitive to changes in their environment provides the opportunity for selecting one or more measures of them or of their activity (collectively or individually), to identify the impact of soil management practices.

Are individual organisms useful indicators of the biological state of soil?

It is not possible to select a single species as a sole indicator of the biological status of soil. Nevertheless, the abundance and activity of a number of individual organisms taken collectively may provide some indication of the health of a soil.

Earthworm abundance may appear to be an easy measure of biological fertility of soil. It is relatively easy to count earthworms in soil compared to assessing the abundance of many other soil animals or bacteria and fungi. However, there is much scientific evidence that suggests that earthworms are not necessarily reliable indicators of soil biological fertility; they are very diverse in their ecology and physiology, as well as in their distribution.

Single species of bacteria are inappropriate as indicators of soil biological fertility because many species are involved in most biological processes in soil; the absence of one may have little effect on whether the biological processes occur or not.

Groups of organisms such as rhizobia can be used to indicate the likelihood that symbiotic nitrogen fixation will occur. Thus, information about some groups of organisms contributes to a suite of indicators. The abundance of these bacteria in relation to the number required for effective nodulation of legumes can be assessed.

AM fungi and ectomycorrhizal fungi could also be included in a suite of biological indicators. A measure of the abundance of fungi as well as their capacity to function within the ecosystem would be desirable. Quantification of mycorrhizal fungi is relatively easy but measurement of their contribution under field conditions is complicated.

Assays of plant pathogens are important and practical indicators of the potential for root disease to occur in both agricultural and natural ecosystems. These assays are not useful unless calibrated against known levels of disease.

Is a food-web a useful indicator of the biological state of soil?

The food-web approach to selecting biological indicators is based on the premise that soil organisms form part of a food chain, with predators being key species that control the abundance of organisms they feed on and vice versa. If the structure of soil food-webs is well known, indicator species could be used to determine whether all processes are functioning ‘normally’ or whether there are gaps that represent disruption to parts of the system. As species of soil fauna differ in different soils and in different ecosystems, detailed knowledge of food chains representative of each soil type and climate are needed.

Is soil biological diversity a useful indicator of the biological state of soil?

Several methods are available to measure the diversity of organisms in soil. A recent approach compares the capacity of the soil population to use a wide range of organic molecules as carbon substrates over a short period of time (Stephenson et al. 2004). The use of a range of substrates has the advantage of better indicating of the diversity of organisms in the soil community than measures that assess only one factor.

This functional approach to assessing biological diversity in soil has the advantage that it does not rely on an ability to identify organisms or their ability to grow in selective media. The patterns that are obtained using this approach are converted into values that can be compared between soils with different land use such as cropping frequency, burning, fertiliser application, or method of incorporation of organic matter. The values obtained using this approach need to be calibrated for a large number of soils and conditions if they are to be used to predict the effects of land management.

Although assessing functional diversity in soil is rather complicated and needs equipment that cannot be used in the field, this approach is important for providing the level of detail required to monitor the effects of land use on soil biological fertility. Simple measures suitable for field use usually offer less precision and less scientific value for predicting long-term changes in the biological state of a soil.

Another approach to assessing biological diversity in soil is to compare gel profiles of DNA extracts from soil. These molecular techniques allow the soil community to be described in terms of the diversity of genes present within organisms rather than the organisms themselves. There is also the possibility to monitor the potential of the community to function in various ways, depending on the nature of the molecular probes used to characterise the nucleic acid extracted from soil. This is a time consuming and expensive approach and not easily applied in the field. Nevertheless, it is an important approach and the techniques it uses are advancing rapidly.

The diversity of specific groups of soil organisms can be included in the suite of indicators that measure the biological state of a soil. For example, nematodes of many types and functions occur in soils. Most are not detrimental and participate in the food-web through their degradation of organic matter and grazing on soil microorganisms. A measure of the diversity of nematodes in soil can be used to indicate the relative abundance of plant parasitic and other types of nematodes. Species of nematodes can be identified by experts using microscopic techniques and the number of species and their abundance can be estimated and compared for soils under different land use in agriculture and in managed natural ecosystems.

Is a measure of the quantity of soil organisms a useful indicator of the biological state of soil?

