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6.2 Direct microbial manipulation

The classic example of widespread and successful introduction of beneficial organisms into the soil is inoculation with rhizobia and bradyrhizobia. However, this is the exception. Generally, there has been little long-term benefit of introducing specific organisms into soil on a large scale. Experimentation with inoculation of Azospirillum, to fix nitrogen in soil, and mixtures of soil organisms selected to enhance a range of soil biological processes have been a focus of some microbiologists for many years with mixed success. Recent interest has centred on the creation of genetically altered organisms for field application to overcome problems of plant disease or to enhance plant growth. Experimental evidence of the long-term success of these initiatives is limited or has not been sought, although specific cases of success have been demonstrated.

How are microorganisms selected for inoculation?

Conventional selection of inoculant organisms

The process of selecting inoculants requires a detailed understanding of the biology of organisms, their suitability to different soil conditions, their effectiveness at performing the required activity, and their ability to persist in soil from year to year if it is not practical for re-inoculation at intervals.

A summary of the characteristics of selected strains of root nodule bacteria demonstrates the type of information that is required (Brockwell et al. 1995). These characteristics are all essential for a bacterial strain to be a successful inoculant. A strain of root nodule bacteria may be identified that is highly effective at fixing nitrogen with a particular legume, but if it grows poorly in artificial media during the preparation of the commercial inoculum, it will not be a suitable inoculant. The range of criteria used to select quality inoculant strains of rhizobia applies equally to inocula of other soil organisms.

Genetic engineering of inoculant organisms

Recent advances in understanding the genetic basis of the physiology of many soil organisms have provided the opportunity for altering existing organisms by inserting genes from other organisms that have desired characteristics. An example is the introduction of genes for increased tolerance of acid soil conditions. The potential exists for genetically altering soil organisms for many different purposes, such as making rhizosphere organisms more effective at competing with pathogenic fungi and bacteria, and increasing the effectiveness of microbial dissolution of insoluble rock phosphate fertiliser. Whatever the possibilities, there is a need to consider whether the altered organism provides a benefit over the existing soil population, survives in soil, remains stable or transfers genetic information to other organisms and contributes to sustainable land use?

Although genetic alteration of soil organisms appears to be a great technological advance for agricultural production, there are different ways in which organisms can be altered and some have greater environmental consequences than others do. Guidelines and regulations are in place in most countries that restrict the use of genetically altered organisms unless scientific evidence for their harmlessness to non-target organisms is demonstrated. Questions that need answers before widespread use of altered organisms is practised include: (i) Are they really necessary? (ii) Do they represent a short-term solution to a more complex problem that needs to be addressed in terms of land use economics and values? (iii) Can less complicated solutions be found to land degradation issues? (iv) Is it necessary to genetically alter an organism to survive in acid soil conditions if it is already possible to find acid tolerant species of bacteria among existing communities of rhizobia? (v) Will problems arise if genetic material is transferred to other organisms in soil?

How are inoculant organisms used in the environment?

Inoculation of field soils with microorganisms is practised either to introduce specific organisms (e.g. rhizobia, mycorrhizal fungi or biological control organisms) or to enhance the overall biological activity in the soil (e.g. commercial microbial mixtures). The first step in the process is to identify whether there is a need for inoculation. For symbiotic associations, an indicator of the requirement for inoculation may be the absence of nodules on roots or the absence of mycorrhizas. Nutrient deficiency is also an indication that the plant may benefit from the introduction of rhizobia (nitrogen deficiency) or arbuscular mycorrhizal fungi (phosphorus deficiency). The value of mixed microbial inoculants needs to be based on their capacity to enhance overall microbial activity, stimulate nutrient cycling, increase disease resistance and/or improve physical soil conditions mediated by biological processes.

Inoculation with rhizobia (eg in south-western Australia)

The widespread use of legumes in Australian agriculture has underpinned the development of a profitable and efficient industry. In the south-west of Western Australia, the introduction of subterranean clover required an inoculant bacterium that could survive in a Mediterranean climate of hot and dry summers and wet winters. The first commercial inoculant for subterranean clover (strain TA1) did not survive the hot and dry summer period, leading to mortality of clover in the following year. A second problem in the establishment of pastures of subterranean clover in this region was the negative effect of naturally occurring saprophytic fungi that colonised newly cleared land and produced compounds toxic to clover.

The success of inoculated legumes in south-western Australia was delayed until the factors that allowed the bacteria to survive and persist in the hot and dry summer conditions were understood. Key steps in the research were: (i) identification that saprophytic fungi were antagonistic to rhizobia (Holland 1962), (ii) Recognition of second-year mortality of subterranean clover (Marshall et al. 1963), (iii) Recognition of the requirement for colonization of soil and plant rhizospheres by rhizobia (Chatel and Parker 1973), (iv) Identification of lack to tolerance of TA1 to high soil temperatures (Marshall et al. 1993, Marshall 1964), and (v) Identification of the need for saprophytic competence in rhizobia (Chatel et al. 1968).

Inoculation with ectomycorrhizal fungi (e.g. in North America)

Commercial inoculation with ectomycorrhizal fungi has been practised for many years. The simple practice of transferring soil from a forest site containing ectomycorrhizal fungi into a new tree plantation has been highly effective in introducing appropriate ectomycorrhizal fungi. More sophisticated technology is now available. The selection of suitable fungi to match the trees being grown follows similar procedures to those outlined for the selection of rhizobia. The fungi need to be able to survive during inoculum production and out-planting with seedlings.

The success of plantations of ectomycorrhizal trees in the USA has been paralleled by research into inoculation with suitable fungi.

Introduction of 'microbial mixtures'

Inoculation with organisms for biological control and general mixtures of microorganisms for enhancing soil biological fertility are examples of direct attempts to alter soil biological fertility. Similarly, bacteria that degrade toxic contaminants have been applied in field situations. The success of these procedures depends on: (i) selection of appropriate organisms; (ii) introduction of organisms into soil under conditions that will allow them to survive; and (iii) provision of additional nutrients to support the growth of the organisms if necessary.

Inoculation of legumes with root nodule bacteria is the most widespread microbial inoculation program.

How are organisms which are released into the environment traced?

An important component of recent research has been developing ways of tracking organisms that have been introduced into the environment. This is of particular importance where genetically altered microorganisms have been released. The high probability of genetic exchange among soil organisms and the potential for loss of useful characteristics necessitates close monitoring of introduced organisms. Many countries have strict codes of practice that relate to the introduction of larger ‘foreign’ organisms such as plants and animals. Similar programs are essential for soil organisms, although management of such programs is more difficult owing to the greater difficulty in studying organisms in the soil.

Some of the techniques already described for identifying soil organisms can be applied to tracking inoculant organisms in the surface layers of soil and the regolith. In particular, the tools of molecular biology and serology are particularly useful.

Summary Points (6.2)

• The selection of inoculant soil organisms is a highly developed technology.

• Detailed study of the biology of inoculants and associated indigenous soil organisms are important for successful field introductions.

• Genetically engineered soil organisms appear to be of considerable interest, but their benefits in sustainable agricultural farming systems remain controversial and are yet to be resolved.

• Case studies of the introduction of rhizobia into soils of south-western Australia and ectomycorrhizal fungi in the USA illustrate progress made by well organised inoculant industries using naturally occurring organisms selected elsewhere.

• The ecological significance of introducing foreign soil organisms into any environment needs to be carefully evaluated.

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