AGP - Agriculture and soil biodiversity

Our agricultural activities exert an important influence on the soil biota, their activities and diversity (see top figure right; table). Clearing forested or grassland for cultivation drastically affects the soil environment and hence reduces the number and species of soil organisms. The reduction of quantity and quality of plant residues and the number of higher plants species leads to a reduction in the range of habitats and foods for soil organisms.

Different types of agricultural practices and systems affect the soil biota in different ways and the response (see bottom figure right) may be either positive or negative depending on which part of the soil the biota, e.g. fungal or bacterial, is affected. For example, organisms which are sensitive to pH will be affected by the addition of lime; the bacterial: fungal ratio will be affected by the addition of fertilizers and manures which alter the C:N ratio as will the effects of tillage. Tilling the soil will reduce the number of fungal hyphens, because soil aggregates, which are held together by these hyphens, are broken down.

The consequences of agricultural practices on soil biota may be direct and far reaching. Organisms which are of benefit to agriculture and which may be affected include those responsible for

  • organic matter decomposition and soil aggregation;
  • breakdown of toxic compounds both metabolic by-products of organisms and agrochemicals;
  • inorganic transformations that make available nitrates, sulphates, and phosphates as well as essential elements such as iron and manganese;
  • nitrogen fixation into forms usable by higher plants

Agricultural practices that use high amounts of external-inputs, such as inorganic fertilizers, pesticides, and other amendments, can overcome specific soil constraints to crop production. These practices have led to considerable increases in overall food production in Europe, Asia and the Americas. However, especially in the most intensively managed systems, this has resulted in continuous environmental degradation, particularly of soil, vegetation and water resources, such as in the state of Haryana in India. Soil organic matter levels are declining and the use of chemical inputs is intensifying (Singh, 2000).
Any misuse of high external inputs for crop production has far reaching effects, which include:

  • Deterioration of soil quality and reduction in agricultural productivity due to nutrient depletion, organic matter losses, erosion and compaction
  • Pollution of soil and water through the over use of fertilizers and the improper use and disposal of animal wastes
  • Increased incidence of human and ecosystem health problems due to the indiscriminate use of pesticides and chemical fertilizers
  • Loss of biodiversity due to the use of reduced number of species being cultivated for commercial purposes
  • Loss of adaptability traits when species that grow under specific local environmental conditions become extinct
  • Loss of beneficial crop-associated biodiversity that provides ecosystem services such as pollination, nutrient cycling and regulation of pest and disease outbreaks
  • Soil salinisation, depletion of freshwater resources and reduction of water quality due to unsustainable irrigation practices throughout the world
  • Disturbance of soil physicochemical and biological processes as a result of intensive tillage and slash and burning.

Although humans generally begin their influence on soil biodiversity with naturally-present communities at a particular site (resulting essentially from ecological and evolutionary forces), they also have the ability to introduce new organisms and, through imposition of different management practices, put selective pressures on the naturally-present or introduced soil biota. This provides the opportunity to manage soil organisms and their activities to enhance soil fertility and crop growth. In theory, probably enough is known to manage these communities, yet considerable basic and applied research is needed to reach appropriate levels of biological husbandry and optimal management of these biological resources (Hendrix et al., 1990).

Agriculture and Soil Health
Agriculture and other users of land are 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 agricultural sustainability, environmental quality and as a consequence of both plant, animal and human health.

A healthy soil has the ability to perform or function according to its potential, and to change over time due to human use and management or to natural events. Soil health is enhanced by management and land-use decisions that consider the multiple functions of soil and that take into account that soil is a living organism. It is impaired by overuse of one input factor in order to reach the maximum crop yield potential . 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 healthily 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, is important in order to sustain plant growth in the long-term.

Improving Soil Management
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 and inorganic fertilizers to soil, tillage, 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 greater 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 mineral fertilizers (TSBF, 2000).

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 use of mineral fertilisers, crop rotations, irrigation in dry and drainage in wet areas generally have positive impacts on soil organism densities, diversity and activity.