Research in the 1970s on soil microbial biomass alerted soil biologists and others to the potential for using a measure of the quantity of the carbon in the microbial fraction to predict the long-term impacts of land management practices on the carbon status of a soil. Although the carbon and nutrients present in soil organisms represents only a small proportion of the total carbon in the soil, the nutrients contained in them are rapidly mineralised when the organisms die. The turnover of nutrients stored temporarily in microbial biomass is the focal point of nutrient cycling within the soil. It has flow on effects to other important transformations such as nitrification.

The addition of organic matter to a soil in any ecosystem can immobilise nutrients by increasing the activity of soil organisms. The relative proportions of carbon, nitrogen and phosphorus in different pools in soil have been studied for many years. Now that there is greater understanding of the small but very important microbial pool of nutrients, it is easier to comprehend its importance.

Is a measure of activity of soil organisms a useful indicator of the biological state of soil?

The presence of organisms in soil provides little information about the contribution that they make to soil processes, except as a pool of nutrients. An indicator that assesses how the organisms are functioning may be more useful in predicting the effects of land management on soil biological and chemical fertility.

One such indicator is soil respiration, which is a measure of the release of CO2 from the biological component of soil. Roots can be excluded to provide an estimate of the activity of soil organisms only. Perhaps a more useful measure is the rate of respiration calculated in proportion to the amount of microbial biomass in the soil. It is possible to have a small biomass that has a high respiration rate and vice versa. The quotient qCO2 (CO2 respired in relation to the microbial biomass present) and other measures of the activity of soil organisms such as enzyme activity are potentially useful indicators, but are difficult to apply routinely in the field.

The cotton strip assay is a practical measure of the potential of the soil organisms to degrade cellulose. The time taken to degrade a strip of cotton fabric gives a relative measure of the activity of one component of the soil community. However, addition of cellulose increases the activity of these organisms to levels higher than would occur naturally in the absence of the cotton strip. The technique can to be calibrated to indicate the potential of the soil community to degrade high cellulose-containing organic matter such as straw.

How can biological indicators be used in association with chemical and physical indicators of the state of soil?

A suite of biological indicators is likely to be necessary to assess the state of soil in terms of its suitability for a particular land use. However, further research is needed to determine the usefulness of a particular suite of indicators.

The existing expertise of land managers expressed by their keen vision, experience and interpretation of soil quality is a highly skilled and integrated approach to identifying soil biological characteristics. A major problem is that ‘good quality’ soils are not well defined in biological terms. As a result, there are few reference points to determine the extent to which biological measurements approach what is possible for a particular soil type under a defined land use. Until this is known, it is difficult to determine what proposed ‘indicators’ actually indicate. For practical purposes, suites of biological indicators need to be calibrated for reference sites on different soil types and land uses.

Summary points (7.1)

• Various approaches can be taken for identifying indicators of soil biological fertility. A single indicator is unlikely to be useful for identifying the overall biological fertility of soil.

• The single organism approach is useful for identifying the presence of specific organisms such as plant pathogens, mycorrhizal fungi or root nodule bacteria.

• The food-web approach is useful for assessing the soil community in terms of the inter-dependence of species across the spectrum from bacteria to larger soil animals.

• The biological diversity approach offers the potential to discriminate among soils in terms of the abundance of organisms with different functions. This may also include relative abundance of groups of organisms (e.g. bacteria and fungi, or mites and collembola).

• The microbial biomass approach allows comparisons to be made of the quantity of carbon, nitrogen and phosphorus in the most easily degraded component of the soil organic matter.

• The biological activity approach adds the dimension of activity to the measure of biomass. As most organisms can be inactive in soil at any time, it is useful to know how active soil organisms are under particular conditions. Measures of activity usually indicate potential activity rather than current activity because of the disturbances that are imposed during their assessment.

• The cotton-strip assay is a simple and practical measure of the potential for organisms to degrade cellulose in the soil.

• A suite of biological indicators will be more useful than a single indicator, however, many indicators of biological processes or organisms in soil are complicated and are impractical for easy field use.

• Difficulties in using biological indicators in the field are not an excuse for ignoring them. Indeed, they demonstrate the necessity for even greater investigation because they hold the key to assessing an important impact of land use on the soil environment.

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