Integrated soil biological management practices and enhancement of soil biota functions

Sustainable Agriculture and Soil Health
Sustainable Agricultural Practices
Soil Biodiversity and Agriculture Interactions
The Challenge of Managing Soil Biota: Integrated and Locally Appropriate Approaches
Agro-ecological Farming Options and Opportunities
References

Agriculture, and society in general, is challenged to develop strategies for sustainability that conserve non-renewable natural resources such as soil. Much attention has been paid in recent decades to mitigating soil erosion through physical conservation measures and to providing supplementary nutrients and water to meet crop needs. Less consideration has been paid to the soil as a dynamic living resource, although its condition is vital to both the production of food and fibre and to global balance and ecosystem function. The quality and health of soil determine agriculture sustainability, environmental quality and, as a consequence of both - plant, animal and human health (Haberem, 1992).

	Box 1. What is a healthy soil? Soil health can be defined as the "the continued capacity of soil to function as a vital living system, within ecosystem and land-use boundaries, to sustain biological productivity, promote the quality of air and water environments, and maintain plant, animal, and human health" (Pankhurst et al., 1997). Two elements of this definition of soil health distinguish it from the definition of soil quality: (i) the inclusion of a time component (e.g. ''the continued capacity of'' - reflecting the importance of the soil in being able to continue to function over time); and (ii) recognition of soil "as a vital living system" (emphasising the importance of the soil biota to soil functioning). The concept of soil health captures the ecological attributes of the soil, which have implications beyond its quality or capacity to produce a particular crop. These attributes are chiefly those associated with the soil biota; its biodiversity, its food web structure, its activity and the range of functions it performs. For example, soil biodiversity is not a soil property that is critical for the production of a given crop, but it is a property that may be important for the continued capacity of the soil to produce that crop.

Soil health concerns the ability of soil to perform or function according to its potential, and to changes over time due to human use and management or to natural events, see Box 1. Soil health is enhanced by management and land-use decisions that consider the multiple functions of soil. It is impaired by decisions which focus only on single functions, such as crop productivity. The time scale is an important consideration as seasonal and yearly changes in crop/land use patterns can be effectively managed to compensate for changes in soil condition and to restore a healthy functioning soil. Without maintenance of biodiversity, the soil's capacity to recover from natural or anthropogenic perturbations may well be reduced. Similarly, maintenance of the soil's capacity to perform functional processes such as those associated with nutrient cycling and the breakdown of organic matter are important if the soil is to be able to sustain plant growth in the long-term.

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Sustainable Agricultural Practices

The development of sustainable agricultural practices depends largely on promoting long term fertility and productivity of soil at economically viable levels through, for example (Beare, 1997):

1. Matching the supply of soil nutrients with nutrient demands of crop, fodder and pasture plants: through optimising return of crop residues and animal wastes to the land and through greater reliance on biologically fixed and recycled nutrients instead of fertiliser inputs;

2. Maintaining acceptable pest tolerance levels: through reliance on crop rotations and biocontrol agents and hence reducing or maintaining low pesticide use;

3. Maintaining soil physical properties conducive to plant growth and to soil ecosystem functioning (aeration, water infiltration and retention, nutrient availability, etc.) through decreasing or maintaining low frequency and intensity of tillage and reducing erosion and leaching.

Farming can be considered essentially as an ecological activity in which natural ecosystems open to influences of climate, substrate and wild biota are modified to increase yields of desired food and fiber products. The greater the change to natural ecosystem the greater the human effort to maintain the agricultural system. It has been shown that conventional agriculture results in greater ecological disturbance and may be less sustainable compared to low external input agricultural (LEIA) systems. LEIA systems have high genetic and cultural diversity, multiple use of resources and efficient nutrient and mineral recycling (Altieri 1987) The search for biological alternatives to improve and maintain yields is a high priority. In order to find alternatives for different environments and agricultural systems we need to understand the effect of different practices on soil organisms, their functions and processes and their influence on plant nutrition and soil stability.