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:

  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, and judicious use of mineral fertilisers;
  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 activity that modifies natural ecosystems to agro-ecosystems by  influencing and managing micro-climate, substrate and wild biota so as to increase the yields of desired food and fiber crops. The greater the change to the natural ecosystem the more material inputs and energy humans have to supply to maintain productivity of the agro-ecosystem and the less likely is its resilience to stress and its sustainability. It has been shown that high external conventional agriculture results in greater ecological disturbance and may be less sustainable compared to low external input agricultural (LEIA) and Organic Agricultural systems. LEIA systems have high genetic and cultural diversity, multiple use of resources and efficient nutrient and mineral recycling (Altieri 1999). 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. It has been shown that with minimal soil disturbance and maximum retention of crop residues on the soil surface there is much greater spatial and temporal differentiation of belowground food webs and processes compared to conventionally cultivated soils. Bacteria based food webs play a greater role in conventionally tilled soils, especially in the tilled layer, and as a result of more intense oxidation, may lead to greater organic matter loss and subsequent lower nutrient retention. Fungal based food webs are more important in no-till systems, which influence nutrient availability and soil aggregate stability and tend to increase N retention and reduced leaching.

Agro-ecological Farming Practices and Opportunities
There are many approaches to make agricultural production more sustainable. Agroecology has greatly contributed over the last few years to elucidate the role of ecosystem services and soil biodiversity in sustaining crop production (Altieri, 1995; 2002, Swift et al., 2004, Pretty 2006). Farming practices range from strictly limiting the use of external inputs, such as in Organic Agriculture, to LEIA systems and approaches that advocate the  judicious use of inputs for sustainable intensification of crop production. The latter has recently been promoted by FAO, when it launched its 'Save and Grow' book for policymakers. Common to all approaches is the goal of reducing environmental degradation, but they differ in their aim and their means to intensify production.

Human efforts can lead to highly intensive systems, despite no use of external inputs. For example, about 110,000 farmers in Cuba linked to ANAP (Asociacion Nacional de Agricultores Pequenos) manage their soils in rural and peri-urban areas of Havana and other major cities without any use of external inputs, simply because they cannot afford nor have access to them. Yet their system is highly productive; they produce on average 16-20 kg of food per m2 per year using a series of organic material, such as vermin-compost, green manures, and compost teas. Studies have shown that these farmers managing such diversified low external input systems can produce on average per hectare enough food to feed 10-15 people per year (Funes-Monzote, 2008).
However, such approaches cannot be transferred to large fields, because either labour and transport costs are too high or soils used for crop production are so degraded or mined of nutrients that they need to be brought to a higher fertility level by other means, before in-situ biomass production is high enough. That is the situation in vast areas of sub-Saharan African savannas. Nutrient mining was so intense in the last decennia’s (Smaling et al 1997) that these 'non-responsive' soils (Vanlauwe et al., 2010) need to be replenished with external nutrients.

The new paradigm of crop production, taking into account ecosystem approaches and biodiversity, should be able to balance production goals with ecological and socio-economic requirements.

A short chronicle of human effects on soil biodiversity
Humans affect soil biodiversity through their agricultural activities. The biodiversity of plants and animals at large was changed when humans first started the domestication process over 7000 years ago (Solbrig and Solbrig, 1994). By identifying a few seemingly more useful or edible species, these ancient agriculturists began the selection process which still continues today as farmers, researchers and companies look for more productive plants and animals. This process necessarily involves a reduction and simplification of the immense biological diversity of nature, at both the species and genetic level. However, farmers’ first activities had only little impact or these impacts were limited on a geographic scale, because they used a few simple tools and mostly organic inputs. There are still examples today of cultures that continue to practice this small-scale, limited-impact agriculture (Denevan, 1995; Redford and Mansour, 1996).

The growth in population and the increasing urbanization and specialization led to the need to produce larger quantities of food being transported over longer distances. Larger areas of land were converted towards agricultural activities, and animal traction, heavy machines, irrigation canals or other intensification techniques were used. The change in land use through clearing forests or converting grassland affect drastically the soil environment and change the range of habitats and foods for soil organisms. Agricultural practices, such as intercropping, crop rotation, residue management, tillage with the moldboard plow, fertilizer application, pesticide use, irrigation or drainage and grazing techniques, have all a bearing on the composition and functioning of soil organisms as well as the physical and chemical constituencies of the soil environment.

Today, some 7 billion humans rely on biodiversity for its goods and services. The population doubled since 1950 and the UN forecasts a population of 9.2 billion for the year 2050. The demands on natural resources are growing even faster, because the global economy has quintupled in the last 50 years.  As the amount of land available for agricultural use continues to decrease worldwide, more pressure on the soil resource base and the environment is to be expected (Lavelle, 2000; Young, 1998).

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Hierarchical organization of soil ecosystem function

from Lavelle, 1996 Click to enlarge

Response of soil biota to disturbance

click to enlarge

The figure illustrates the effects of agricultural practices on the soil biota after an initial disturbance. 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). These responses are dependent upon on local climate or soil conditions and not applicable to all of the soil biota.