Understanding how agricultural management practices contribute to sustained fertility and productivity of arable soils requires a knowledge of below ground food webs. Trials have helped to illustrate effects of tillage on structure and function of such food webs and identify key mechanisms by which fungal and bacterial based food webs regulate soil processes. It is an important area for further research. Where cultivation is minimised and crop residues retained on the soil surface it has been shown that there is much greater spatial and temporal differentiation of belowground food webs and processes compared to conventional cultivated soils. In conventional tillage bacteria based food webs play a greater role especially in the tilled layer, and as result of flushes of mineralisation related to tillage events may lead to greater organic matter loss and lower nutrient retention. In no tillage systems fungal based food webs are more important which influence nutrient availability and soil aggregate stability, tending to increase N retention and reduce leaching.

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Soil Biodiversity and Agricultural Interactions

Changing land use through clearing forested or grassland for cultivation drastically affects the soil environment and hence the number and kinds of soil organisms. In general, through cultivation, the quantity and quality of plant residues and the number of species of higher plants is greatly reduced thus the range of habitats and foods for soil organisms is significantly reduced.

Different types of agricultural practices and systems also greatly influence the soil biota. Practices such as adding lime, fertilisers, manure and other organic materials, tillage practices, the use of pesticides and so forth, change the physical and chemical environment This results in significant alteration to the ratio of different organisms and their interactions. Some other practices that also affect the soil environment include the crop rotation and mixes, grazing practices, residue management, irrigation and drainage. Table 1 outlines the different effects of agricultural management practices on soil biota and soil function and constraints to use them.

Through land use and management practices the beneficial effects of soil organisms on agricultural productivity and ecological functioning may be affected, including:

• organic matter decomposition and soil aggregation;

• breakdown of toxic compounds both metabolic by-products of organisms and agro-chemicals;

• inorganic transformations that make available nitrates, sulphates, and phosphates as well as essential elements such as iron and manganese; and

• nitrogen fixation into forms usable by higher plants.

Many soil organisms are also detrimental to plant production. For example some moles and rodents may seriously damage crops, snails and slugs are serious pests as well as some ants, aphids and nematodes. As for microflora, bacteria and actinomycetes cause some plant diseases, but most damage is caused by fungi which account for the majority of soil borne crop diseases such as wilts, root rot, club rot, and blight. Soil organisms may compete for nitrogen with higher plants and, under conditions of poor drainage, soil organisms may compete for limited oxygen.

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Direct and Indirect biological soil management strategies

There are many different options to improve biological soil management. These include both direct and indirect interventions.

Direct methods of intervening in the production system attempt to alter the abundance or activity of specific groups of organisms (Hendrix et al., 1990). Examples of direct interventions include: (a) inoculation of seeds or roots with rhizobia, mycorrhizae, fungi and rhizobacteria, for enhanced soil fertility and (b) inoculation of soil or the environment with biocontrol agents (pest or disease) antagonists or beneficial fauna (e.g., earthworms).

Indirect interventions are means of managing soil biotic processes by manipulating the factors that control biotic activity (habitat structure, microclimate, nutrients & energy resources) rather than the organisms themselves (Hendrix et al., 1990). Examples of indirect interventions include most agricultural practices such as application of organic materials to soil, tillage, fertilisation, irrigation, green manuring and liming as well as cropping system design and management. More recent techniques include genetic control of soil function by manipulating resistance to disease, residue and rhizosphere quality (root exudates).

Some of these interventions, particularly direct ones, such as rhizobia inoculation in grain legumes, mycorrhiza inoculation for tree establishment and bio-control agents for disease and pest control are already well developed techniques, widely used by farmers in many developed and some developing countries. Nevertheless, these applications continue to be under-utilised in many less developed countries, particularly by resource-poor farmers. The potential for the use of these direct techniques is important and should be promoted by the relevant institutions and governments responsible for agricultural development.

Perhaps even great benefits, particularly over the long term, are likely to come from indirect interventions such as: choice of crops and their spatio-temporal organisation the enhancement of their natural ability to resist disease, improvements in the quality of the organic matter they produce, and by management of organic matter and other external inputs including fertilisers (TSBF, 1999).

Genetic manipulation of crops provides immense opportunities to improve their abilities to resist adverse environmental conditions (climatic, edaphic, biological), as well as improve the quality of the residues (above- and below-ground).

Tillage, monoculture, pesticide use, erosion and soil contamination or pollution generally have negative effects on most soil organisms, reducing the soil's capacity to maintain its function. This has numerous facets including decreased soil organic matter content, loss of soil structure, loss of soil through wind and water erosion, development of acidic, saline and sodic soils, and soil contamination with pesticide residues and heavy metals (Doran and Parking, 1994). On the other hand, the application of organic wastes, moderate fertiliser use, crop rotations, irrigation in dry and drainage in wet areas generally have positive impacts on soil organism densities, diversity and activity.

Trials have helped to illustrate effects of tillage on structure and function of such food webs and identify key mechanisms by which fungal- and bacterial- based food webs regulate soil processes. It is an important area for further research. Where cultivation is minimised and crop residues retained on the soil surface it has been shown that there is much greater spatial and temporal differentiation of below ground food webs and processes compared to conventional cultivated soils. In conventional tillage bacteria-based food webs play a greater role especially in the tilled layer, and as result of flushes of mineralisation related to tillage events may lead to greater organic matter loss and lower nutrient retention. In no-tillage systems fungal-based food webs are more important which influence nutrient availability and soil aggregate stability, tending to increase N retention and reduce leaching.

Table 1. Effects of different management practices on soil biota and soil function and constraints to using them (expanded from Swift, 1997).

Management practice	Effect on biota & function	Constraints to use
Tillage	More rapid decomposition of OM, higher ratio of bacteria/fungi, lower populations of macro- & meso-fauna, short-term increase in nutrient availability but increase in long-term losses, better root growth in tilled layer, higher erosion risks	Labor, tools & machinery, cost, soil-borne diseases, sloping lands
No-tillage	Higher populations of macro-meso and microfauna, greater ratio of fungi/bacteria, organic matter accumulation on soil surface, nutrient conservation, lower runoff & erosion, increase in presence and incidence of pests and diseases	Machinery, cost, soil compaction & heavy textures, pest management
Organic matter input	Changes in decomposition rates & organism populations (some increase, others decrease, depending on the type of material), increased nutrient availability, storage and exchanges, improved soil physical structure and water relations, reduction in acidity & Al toxicity, greater microbial and fauna activity, esp. detritivores	Availability, labor, livestock presence, cost
Fertilization	Usually reduction in mycorrhization & N2 fixation (with P & N, respectively), mineralization-immobilization balance changes, increased plant production & organic matter inputs, increases in populations of some organisms through greater food supply	Availability, cost
Pesticides	Reduced incidence of diseases and pest, parasites & pathogenic organisms, but negative effects on non-target biota such as beneficial insects & earthworms, improved plant production but often creation of dependence, destabilization of nutrient cycles, loss of soil structure, long-term increased resistance of target biota	Cost, environmental & health impacts
Irrigation/Flooding	Increased water availability, pH neutralization, changes in nutrient cycling (often higher anaerobic processes) and availability, higher asymbiotic N2 fixation, increased populations of drought-stressed biota, lower numbers of sensitive biota, lower organic matter decomposition rates, depression of soil-borne diseases & weeds	Cost, available water, labor, tools
Crop rotations	The "rotation effect", improved pest & disease management, more efficient soil nutrient utilization, greater diversity above- & below-ground, higher populations, biomass and activity of most organisms (esp. with legumes), improved soil aggregation & infiltration, reduced bulk density, higher organic matter	Social acceptability, opportunity costs, agroecosystem compatibility, climate, soil conditions
Inoculation of selected soil biota (e.g., rhizobia, mycorrhizae, earthworms, rhizo-bacteria, antagonists, bio-control agents)	Increased N fixation, nutrient availability in soil, water uptake & efficiency of nutrient acquisition by plants, higher yields, increased heavy metal tolerance, better resistance to plant diseases, pests and parasites, increased soil porosity, aeration, aggregate stability, water infiltration & holding capacity, faster decomposition rates & nutrient cycling	Cost, availability, environmental adaptability, competition with and/or replacement of native biota, adequate soil conditions

Different response of diverse soil organisms to agricultural practices

Figure 1. Different response dynamics of soil biota to disturbance.

Figure 1 illustrates the effects of agricultural practices on the soil biota, this information is not available for all groups of the soil biota, and there can also be important differences in the effects on the same organism depending on local climate or soil conditions (Figure 1). Some organisms are susceptible to certain land management practices and become locally extinct, while others are opportunistic and take advantage of the modified conditions to increase their abundance, biomass and activity. Some organisms may increase or decrease in numbers and biomass for a short period (temporary or elastic) but then return to normal proportions, while others remain unchanged or slightly unchanged (persistent or resistant).

A proper study of these phenomena and the understanding of the basic requirements of different organisms in a variety of land use types and systems is desirable to assess the overall effect of a particular land management decision on the soil biotic community. This is a complicated, if not impossible task, even for a group of interdisciplinary scientists working at one site for a long period, and is definitely not feasible for most farmers. Nevertheless, there are a few general rules that apply, and can be used in predicting management effects and in choosing potential solutions, as illustrated in Figure 2 and Table 1.

Figure 2. The effect of different agricultural management practices on soil biota (modified from Hendrix et al., 1990)

Hierarchical Levels of Management

The management of organic matter inputs, cropping system design, fertilisation, etc must not be conducted independently, but in a holistic fashion, especially because of the recurrent interactions between different management strategies, different hierarchical levels of management, and between different soil organisms (Swift, 1999).

Manipulation of the system at the highest level (e.g., the crop system) will influence all the other levels of management, and will generally lead to more rapid system responses than manipulations at lower levels (e.g., organic matter management, tillage, soil fauna inoculation). The goal is to establish the most direct link possible between the management intervention and the target; the more specific the intervention, the more likely it is to be successful (Swift, 1999).

Thus, a hierarchical organisation of the limitations and potential alternatives, adapted to the local human, climate, soil and agro-ecosystem conditions, could be drawn up to guide farmers and land use decision makers to the potential practices that can be adopted or changed. At this point, an understanding of how limitations to agricultural production at various levels (social, cultural, economic, political, agronomic, biological, environmental, edaphic, genetic), can be overcome using local or imported resources, knowledge and capacity, as well as how agricultural practices separately and cumulatively, affect soil biota and their activity, is essential to predict possible management options and other solutions.

The Challenge of Managing Soil Biota: Integrated and Locally Appropriate Approaches

As illustrated in Figure 3, the key to successful soil biological management is its development in an integrated manner (TSBF, 1999).

Figure 3. The seven step process to optimum soil biological management and conservation (expanded from Swift, 1997).

Integrated management of soil biodiversity in agricultural systems is a holistic process that relies largely on locally available resources, climate, socio-economic conditions, and direct participation of different stakeholders, especially farmers. (Figure 3).

For agro-ecological approaches several aspects of traditional knowledge systems are relevant, such as knowledge of farming practices and the physical environment, folk taxonomic systems and biological classifications, and the use of low-input technologies. Considerations of traditional agriculture include aspects such as ability to bear risk, production efficiencies of symbiotic crop mixtures, recycling of materials, reliance on local resources and germplasm, exploitation of full range of micro-environments, etc.. By understanding and obtaining information on such considerations, it is possible to obtain important information that may be used for developing appropriate agricultural strategies tailored to the needs, preferences and resources bases of specific farmers groups and regional agro-ecosystems (Altieri, 1995).

If farmers understand the effects of their different management practices on key categories of soil biota and their functions, and if they know how to observe and assess what is happening in the soil, then they can more successfully develop and adopt beneficial practices. However, it is not only the biophysical factors that affect farmers’ decisions but also socio-economic considerations. Common constraints to the use of different soil biological management practices include the monetary cost (purchased inputs), labour and time costs, the availability of the resources and the tools to implement them, as well as social acceptability.

More information is provided in the section on Promotion and Integration, which outlines participatory processes and integration with other agricultural practices/technologies including integrated research and development on soil management considering physical, biological and chemical issues.

Agro-ecological Farming Options and Opportunities

Farming can be considered essentially as an ecological activity in which natural ecosystems open to influences of climate, soil processes and wild biota are modified to increase yields of desired food and fibre products. The greater the change to natural ecosystem the greater the human effort to maintain the agricultural system. It has been shown that conventional agriculture relying on tillage to enhance productivity results in greater ecological disturbance, and may be less sustainable in the long term compared to Low External Input Agricultural (LEIA) systems. LEIA systems are characterised by high genetic and cultural diversity, multiple use of resources and efficient nutrient and mineral recycling (Altieri 1987). There are many approaches to sustainable agriculture with the goal of reducing environmental degradation, through appropriate input technologies or farming techniques.

The search for biological alternatives to improve and maintain yields is becoming a high priority in view of increasing problems of pollution such as nitrate leaching into ground and surface water sources, soil degradation and productivity decline, disturbed hydrological regimes and major pest and disease outbreaks. In order to find alternatives for different environments and agricultural systems we need to understand the effect of different practices on soil organisms, their functions and processes and their influence on plant nutrition and soil stability. Understanding how agricultural management practices contribute to sustained fertility and productivity of arable soils requires knowledge of below ground food webs.

	Box 2. "The Tropical Soil Biology and Fertility Programme" or TSBF An international research institution whose mission is to contribute to human welfare and the conservation of environments in the tropics by developing improved practices for sustaining tropical soil fertility through the management of the soil biota, biological processes and natural resources in combination with judicious use of inorganic inputs. Biological management of soil fertility is addressed as an integral component of sustainable agriculture The TSBF program was initiated in 1984, under the patronage of the 'Man and Biosphere' program of United Nations Educational Scientific and Cultural Organization (UNESCO) and the 'Decade of the Tropics' initiative of the International Union of Biological Sciences (IUBS). The Programme is hosted by UNESCO at UNON, Nairobi, and activities have been funded by multiple donors. Over the last 15 years the work of the TSBF, has focused extensively on indirect techniques, particularly the manipulation of organic matter decomposition. It aims at optimum synchrony between the decomposition, immobilization and mineralization processes, and the nutrient demands of growing plants (Myers et al., 1994; Palm et al., 2000). A global GEF/UNEP/TSBFproject has been approved on the Conservation and Sustainable Management of Below-Ground Biodiversity in Brazil, Côte d'Ivoire, Indonesia, India, Kenya, Mexico, Uganda (Previously known as MAGLUS).

Organic agriculture is a holistic production management system which promotes and enhances agro-ecosystems health, including biodiversity, biological cycles, and soil biological activity. It emphasises the use of management practices in preference to the use of off-farm inputs, taking into account that regional conditions require locally adapted system. This is accomplished by using, where possible, agronomic, biological, and mechanical methods, as opposed to using synthetic material, to fulfil any specific function within the system (Codex, 1999). Further information on Organic Agriculture at FAO.

Conservation tillage, including zero and reduced tillage, and wider conservation agriculture techniques, including the management of rotations, weeds, crop cover and rooting systems, are being adopted worldwide. Its uptake by farmers in some parts of Latin America is spontaneous and escalating in view of the multiple production, environmental and labour benefits. Where cultivation is minimised and crop residues retained on the soil surface it has been shown that there is much greater spatial and temporal differentiation of below ground food webs and processes compared to conventional cultivated soils. In conventional tillage bacteria-based food webs play a greater role especially in the tilled layer, and as result of flushes of mineralisation related to tillage events may lead to greater organic matter loss and lower nutrient retention. In no-tillage systems fungal-based food webs are more important which influence nutrient availability and soil aggregate stability, tending to increase N retention and reduce leaching.

Conservation agriculture approaches are being adopted worldwide, as they not only allow sustainable production but also reduce labour, inputs and costs. Integrated management of soil biodiversity in agricultural systems is a holistic process that relies largely on locally available resources, climate, socio-economic conditions, and direct participation of different stakeholders, especially farmers. Further information on Conservation Agriculture at FAO.

The importance of soil biota for sustaining the fertility and productivity of soils has also been the focus of several major programmes on the ecology of arable farming systems.

Agroecology and the farming systems approaches have greatly contributed over the last few years to the design of more sustainable and productive agro-ecosystems (Pimbert, Altieri, et al). More recently spatial statistics have been used to predict soils and regions within landscapes or fields that are more or less productive, helping farmers to decide where they should plant their crops and in what densities, and at what times of the year.

The biodiversity and agro-ecological revolution in agriculture should result in a definition of a set of new guiding principles and optimizing parameters for agricultural techniques. Alternative agricultural techniques, which aim, inter alia at the preservation of biodiversity as well as productivity, should be able to balance their performance against existing ecological and socio-economic constraints.

References

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